diff --git a/apollo_sv-base.json b/apollo_sv-base.json
index 504ba22..76b019d 100644
--- a/apollo_sv-base.json
+++ b/apollo_sv-base.json
@@ -52,9 +52,9 @@
         "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl.  When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)."
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2024-12-24"
+        "val" : "2026-03-13"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv-base.json"
+      "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv-base.json"
     },
     "nodes" : [ {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000000",
@@ -238,7 +238,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000011",
-      "lbl" : "control strategy reactive start time information",
+      "lbl" : "obsolete control strategy reactive start time information",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -263,7 +263,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A number of time step units in a time step of a simulation.  \n\nFor example, if the time step is 6 hours, then this value is 6.\n"
+          "val" : "A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "numberOfUnitsOfTimeInOneSimulatorStep"
@@ -308,7 +308,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The number of time steps in a simulator run.\n\nFor example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.\n"
+          "val" : "The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "runLength"
@@ -348,7 +348,7 @@
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  \n\nNote that the susceptible and infected organisms can be of different species.\n\n"
+          "val" : "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "latentPeriodDuration"
@@ -402,13 +402,13 @@
         "definition" : {
           "val" : "The count of (simulated organisms) in a simulated population."
         },
-        "comments" : [ "MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n" ],
+        "comments" : [ "MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The number of simulated organisms in a simulated population.  The number does not have to be an integer.  "
+          "val" : "The number of simulated organisms in a simulated population.  The number does not have to be an integer."
         } ]
       }
     }, {
@@ -421,7 +421,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. "
+          "val" : "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism."
         } ]
       }
     }, {
@@ -432,7 +432,7 @@
         "definition" : {
           "val" : "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination."
         },
-        "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.\n" ],
+        "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint."
@@ -485,11 +485,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  "
+          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  "
+          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease."
         } ]
       }
     }, {
@@ -631,11 +631,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A simulated organism in a simulated population that is not susceptible. "
+          "val" : "A simulated organism in a simulated population that is not susceptible."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.\n"
+          "val" : "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage."
         } ]
       }
     }, {
@@ -663,7 +663,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. "
+          "val" : "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
@@ -753,11 +753,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. "
+          "val" : "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. "
+          "val" : "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection."
         } ]
       }
     }, {
@@ -771,7 +771,7 @@
         "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2.  If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. "
+          "val" : "The fraction of individuals in a simulated population that will accept antiviral treatment if offered."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "antiviral cm compliance"
@@ -783,7 +783,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "An action specification giving the number of doses of an antiviral to be made available during a specific time interval. "
+          "val" : "An action specification giving the number of doses of an antiviral to be made available during a specific time interval."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
@@ -897,9 +897,9 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The simulation of an antiviral control measure. "
+          "val" : "The simulation of an antiviral control measure."
         },
-        "comments" : [ "MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.\n" ],
+        "comments" : [ "MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism."
@@ -952,7 +952,7 @@
         "definition" : {
           "val" : "A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation."
         },
-        "comments" : [ "MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.\n" ],
+        "comments" : [ "MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation."
@@ -1027,11 +1027,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A purely intentional entity that simulates an entity and its properties.\n\n"
+          "val" : "A purely intentional entity that simulates an entity and its properties."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A purely intentional entity that simulates an entity and its properties.\n\n"
+          "val" : "A purely intentional entity that simulates an entity and its properties."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "simulation"
@@ -1109,7 +1109,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000076",
-      "lbl" : "μ",
+      "lbl" : "obsolete μ",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1123,7 +1123,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000077",
-      "lbl" : "σ",
+      "lbl" : "obsolete σ",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1150,7 +1150,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000079",
-      "lbl" : "deprecated log normal distribution",
+      "lbl" : "obsolete log normal distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1221,7 +1221,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. "
+          "val" : "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism."
         } ]
       }
     }, {
@@ -1291,7 +1291,7 @@
         "definition" : {
           "val" : "A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study."
         },
-        "comments" : [ "1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.\n" ],
+        "comments" : [ "1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A vaccination efficacy that results from a vaccination efficacy study."
@@ -1377,7 +1377,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000095",
-      "lbl" : "deprecated discrete probability distribution",
+      "lbl" : "obsolete discrete probability distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1406,11 +1406,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The sum of all biotic and abiotic entities in a geographical region. "
+          "val" : "The sum of all biotic and abiotic entities in a geographical region."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The sum of all biotic and abiotic entities in a geographical region. "
+          "val" : "The sum of all biotic and abiotic entities in a geographical region."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "Ecosystem"
@@ -1662,15 +1662,15 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources"
+          "val" : "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources."
         },
-        "comments" : [ "Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing. \n", "Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing" ],
+        "comments" : [ "Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing.", "Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species.\n\n"
+          "val" : "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "InfectionAcquisition"
@@ -1785,7 +1785,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000125",
-      "lbl" : "school calendar",
+      "lbl" : "obsolete school calendar",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1871,7 +1871,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc.\n"
+          "val" : "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "reactiveControlMeasureThreshold"
@@ -1945,7 +1945,7 @@
       "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "the number of distinct antigenic strains in a vaccine product "
+          "val" : "The number of distinct antigenic strains in a vaccine product."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "valence"
@@ -2025,7 +2025,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000143",
-      "lbl" : "vaccine disposition",
+      "lbl" : "obsolete vaccine disposition",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "replaced with VO 'vaccine function'" ],
@@ -2069,7 +2069,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000146",
-      "lbl" : "beta",
+      "lbl" : "obsolete beta",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "it is the same thing as transmission coefficient" ],
@@ -2094,7 +2094,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000148",
-      "lbl" : "random number seed",
+      "lbl" : "obsolete random number seed",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -2272,7 +2272,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000161",
-      "lbl" : "MIDAS scenario",
+      "lbl" : "obsolete MIDAS scenario",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -2372,7 +2372,7 @@
         "definition" : {
           "val" : "An independent continuant that is the localization of a pathogen, but is not undergoing an infection."
         },
-        "comments" : [ "A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    " ],
+        "comments" : [ "A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
@@ -2691,7 +2691,7 @@
         "definition" : {
           "val" : "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero."
         },
-        "comments" : [ "Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.", "This census should exclude infection, immunity, treatment, or contamination.  " ],
+        "comments" : [ "Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.", "This census should exclude infection, immunity, treatment, or contamination." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero."
@@ -2819,11 +2819,11 @@
       "lbl" : "agent level population and environment census",
       "type" : "CLASS",
       "meta" : {
-        "comments" : [ "An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. " ]
+        "comments" : [ "An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved." ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000198",
-      "lbl" : "agent model ecosystem census description",
+      "lbl" : "obsolete agent model ecosystem census description",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics." ],
@@ -2831,7 +2831,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000199",
-      "lbl" : "compartment model population and environment census",
+      "lbl" : "obsolete compartment model population and environment census",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census)." ],
@@ -2868,7 +2868,7 @@
       "lbl" : "indexable Apollo item",
       "type" : "CLASS",
       "meta" : {
-        "comments" : [ "A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. " ],
+        "comments" : [ "A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "ApolloIndexableItem"
@@ -3100,14 +3100,14 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. "
+          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://en.wikipedia.org/wiki/Probability_distribution"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. "
+          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "ProbabilityDistribution"
@@ -3686,7 +3686,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000249",
-      "lbl" : "nonparametric probability distribution",
+      "lbl" : "obsolete nonparametric probability distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -3978,7 +3978,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious.\n"
+          "val" : "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "InfectionAcquisitionFromInfectedHost"
@@ -4036,7 +4036,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated.\n"
+          "val" : "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "timeScale"
@@ -4429,7 +4429,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'.\n"
+          "val" : "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "supplyScheduleUnits"
@@ -4496,7 +4496,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.\n"
+          "val" : "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "CaseDefinition"
@@ -5867,7 +5867,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000370",
-      "lbl" : "deprecated homeostasis",
+      "lbl" : "obsolete homeostasis",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -6426,7 +6426,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000399",
-      "lbl" : "deprecated infection case count",
+      "lbl" : "obsolete infection case count",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -7201,7 +7201,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000435",
-      "lbl" : "closure period",
+      "lbl" : "obsolete closure period",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -8070,7 +8070,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000475",
-      "lbl" : "gonotrophic period duration",
+      "lbl" : "obsolete gonotrophic period duration",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -8482,7 +8482,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000496",
-      "lbl" : "ORCID",
+      "lbl" : "obsolete ORCID",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -10380,9 +10380,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "treatment facilities census"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "treatment facility census"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A census that counts the number of treatment facilities of some kind in a particular geographical region."
@@ -11591,6 +11588,9 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/CHEBI_36044",
       "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/COB_0000035",
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/DOID_3292",
       "type" : "CLASS"
@@ -11630,15 +11630,15 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/GO_0019954",
       "type" : "CLASS"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/GO_0032504",
-      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/GO_0044409",
       "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/GO_0044419",
       "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_0048609",
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/GO_0051701",
       "type" : "CLASS"
@@ -11847,13 +11847,13 @@
       "id" : "http://purl.obolibrary.org/obo/UBERON_0000061",
       "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/UBERON_0000479",
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0000071",
       "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/UBERON_0002405",
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0000479",
       "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/UBERON_0035944",
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0002405",
       "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/UO_0000000",
@@ -11872,7 +11872,7 @@
       "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000004",
-      "lbl" : "basis of",
+      "lbl" : "obsolete basis of",
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
@@ -11884,7 +11884,7 @@
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
-        "comments" : [ "p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. " ],
+        "comments" : [ "p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption." ],
         "deprecated" : true
       }
     }, {
@@ -11911,7 +11911,7 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "definition" : {
-          "val" : "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. "
+          "val" : "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times."
         },
         "comments" : [ "Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222." ]
       }
@@ -11927,7 +11927,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000116",
-      "lbl" : "causally_precedes",
+      "lbl" : "obsolete causally_precedes",
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
@@ -12153,7 +12153,7 @@
         "comments" : [ "This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "National Library of Medicine Identifier\n"
+          "val" : "National Library of Medicine Identifier"
         } ]
       }
     }, {
@@ -12362,6 +12362,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000007",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000594"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008",
       "pred" : "is_a",
@@ -12486,6 +12490,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032",
       "pred" : "http://purl.obolibrary.org/obo/OBI_0000312",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033",
       "pred" : "is_a",
@@ -12622,6 +12630,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000066",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000070"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000066",
+      "pred" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000067",
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000038"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000068",
       "pred" : "is_a",
@@ -12730,6 +12742,14 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000109"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089",
+      "pred" : "http://purl.obolibrary.org/obo/IAO_0000136",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000025"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090",
       "pred" : "is_a",
@@ -12758,6 +12778,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000094",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000027"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000094",
+      "pred" : "http://purl.obolibrary.org/obo/RO_0002351",
+      "obj" : "http://purl.obolibrary.org/obo/PCO_0000001"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000095",
       "pred" : "is_a",
@@ -13178,6 +13202,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000183",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000183",
+      "pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000015"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184",
       "pred" : "is_a",
@@ -13222,6 +13250,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000193",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000027"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000086"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000195",
       "pred" : "is_a",
@@ -13729,7 +13761,7 @@
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000312",
       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/GO_0032504"
+      "obj" : "http://purl.obolibrary.org/obo/GO_0048609"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000312",
       "pred" : "http://purl.obolibrary.org/obo/RO_0002218",
@@ -15154,6 +15186,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000795",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000794"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796",
       "pred" : "is_a",
@@ -15162,6 +15198,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796",
       "pred" : "http://purl.obolibrary.org/obo/OBI_0000299",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000100"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000797",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000797",
       "pred" : "is_a",
diff --git a/apollo_sv-base.obo b/apollo_sv-base.obo
index 3582af5..96dc44d 100644
--- a/apollo_sv-base.obo
+++ b/apollo_sv-base.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: apollo_sv/releases/2024-12-24/apollo_sv-base.owl
+data-version: apollo_sv/releases/2026-03-13/apollo_sv-base.owl
 idspace: ace_lexicon http://attempto.ifi.uzh.ch/ace_lexicon# 
 idspace: dc http://purl.org/dc/elements/1.1/ 
 idspace: doap http://usefulinc.com/ns/doap# 
@@ -21,7 +21,7 @@ property_value: dc:contributor "Shawn T. Brown" xsd:string
 property_value: dc:contributor "William R. Hogan" xsd:string
 property_value: dc:creator "Mathias Brochhausen" xsd:string
 property_value: dc:type IAO:8000001
-property_value: owl:versionInfo "2024-12-24" xsd:string
+property_value: owl:versionInfo "2026-03-13" xsd:string
 property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI
 property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string
 property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string
@@ -98,6 +98,7 @@ property_value: IAO:0000600 "A software application that provides a model of a r
 id: APOLLO_SV:00000008
 name: software development
 def: "A planned process that has specified output a software product and that involves the creation of source code." []
+is_a: COB:0000035
 is_a: OBI:0000011
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -124,7 +125,7 @@ property_value: IAO:0000600 "An identifier that refers to all versions of a spec
 
 [Term]
 id: APOLLO_SV:00000011
-name: control strategy reactive start time information
+name: obsolete control strategy reactive start time information
 def: "A control strategy start time information item that is based on a condition that triggers the control strategy." []
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A control strategy start time information item that is based on a condition that triggers the control strategy." xsd:string
@@ -136,7 +137,7 @@ name: simulation time step value
 def: "A numeral that is part of a simulation time step action specification." []
 is_a: IAO:0000029
 property_value: APOLLO_SV:0000040 "numberOfUnitsOfTimeInOneSimulatorStep" xsd:string
-property_value: IAO:0000600 "A number of time step units in a time step of a simulation.  \n\nFor example, if the time step is 6 hours, then this value is 6.\n" xsd:string
+property_value: IAO:0000600 "A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6." xsd:string
 
 [Term]
 id: APOLLO_SV:00000013
@@ -161,7 +162,7 @@ def: "The action specification that specifies the number of time steps a simulat
 is_a: APOLLO_SV:00000793 ! epidemic simulator action specification
 relationship: BFO:0000051 APOLLO_SV:00000068 ! simulation time step action specification
 property_value: APOLLO_SV:0000040 "runLength" xsd:string
-property_value: IAO:0000600 "The number of time steps in a simulator run.\n\nFor example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.\n" xsd:string
+property_value: IAO:0000600 "The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero." xsd:string
 
 [Term]
 id: APOLLO_SV:00000016
@@ -178,11 +179,10 @@ id: APOLLO_SV:00000017
 name: latent period duration
 def: "A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts." []
 comment: MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs
-comment: The duration of the period between when an organism becomes infected and when it becomes infectious.
 is_a: APOLLO_SV:00000243 ! duration
 property_value: APOLLO_SV:0000040 "latentPeriodDuration" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  \n\nNote that the susceptible and infected organisms can be of different species.\n\n" xsd:string
+property_value: IAO:0000600 "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species." xsd:string
 
 [Term]
 id: APOLLO_SV:00000018
@@ -212,23 +212,22 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 id: APOLLO_SV:00000022
 name: count of simulated population
 def: "The count of (simulated organisms) in a simulated population." []
-comment: MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n
+comment: MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "The number of simulated organisms in a simulated population.  The number does not have to be an integer.  " xsd:string
+property_value: IAO:0000600 "The number of simulated organisms in a simulated population.  The number does not have to be an integer." xsd:string
 
 [Term]
 id: APOLLO_SV:00000023
 name: vaccination dose schedule
 def: "An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent." []
 is_a: APOLLO_SV:00000084 ! control strategy dose schedule
-property_value: IAO:0000600 "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. " xsd:string
+property_value: IAO:0000600 "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism." xsd:string
 
 [Term]
 id: APOLLO_SV:00000024
 name: vaccination compliance
 def: "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination." []
 comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
-comment: MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.\n
 is_a: OBI:0302867
 property_value: IAO:0000600 "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint." xsd:string
 
@@ -236,7 +235,6 @@ property_value: IAO:0000600 "The fraction of individuals in a population who are
 id: APOLLO_SV:00000025
 name: vaccination efficacy
 def: "The infectious disease treatment efficacy of a vaccine." []
-comment: need to generate class restriction.  Something like:\n\n'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance'))\n\nwe'd also like to say that the protective resistance disposition began to exist during the process.  \n\ncan't recall whether we should use process or processual_entity for future BFO compatibility.
 comment: Notes: \n1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer
 is_a: APOLLO_SV:00000227 ! infectious disease treatment efficacy
 property_value: APOLLO_SV:0000040 "vaccinationEfficacies" xsd:string
@@ -265,9 +263,9 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 [Term]
 id: APOLLO_SV:00000029
 name: infectious disease control strategy execution
-def: "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  " []
+def: "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease." []
 is_a: OBI:0000011
-property_value: IAO:0000600 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  " xsd:string
+property_value: IAO:0000600 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease." xsd:string
 
 [Term]
 id: APOLLO_SV:00000030
@@ -305,6 +303,7 @@ property_value: IAO:0000600 "A measurement datum that is the output of counting.
 id: APOLLO_SV:00000033
 name: counting
 def: "The planned process of finding the number of elements in a finite set of objects." []
+is_a: COB:0000035
 is_a: OBI:0000011
 intersection_of: OBI:0000011
 intersection_of: OBI:0000299 APOLLO_SV:00000032 ! count
@@ -356,9 +355,9 @@ property_value: IAO:0000600 "A simulated organism in a simulated population that
 [Term]
 id: APOLLO_SV:00000041
 name: simulation of recovered organism
-def: "A simulated organism in a simulated population that is not susceptible. " []
+def: "A simulated organism in a simulated population that is not susceptible." []
 is_a: APOLLO_SV:00000034 ! simulation of organism
-property_value: IAO:0000600 "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.\n" xsd:string
+property_value: IAO:0000600 "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage." xsd:string
 
 [Term]
 id: APOLLO_SV:00000042
@@ -372,7 +371,7 @@ property_value: IAO:0000600 "The disease being simulated." xsd:string
 [Term]
 id: APOLLO_SV:00000043
 name: reproduction number
-def: "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. " []
+def: "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection." []
 property_value: APOLLO_SV:0000040 "ReproductionNumber" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "The number of susceptible organisms that each infected organism infects.  ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation." xsd:string
@@ -419,24 +418,23 @@ property_value: IAO:0000600 "The degree to which a particular antiviral drug red
 [Term]
 id: APOLLO_SV:00000049
 name: antiviral efficacy delay
-def: "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. " []
+def: "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role." []
 is_a: APOLLO_SV:00000243 ! duration
-property_value: IAO:0000600 "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. " xsd:string
+property_value: IAO:0000600 "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection." xsd:string
 
 [Term]
 id: APOLLO_SV:00000050
 name: antiviral compliance
 def: "The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible." []
 comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
-comment: MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2.  If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population
 is_a: OBI:0302867
 property_value: APOLLO_SV:0000040 "antiviral cm compliance" xsd:string
-property_value: IAO:0000600 "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. " xsd:string
+property_value: IAO:0000600 "The fraction of individuals in a simulated population that will accept antiviral treatment if offered." xsd:string
 
 [Term]
 id: APOLLO_SV:00000051
 name: antiviral supply schedule
-def: "An action specification giving the number of doses of an antiviral to be made available during a specific time interval. " []
+def: "An action specification giving the number of doses of an antiviral to be made available during a specific time interval." []
 is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
 property_value: IAO:0000600 "Counts of antiviral doses that become available in a specific location per time step unit." xsd:string
 
@@ -452,7 +450,6 @@ id: APOLLO_SV:00000053
 name: simulation of organism awaiting control measure
 def: "A simulated organism that is assumed “eligible, willing and able” to participate with a particular control measure." []
 comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
-comment: This class will need more ontological reasoning, since the "willing" part of the definition is not representable in BFO to date.
 is_a: APOLLO_SV:00000034 ! simulation of organism
 disjoint_from: APOLLO_SV:00000058 ! simulation of organism not awaiting control measure
 property_value: IAO:0000600 "A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure." xsd:string
@@ -492,7 +489,6 @@ id: APOLLO_SV:00000058
 name: simulation of organism not awaiting control measure
 def: "A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular control measure." []
 comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
-comment: This class will need more ontological reasoning, since the "unwilling" part of the definition is not representable in BFO to date.
 property_value: IAO:0000600 "A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure." xsd:string
 
 [Term]
@@ -505,8 +501,8 @@ property_value: IAO:0000600 "This concept represents a simulated organism that h
 [Term]
 id: APOLLO_SV:00000060
 name: simulation of antiviral control measure
-def: "The simulation of an antiviral control measure. " []
-comment: MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.\n
+def: "The simulation of an antiviral control measure." []
+comment: MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.
 is_a: APOLLO_SV:00000070 ! simulation
 property_value: APOLLO_SV:0000040 "antiviral control measure" xsd:string
 property_value: IAO:0000600 "A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism." xsd:string
@@ -536,7 +532,7 @@ property_value: IAO:0000600 "A simulated organism in a simulated population has
 id: APOLLO_SV:00000064
 name: simulation time series
 def: "A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation." []
-comment: MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.\n
+comment: MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.
 is_a: IAO:0000584
 property_value: IAO:0000600 "A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation." xsd:string
 
@@ -557,6 +553,7 @@ id: APOLLO_SV:00000066
 name: simulation of time step
 def: "A purely intentional entity that simulates a temporal interval of pre-specified length." []
 is_a: APOLLO_SV:00000070 ! simulation
+relationship: APOLLO_SV:00000067 BFO:0000038 ! simulates
 property_value: APOLLO_SV:0000040 "simulation time step" xsd:string
 property_value: IAO:0000600 "A purely intentional entity that simulates a temporal interval of pre-specified length." xsd:string
 
@@ -587,13 +584,13 @@ property_value: IAO:0000600 "The time step number of a simulation." xsd:string
 [Term]
 id: APOLLO_SV:00000070
 name: simulation
-def: "A purely intentional entity that simulates an entity and its properties.\n\n" []
+def: "A purely intentional entity that simulates an entity and its properties." []
 is_a: APOLLO_SV:00000000 ! purely intentional entity
 intersection_of: APOLLO_SV:00000000 ! purely intentional entity
 intersection_of: APOLLO_SV:00000067 BFO:0000001 ! simulates
 relationship: APOLLO_SV:00000067 BFO:0000001 ! simulates
 property_value: APOLLO_SV:0000040 "simulation" xsd:string
-property_value: IAO:0000600 "A purely intentional entity that simulates an entity and its properties.\n\n" xsd:string
+property_value: IAO:0000600 "A purely intentional entity that simulates an entity and its properties." xsd:string
 
 [Term]
 id: APOLLO_SV:00000071
@@ -638,7 +635,7 @@ property_value: IAO:0000600 "an objective of achieving satisfactory control of e
 
 [Term]
 id: APOLLO_SV:00000076
-name: μ
+name: obsolete μ
 is_a: oboInOwl:ObsoleteClass
 property_value: APOLLO_SV:0000040 "μ" xsd:string
 property_value: IAO:0000600 "the mean or expectation of a distribution" xsd:string
@@ -646,7 +643,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000077
-name: σ
+name: obsolete σ
 is_a: oboInOwl:ObsoleteClass
 property_value: APOLLO_SV:0000040 "sigma" xsd:string
 property_value: IAO:0000600 "standard deviation" xsd:string
@@ -661,7 +658,7 @@ property_value: IAO:0000600 "A continuous probability distribution whose charact
 
 [Term]
 id: APOLLO_SV:00000079
-name: deprecated log normal distribution
+name: obsolete log normal distribution
 is_a: oboInOwl:ObsoleteClass
 property_value: IAO:0000600 "a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm" xsd:string
 is_obsolete: true
@@ -700,7 +697,7 @@ name: control strategy dose schedule
 def: "An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism." []
 is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
 relationship: BFO:0000050 APOLLO_SV:00000086 ! infectious disease control strategy
-property_value: IAO:0000600 "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. " xsd:string
+property_value: IAO:0000600 "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism." xsd:string
 
 [Term]
 id: APOLLO_SV:00000085
@@ -740,8 +737,9 @@ property_value: IAO:0000600 "The count of individuals in an exposed population (
 id: APOLLO_SV:00000089
 name: measured vaccination efficacy
 def: "A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study." []
-comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.\n
+comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.
 is_a: IAO:0000109
+relationship: IAO:0000136 APOLLO_SV:00000025 ! vaccination efficacy
 property_value: APOLLO_SV:0000040 "VaccinationEfficacyMeasured" xsd:string
 property_value: IAO:0000600 "A vaccination efficacy that results from a vaccination efficacy study." xsd:string
 
@@ -749,6 +747,7 @@ property_value: IAO:0000600 "A vaccination efficacy that results from a vaccinat
 id: APOLLO_SV:00000090
 name: vaccination efficacy study design execution
 def: "a study design execution that has as its specified output one or more measured vaccination efficacy data items" []
+is_a: COB:0000035
 is_a: OBI:0000471
 intersection_of: OBI:0000471
 intersection_of: BFO:0000051 APOLLO_SV:00000142 ! vaccination
@@ -785,13 +784,14 @@ id: APOLLO_SV:00000094
 name: community
 def: "Two or more distinct populations that are part of the same biotic ecosystem." []
 is_a: BFO:0000027
+relationship: RO:0002351 PCO:0000001
 property_value: APOLLO_SV:0000040 "community" xsd:string
 property_value: dc:creator "William R. Hogan" xsd:string
 property_value: IAO:0000600 "Two or more distinct populations that are part of the same biotic ecosystem." xsd:string
 
 [Term]
 id: APOLLO_SV:00000095
-name: deprecated discrete probability distribution
+name: obsolete discrete probability distribution
 is_a: oboInOwl:ObsoleteClass
 property_value: APOLLO_SV:0000040 "discrete probability distribution" xsd:string
 property_value: IAO:0000600 "a probability distribution over a discrete random variable" xsd:string
@@ -806,11 +806,11 @@ is_obsolete: true
 [Term]
 id: APOLLO_SV:00000097
 name: ecosystem
-def: "The sum of all biotic and abiotic entities in a geographical region. " []
+def: "The sum of all biotic and abiotic entities in a geographical region." []
 is_a: BFO:0000040
 property_value: APOLLO_SV:0000040 "Ecosystem" xsd:string
 property_value: dc:creator "William R. Hogan" xsd:string
-property_value: IAO:0000600 "The sum of all biotic and abiotic entities in a geographical region. " xsd:string
+property_value: IAO:0000600 "The sum of all biotic and abiotic entities in a geographical region." xsd:string
 
 [Term]
 id: APOLLO_SV:00000098
@@ -885,7 +885,6 @@ id: APOLLO_SV:00000107
 name: atmosphere
 def: "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force" []
 comment: atmosphere of Earth, Earth's moon, Saturn, Titan, etc.
-comment: outer, gaseous layers of exoplanets are called extraterrestrial atmosphere.
 is_a: BFO:0000024
 property_value: dc:creator "William R. Hogan" xsd:string
 property_value: IAO:0000600 "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force" xsd:string
@@ -948,14 +947,13 @@ property_value: IAO:0000600 "A process of reproduction of a particular pathogen
 [Term]
 id: APOLLO_SV:00000115
 name: infection acquisition
-def: "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources" []
-comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing. \n
-comment: Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing
+def: "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources." []
+comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing.
 is_a: GO:0044409
 relationship: RO:0002411 APOLLO_SV:00000114 ! infection
 property_value: APOLLO_SV:0000040 "InfectionAcquisition" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species.\n\n" xsd:string
+property_value: IAO:0000600 "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species." xsd:string
 
 [Term]
 id: APOLLO_SV:00000117
@@ -1020,7 +1018,7 @@ property_value: IAO:0000600 "The number of time steps that a school closure cont
 
 [Term]
 id: APOLLO_SV:00000125
-name: school calendar
+name: obsolete school calendar
 property_value: IAO:0000600 "The time steps that a school will be in session." xsd:string
 is_obsolete: true
 
@@ -1067,7 +1065,7 @@ name: reactive control strategy threshold
 def: "A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy." []
 is_a: IAO:0000027
 property_value: APOLLO_SV:0000040 "reactiveControlMeasureThreshold" xsd:string
-property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc.\n" xsd:string
+property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc." xsd:string
 
 [Term]
 id: APOLLO_SV:00000132
@@ -1110,7 +1108,7 @@ id: APOLLO_SV:00000137
 name: vaccine valence
 is_a: APOLLO_SV:00000032 ! count
 property_value: APOLLO_SV:0000040 "valence" xsd:string
-property_value: IAO:0000600 "the number of distinct antigenic strains in a vaccine product " xsd:string
+property_value: IAO:0000600 "The number of distinct antigenic strains in a vaccine product." xsd:string
 
 [Term]
 id: APOLLO_SV:00000138
@@ -1124,7 +1122,6 @@ id: APOLLO_SV:00000139
 name: control strategy compliance
 def: "A measurement datum about the fraction of individuals in a population that elect to participate in a control strategy when offered." []
 comment: the class restriction can be made more precise AH
-comment: the fraction of some population that is targeted for a control strategy that accepts it.  It can obviously also be interpreted as a probability that the average individual in the targeted population accepts/complies with the control strategy.  It is not simulated
 property_value: APOLLO_SV:0000040 "compliance" xsd:string
 property_value: IAO:0000600 "A fraction of eligible individuals in a population who receive an intervention or participate in a control strategy." xsd:string
 
@@ -1154,7 +1151,7 @@ property_value: IAO:0000600 "A treatment of an individual with antigenic materia
 
 [Term]
 id: APOLLO_SV:00000143
-name: vaccine disposition
+name: obsolete vaccine disposition
 comment: replaced with VO 'vaccine function'
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_obsolete: true
@@ -1180,7 +1177,7 @@ property_value: IAO:0000600 "The dispostion of an organism of a particular biolo
 
 [Term]
 id: APOLLO_SV:00000146
-name: beta
+name: obsolete beta
 comment: it is the same thing as transmission coefficient
 property_value: IAO:0000600 "Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons." xsd:string
 is_obsolete: true
@@ -1194,7 +1191,7 @@ property_value: IAO:0000600 "Transmission parameter" xsd:string
 
 [Term]
 id: APOLLO_SV:00000148
-name: random number seed
+name: obsolete random number seed
 property_value: IAO:0000600 "random number seed" xsd:string
 is_obsolete: true
 
@@ -1253,7 +1250,6 @@ id: APOLLO_SV:00000155
 name: population infection survey
 def: "A population survey that counts the number of individuals in the population who are infected with a particular pathogen." []
 comment: Comment from Mike (to do!):\nI checked because an infection and immunity census would involve two different census methods.   One would be some kind of disease surveillance that counts infections.  The other is some kind of immunity census process based on seroprevalence studies or vaccination registries.
-comment: Equivalent class was:\n'population survey' and (has_part some \n(counting and (has_specified_output some \n(count and ('is about' some 'exposed population'))) and (has_specified_output some \n(count and ('is about' some 'infectious population'))) and (has_specified_output some \n(count and ('is about' some 'susceptible population'))) and (has_specified_output some \n(count and ('is about' some 'immune population')))))
 is_a: APOLLO_SV:00000152 ! population survey
 property_value: APOLLO_SV:0000040 "PopulationInfectionSurvey" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1307,7 +1303,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000161
-name: MIDAS scenario
+name: obsolete MIDAS scenario
 def: "An ecosystem in which a population of hosts is undergoing at least one infection." []
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "An ecosystem in which a population of hosts is undergoing at least one infection." xsd:string
@@ -1354,7 +1350,7 @@ property_value: IAO:0000600 "A census that is the specified output of a agent-le
 id: APOLLO_SV:00000166
 name: contaminated thing
 def: "An independent continuant that is the localization of a pathogen, but is not undergoing an infection." []
-comment: A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    
+comment: A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.
 is_a: BFO:0000004
 property_value: APOLLO_SV:0000040 "ContaminatedThing" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1499,6 +1495,7 @@ name: simulator time specification
 def: "An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps)." []
 is_a: APOLLO_SV:00000793 ! epidemic simulator action specification
 relationship: BFO:0000051 APOLLO_SV:00000015 ! simulation run length
+relationship: BFO:0000051 APOLLO_SV:00000015 ! simulation run length
 relationship: BFO:0000051 APOLLO_SV:00000068 ! simulation time step action specification
 property_value: APOLLO_SV:0000040 "SimulatorTimeSpecification" xsd:string
 property_value: IAO:0000600 "An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps)." xsd:string
@@ -1546,7 +1543,6 @@ id: APOLLO_SV:00000188
 name: population and environment census
 def: "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero." []
 comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.
-comment: This census should exclude infection, immunity, treatment, or contamination.  
 is_a: APOLLO_SV:00000173 ! census
 property_value: IAO:0000600 "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero." xsd:string
 
@@ -1595,6 +1591,7 @@ property_value: IAO:0000600 "A data item inferring a vaccination efficacy based
 id: APOLLO_SV:00000194
 name: individual treatment control strategy
 def: "An infectious disease control strategy that immediately targets individuals." []
+is_a: APOLLO_SV:00000086 ! infectious disease control strategy
 property_value: APOLLO_SV:0000040 "IndividualTreatmentControlMeasure" xsd:string
 property_value: IAO:0000112 "vaccination control strategy, antiviral control strategy" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1616,18 +1613,18 @@ is_a: APOLLO_SV:00000136 ! vaccination control strategy
 [Term]
 id: APOLLO_SV:00000197
 name: agent level population and environment census
-comment: An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. 
+comment: An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved.
 is_a: APOLLO_SV:00000188 ! population and environment census
 
 [Term]
 id: APOLLO_SV:00000198
-name: agent model ecosystem census description
+name: obsolete agent model ecosystem census description
 comment: At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics.
 is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000199
-name: compartment model population and environment census
+name: obsolete compartment model population and environment census
 comment: The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census).
 is_obsolete: true
 
@@ -1648,7 +1645,7 @@ property_value: IAO:0000600 "A census about contaminated things of a given type
 [Term]
 id: APOLLO_SV:00000202
 name: indexable Apollo item
-comment: A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. 
+comment: A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved.
 is_a: IAO:0000030
 property_value: APOLLO_SV:0000040 "ApolloIndexableItem" xsd:string
 
@@ -1770,11 +1767,11 @@ property_value: IAO:0000600 "An information content entity that specifies the va
 [Term]
 id: APOLLO_SV:00000215
 name: probability distribution
-def: "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. " []
+def: "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference." []
 is_a: IAO:0000030
 property_value: APOLLO_SV:0000040 "ProbabilityDistribution" xsd:string
 property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Probability_distribution" xsd:string
-property_value: IAO:0000600 "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. " xsd:string
+property_value: IAO:0000600 "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference." xsd:string
 
 [Term]
 id: APOLLO_SV:00000216
@@ -2028,7 +2025,6 @@ id: APOLLO_SV:00000244
 name: disease unique identifier
 def: "a unique identifier that refers to a disease." []
 comment: This class is different from its superclass, in that the identifier is non-redundant with other identifiers in its context (such as a coding system or terminology or ontology).  The superclass admits of natural langugage names of diseases, whereas this one typically does not.
-comment: We still need to decide which coding schema to adopt.-MB
 is_a: APOLLO_SV:00000598 ! disease identifier
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A unique identifier that refers to a particular type of disease." xsd:string
@@ -2070,7 +2066,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000249
-name: nonparametric probability distribution
+name: obsolete nonparametric probability distribution
 property_value: APOLLO_SV:0000040 "NonparametricProbabilityDistribution" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_obsolete: true
@@ -2212,7 +2208,7 @@ def: "An infection acquisition whereby a susceptible host acquires an infection
 is_a: APOLLO_SV:00000115 ! infection acquisition
 property_value: APOLLO_SV:0000040 "InfectionAcquisitionFromInfectedHost" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious.\n" xsd:string
+property_value: IAO:0000600 "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious." xsd:string
 
 [Term]
 id: APOLLO_SV:00000266
@@ -2240,7 +2236,7 @@ def: "An identifier that designates a scale according to which time is measured
 is_a: IAO:0020000
 property_value: APOLLO_SV:0000040 "timeScale" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated.\n" xsd:string
+property_value: IAO:0000600 "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated." xsd:string
 
 [Term]
 id: APOLLO_SV:00000269
@@ -2436,7 +2432,7 @@ def: "The unit of measure for the supply schedule of an individual treatment." [
 is_a: UO:0000000
 property_value: APOLLO_SV:0000040 "supplyScheduleUnits" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'.\n" xsd:string
+property_value: IAO:0000600 "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'." xsd:string
 
 [Term]
 id: APOLLO_SV:00000293
@@ -2469,7 +2465,7 @@ def: "An information content entity that specifies the criteria that an organism
 is_a: IAO:0000030
 property_value: APOLLO_SV:0000040 "CaseDefinition" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.\n" xsd:string
+property_value: IAO:0000600 "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on." xsd:string
 
 [Term]
 id: APOLLO_SV:00000297
@@ -2611,7 +2607,7 @@ id: APOLLO_SV:00000312
 name: individual mosquito reproduction
 def: "A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157)" []
 is_a: APOLLO_SV:00000651 ! reproduction
-is_a: GO:0032504
+is_a: GO:0048609
 intersection_of: APOLLO_SV:00000651 ! reproduction
 intersection_of: RO:0002218 NCBITaxon:7157
 relationship: RO:0002218 NCBITaxon:7157
@@ -2776,7 +2772,6 @@ id: APOLLO_SV:00000335
 name: chemical resistance to infection
 def: "A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism." []
 comment: As with all dispositions, chemical resistance need not be realized to exist.  The presence of cholorquine confers this disposition even if the person is never bitten by a mosquito, let alone a malaria-laden mosquito.
-comment: Examples: chemoprophylaxis of malaria with chloroquine, treatment of infections with antibiotics, antiviral treatment
 property_value: IAO:0000111 "chemical resistance to infection" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "chemoprotection" xsd:string
@@ -3150,7 +3145,7 @@ property_value: IAO:0000600 "An endosymbiotic mutualism that realizes a biologic
 
 [Term]
 id: APOLLO_SV:00000370
-name: deprecated homeostasis
+name: obsolete homeostasis
 def: "A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3415,7 +3410,7 @@ property_value: IAO:0000600 "A data set whose data items are about a host and it
 
 [Term]
 id: APOLLO_SV:00000399
-name: deprecated infection case count
+name: obsolete infection case count
 def: "A count of individuals in a population who meet an infection case definition during a particular time interval." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3457,7 +3452,6 @@ id: APOLLO_SV:00000403
 name: transmission tree
 def: "A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host." []
 comment: Because a set A is a subset of itself, we capture the possibility that all infected organisms in the epidemic are represented in the tree.
-comment: This definition allows for multiple trees in an epidemic because we did not require that the first case infected temporally be the index case, although the ideal situation is that there is one tree for the epidemic that includes the index case.
 is_a: OBI:0000658
 property_value: APOLLO_SV:0000040 "TransmissionTree" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
@@ -3782,7 +3776,7 @@ property_value: IAO:0000600 "A predicted data item that estimates how reliable s
 
 [Term]
 id: APOLLO_SV:00000435
-name: closure period
+name: obsolete closure period
 def: "A one-dimensional temporal region occupied by a place closure control strategy." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -4184,7 +4178,7 @@ property_value: IAO:0000600 "An epidemic simulator action specification that spe
 
 [Term]
 id: APOLLO_SV:00000475
-name: gonotrophic period duration
+name: obsolete gonotrophic period duration
 def: "A time measurement datum of the length of the temporal interval occupied by a gonotropic period." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -4375,7 +4369,7 @@ property_value: IAO:0000600 "An identifier curated by the United States National
 
 [Term]
 id: APOLLO_SV:00000496
-name: ORCID
+name: obsolete ORCID
 def: "An identifier curated by ORCID, Inc. to denote some academic author." []
 property_value: APOLLO_SV:0000040 "orcId" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
@@ -4640,7 +4634,6 @@ id: APOLLO_SV:00000524
 name: compiling software
 def: "A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions." []
 comment: It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code".  Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
-comment: Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
 is_a: APOLLO_SV:00000008 ! software development
 property_value: IAO:0000111 "process of compiling software" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5286,7 +5279,6 @@ property_value: IAO:0000111 "census of treatment facility" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "census of treatment facilities" xsd:string
 property_value: IAO:0000118 "treatment facilities census" xsd:string
-property_value: IAO:0000118 "treatment facility census" xsd:string
 property_value: IAO:0000600 "A census that counts the number of treatment facilities of some kind in a particular geographical region." xsd:string
 
 [Term]
@@ -5593,7 +5585,6 @@ id: APOLLO_SV:00000623
 name: incident epidemic case count
 def: "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." []
 comment: Incident case counts are measured according to regular intervals, typically day or week.
-comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin.
 is_a: APOLLO_SV:00000498 ! count of cases in an epidemic
 is_a: APOLLO_SV:00000649 ! incident case count
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5858,6 +5849,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string
 id: APOLLO_SV:00000796
 name: dataset creating
 def: "A planned process that has a data set as its specified output." []
+is_a: COB:0000035
 is_a: OBI:0000011
 intersection_of: OBI:0000011
 intersection_of: OBI:0000299 IAO:0000100
@@ -5872,6 +5864,7 @@ id: APOLLO_SV:00000797
 name: creating a copyright license
 def: "A planned process that has a copyright license as its specified output." []
 comment: Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time.
+is_a: COB:0000035
 is_a: OBI:0000011
 intersection_of: OBI:0000011
 intersection_of: OBI:0000299 APOLLO_SV:00000798 ! copyright license
@@ -5911,14 +5904,14 @@ property_value: IAO:0000111 "facultative role" xsd:string
 
 [Typedef]
 id: APOLLO_SV:00000004
-name: basis of
+name: obsolete basis of
 is_a: oboInOwl:ObsoleteProperty
 is_obsolete: true
 
 [Typedef]
 id: APOLLO_SV:00000028
 name: obsolete is based on
-comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. 
+comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption.
 is_a: oboInOwl:ObsoleteProperty
 is_obsolete: true
 
@@ -5933,7 +5926,7 @@ is_asymmetric: true
 [Typedef]
 id: APOLLO_SV:00000057
 name: instantiates
-def: "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. " []
+def: "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times." []
 comment: Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.
 domain: BFO:0000001
 is_asymmetric: true
@@ -5948,7 +5941,7 @@ is_asymmetric: true
 
 [Typedef]
 id: APOLLO_SV:00000116
-name: causally_precedes
+name: obsolete causally_precedes
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_a: oboInOwl:ObsoleteProperty
 is_obsolete: true
diff --git a/apollo_sv-base.owl b/apollo_sv-base.owl
index b27f6d3..4321e19 100644
--- a/apollo_sv-base.owl
+++ b/apollo_sv-base.owl
@@ -25,7 +25,7 @@
      xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"
      xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/apollo_sv/apollo_sv-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv-base.owl"/>
         <dc:contributor>Amanda Hicks</dc:contributor>
         <dc:contributor>John Levander</dc:contributor>
         <dc:contributor>Josh Hanna</dc:contributor>
@@ -42,7 +42,7 @@
         <www:RTS_00000001>C87985BA-6A8A-483A-A6B6-63975101F672</www:RTS_00000001>
         <www:RTS_00000002>082D5D78-D916-457E-B4FD-365F86F45B30</www:RTS_00000002>
         <rdfs:comment xml:lang="en">When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl.  When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component&apos;s Uniform Resource Identifier (URI).</rdfs:comment>
-        <owl:versionInfo>2024-12-24</owl:versionInfo>
+        <owl:versionInfo>2026-03-13</owl:versionInfo>
     </owl:Ontology>
     
 
@@ -61,8 +61,7 @@
     <!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000319 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000319">
-        <obo:IAO_0000118 xml:lang="en">National Library of Medicine Identifier
-</obo:IAO_0000118>
+        <obo:IAO_0000118 xml:lang="en">National Library of Medicine Identifier</obo:IAO_0000118>
         <rdfs:comment xml:lang="en">This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed.</rdfs:comment>
         <rdfs:label xml:lang="en">NLM ID</rdfs:label>
     </owl:AnnotationProperty>
@@ -291,7 +290,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation.</rdfs:comment>
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000004">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
-        <rdfs:label xml:lang="en">basis of</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete basis of</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
@@ -301,7 +300,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation.</rdfs:comment>
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000028">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
-        <rdfs:comment xml:lang="en">p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. </rdfs:comment>
+        <rdfs:comment xml:lang="en">p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption.</rdfs:comment>
         <rdfs:label xml:lang="en">obsolete is based on</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
@@ -344,7 +343,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation.</rdfs:comment>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AsymmetricProperty"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#IrreflexiveProperty"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
-        <obo:IAO_0000115 xml:lang="en">A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times.</obo:IAO_0000115>
         <rdfs:comment>Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.</rdfs:comment>
         <rdfs:label xml:lang="en">instantiates</rdfs:label>
     </owl:ObjectProperty>
@@ -369,7 +368,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation.</rdfs:comment>
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000116">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
-        <rdfs:label xml:lang="en">causally_precedes</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete causally_precedes</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
@@ -882,6 +881,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -1024,7 +1024,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
         <obo:IAO_0000115 xml:lang="en">A control strategy start time information item that is based on a condition that triggers the control strategy.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A control strategy start time information item that is based on a condition that triggers the control strategy.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">control strategy reactive start time information</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete control strategy reactive start time information</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -1035,10 +1035,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000012">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000029"/>
         <obo:IAO_0000115 xml:lang="en">A numeral that is part of a simulation time step action specification.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A number of time step units in a time step of a simulation.  
-
-For example, if the time step is 6 hours, then this value is 6.
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>numberOfUnitsOfTimeInOneSimulatorStep</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation time step value</rdfs:label>
     </owl:Class>
@@ -1085,10 +1082,7 @@ For example, if the time step is 6 hours, then this value is 6.
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">The action specification that specifies the number of time steps a simulation is going to run.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The number of time steps in a simulator run.
-
-For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>runLength</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation run length</rdfs:label>
     </owl:Class>
@@ -1149,11 +1143,7 @@ Note that the susceptible and infectious organisms can be of different species.<
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
-        <obo:IAO_0000600 xml:lang="en">A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  
-
-Note that the susceptible and infected organisms can be of different species.
-
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>latentPeriodDuration</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs</rdfs:comment>
         <rdfs:comment xml:lang="en">The duration of the period between when an organism becomes infected and when it becomes infectious.</rdfs:comment>
@@ -1218,11 +1208,10 @@ Note that the susceptible and infected organisms can be of different species.
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">The count of (simulated organisms) in a simulated population.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
-        <obo:IAO_0000600 xml:lang="en">The number of simulated organisms in a simulated population.  The number does not have to be an integer.  </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of simulated organisms in a simulated population.  The number does not have to be an integer.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  
 
-Any ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’
-</rdfs:comment>
+Any ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’</rdfs:comment>
         <rdfs:label xml:lang="en">count of simulated population</rdfs:label>
     </owl:Class>
     
@@ -1233,7 +1222,7 @@ Any ideas?  I’ve considered and rejected allowing individual organisms to be f
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000023">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000084"/>
         <obo:IAO_0000115 xml:lang="en">An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">vaccination dose schedule</rdfs:label>
     </owl:Class>
     
@@ -1248,8 +1237,7 @@ Any ideas?  I’ve considered and rejected allowing individual organisms to be f
         <rdfs:comment xml:lang="en">MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class &quot;eligibility rule&quot; in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.</rdfs:comment>
         <rdfs:comment xml:lang="en">MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.
 
-It is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.
-</rdfs:comment>
+It is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.</rdfs:comment>
         <rdfs:label xml:lang="en">vaccination compliance</rdfs:label>
     </owl:Class>
     
@@ -1381,8 +1369,8 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:someValuesFrom>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">infectious disease control strategy execution</rdfs:label>
     </owl:Class>
     
@@ -1508,6 +1496,7 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -1663,10 +1652,9 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:someValuesFrom>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A simulated organism in a simulated population that is not susceptible. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A simulated organism in a simulated population that is not susceptible.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. 
-Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.
-</obo:IAO_0000600>
+Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">simulation of recovered organism</rdfs:label>
     </owl:Class>
     
@@ -1735,7 +1723,7 @@ Note that the name for this concept, were it to be named based on its intent, wo
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">The number of susceptible organisms that each infected organism infects.  ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ReproductionNumber</apollo_sv:APOLLO_SV_0000040>
@@ -1845,8 +1833,8 @@ Preventable outcomes include but are not limited to infection, infectiousness, s
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000049">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000243"/>
-        <obo:IAO_0000115 xml:lang="en">The value of the time interval between an organism&apos;s taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">The value of the time interval between an organism&apos;s taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">antiviral efficacy delay</rdfs:label>
     </owl:Class>
     
@@ -1857,7 +1845,7 @@ Preventable outcomes include but are not limited to infection, infectiousness, s
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000050">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0302867"/>
         <obo:IAO_0000115 xml:lang="en">The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The fraction of individuals in a simulated population that will accept antiviral treatment if offered. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The fraction of individuals in a simulated population that will accept antiviral treatment if offered.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>antiviral cm compliance</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class &quot;eligibility rule&quot; in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.</rdfs:comment>
         <rdfs:comment xml:lang="en">MW: Since the estimates that modelers use are from real populations, I have two questions:
@@ -1874,7 +1862,7 @@ MB: This issue will need to be taken care of in the axiomatization of simulated
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000051">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000795"/>
-        <obo:IAO_0000115 xml:lang="en">An action specification giving the number of doses of an antiviral to be made available during a specific time interval. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">An action specification giving the number of doses of an antiviral to be made available during a specific time interval.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">Counts of antiviral doses that become available in a specific location per time step unit.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">antiviral supply schedule</rdfs:label>
     </owl:Class>
@@ -2029,13 +2017,12 @@ MB: This issue will need to be taken care of in the axiomatization of simulated
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000060">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000070"/>
-        <obo:IAO_0000115>The simulation of an antiviral control measure. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The simulation of an antiviral control measure.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>antiviral control measure</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn&apos;t able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).
 AND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.
-Maybe we need to discuss this.
-</rdfs:comment>
+Maybe we need to discuss this.</rdfs:comment>
         <rdfs:label xml:lang="en">simulation of antiviral control measure</rdfs:label>
     </owl:Class>
     
@@ -2160,8 +2147,7 @@ Maybe we need to discuss this.
 
 One property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.
 
-While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.
-</rdfs:comment>
+While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.</rdfs:comment>
         <rdfs:label xml:lang="en">simulation time series</rdfs:label>
     </owl:Class>
     
@@ -2223,6 +2209,12 @@ While in many pieces of fiction the order in which the purely intentional entiti
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000067"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000038"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates a temporal interval of pre-specified length.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates a temporal interval of pre-specified length.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>simulation time step</apollo_sv:APOLLO_SV_0000040>
@@ -2320,12 +2312,8 @@ The time step value and unit are specified using a scalar value specification.</
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates an entity and its properties.
-
-</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates an entity and its properties.
-
-</obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates an entity and its properties.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates an entity and its properties.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>simulation</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation</rdfs:label>
     </owl:Class>
@@ -2456,7 +2444,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">the mean or expectation of a distribution</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>μ</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">μ</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete μ</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -2468,7 +2456,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">standard deviation</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>sigma</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">σ</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete σ</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -2490,7 +2478,7 @@ The time step value and unit are specified using a scalar value specification.</
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000079">
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated log normal distribution</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete log normal distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -2551,7 +2539,7 @@ The time step value and unit are specified using a scalar value specification.</
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">control strategy dose schedule</rdfs:label>
     </owl:Class>
     
@@ -2593,6 +2581,33 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                                <owl:someValuesFrom>
+                                    <owl:Class>
+                                        <owl:intersectionOf rdf:parseType="Collection">
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000038"/>
+                                            <owl:Restriction>
+                                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000156"/>
+                                                <owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
+                                                <owl:onClass rdf:resource="http://purl.obolibrary.org/obo/BFO_0000182"/>
+                                            </owl:Restriction>
+                                        </owl:intersectionOf>
+                                    </owl:Class>
+                                </owl:someValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000111 xml:lang="en">age structure data set</obo:IAO_0000111>
         <obo:IAO_0000115>A data set consisting of measurements of age organized in age brackets.</obo:IAO_0000115>
         <obo:IAO_0000600>A data set consisting of measurements of age organized in age brackets.</obo:IAO_0000600>
@@ -2692,13 +2707,44 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000025"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/PCO_0000000"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
+                                <owl:allValuesFrom>
+                                    <owl:Class>
+                                        <owl:intersectionOf rdf:parseType="Collection">
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
+                                            <owl:Restriction>
+                                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000142"/>
+                                            </owl:Restriction>
+                                        </owl:intersectionOf>
+                                    </owl:Class>
+                                </owl:allValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A vaccination efficacy that results from a vaccination efficacy study.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>VaccinationEfficacyMeasured</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’
 
-2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.
-</rdfs:comment>
+2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.</rdfs:comment>
         <rdfs:label xml:lang="en">measured vaccination efficacy</rdfs:label>
     </owl:Class>
     
@@ -2722,6 +2768,7 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000471"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -2796,6 +2843,12 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PCO_0000001"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">Two or more distinct populations that are part of the same biotic ecosystem.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">Two or more distinct populations that are part of the same biotic ecosystem.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>community</apollo_sv:APOLLO_SV_0000040>
@@ -2811,7 +2864,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">a probability distribution over a discrete random variable</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>discrete probability distribution</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label>deprecated discrete probability distribution</rdfs:label>
+        <rdfs:label>obsolete discrete probability distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -2831,8 +2884,8 @@ The time step value and unit are specified using a scalar value specification.</
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000097">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <obo:IAO_0000115 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region. </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region. </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>Ecosystem</apollo_sv:APOLLO_SV_0000040>
         <dc:creator xml:lang="en">William R. Hogan</dc:creator>
         <rdfs:label xml:lang="en">ecosystem</rdfs:label>
@@ -3292,19 +3345,16 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000114"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  
 
-Note that the susceptible and infectious organisms can be of different species.
-
-</obo:IAO_0000600>
+Note that the susceptible and infectious organisms can be of different species.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>InfectionAcquisition</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.
 The likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   
-An infection is acquired from an infectious organism or a contaminated thing. 
-</rdfs:comment>
-        <rdfs:comment xml:lang="en">Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing</rdfs:comment>
+An infection is acquired from an infectious organism or a contaminated thing.</rdfs:comment>
+        <rdfs:comment xml:lang="en">Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing.</rdfs:comment>
         <rdfs:label xml:lang="en">infection acquisition</rdfs:label>
     </owl:Class>
     
@@ -3475,7 +3525,7 @@ An infection is acquired from an infectious organism or a contaminated thing.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000125">
         <obo:IAO_0000600 xml:lang="en">The time steps that a school will be in session.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">school calendar</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete school calendar</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -3545,8 +3595,7 @@ An infection is acquired from an infectious organism or a contaminated thing.
         <obo:IAO_0000115 xml:lang="en">A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.
 
-The event could be infection acquisition, vaccination, antiviral treatment, etc.
-</obo:IAO_0000600>
+The event could be infection acquisition, vaccination, antiviral treatment, etc.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>reactiveControlMeasureThreshold</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">reactive control strategy threshold</rdfs:label>
     </owl:Class>
@@ -3651,7 +3700,7 @@ For example, once a vaccination control strategy starts, individual vaccinations
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000137">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000032"/>
-        <obo:IAO_0000600 xml:lang="en">the number of distinct antigenic strains in a vaccine product </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of distinct antigenic strains in a vaccine product.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>valence</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">vaccine valence</rdfs:label>
     </owl:Class>
@@ -3904,7 +3953,7 @@ For example, once a vaccination control strategy starts, individual vaccinations
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000143">
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <rdfs:comment xml:lang="en">replaced with VO &apos;vaccine function&apos;</rdfs:comment>
-        <rdfs:label xml:lang="en">vaccine disposition</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete vaccine disposition</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -3968,7 +4017,7 @@ Somehow, it&apos;s not innate and it&apos;s temporary, ie, the body will eventua
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000146">
         <obo:IAO_0000600 xml:lang="en">Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">it is the same thing as transmission coefficient</rdfs:comment>
-        <rdfs:label xml:lang="en">beta</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete beta</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -3989,7 +4038,7 @@ Somehow, it&apos;s not innate and it&apos;s temporary, ie, the body will eventua
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000148">
         <obo:IAO_0000600 xml:lang="en">random number seed</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">random number seed</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete random number seed</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -4444,7 +4493,7 @@ I checked because an infection and immunity census would involve two different c
         <obo:IAO_0000115 xml:lang="en">An ecosystem in which a population of hosts is undergoing at least one infection.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An ecosystem in which a population of hosts is undergoing at least one infection.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">MIDAS scenario</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete MIDAS scenario</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -4674,7 +4723,7 @@ I checked because an infection and immunity census would involve two different c
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An independent continuant that is the localization of a pathogen, but is not undergoing an infection.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ContaminatedThing</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:comment xml:lang="en">A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    </rdfs:comment>
+        <rdfs:comment xml:lang="en">A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.</rdfs:comment>
         <rdfs:label xml:lang="en">contaminated thing</rdfs:label>
     </owl:Class>
     
@@ -5100,6 +5149,12 @@ I checked because an infection and immunity census would involve two different c
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000015"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>SimulatorTimeSpecification</apollo_sv:APOLLO_SV_0000040>
@@ -5217,7 +5272,7 @@ The infectious disease scenario typically also includes a lot of additional data
         <obo:IAO_0000115 xml:lang="en">A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.</rdfs:comment>
-        <rdfs:comment xml:lang="en">This census should exclude infection, immunity, treatment, or contamination.  </rdfs:comment>
+        <rdfs:comment xml:lang="en">This census should exclude infection, immunity, treatment, or contamination.</rdfs:comment>
         <rdfs:label xml:lang="en">population and environment census</rdfs:label>
     </owl:Class>
     
@@ -5303,6 +5358,7 @@ Note that the infected and susceptible organisms may be of different species.</o
     <!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000194 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000194">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000086"/>
         <rdfs:subClassOf>
             <owl:Class>
                 <owl:intersectionOf rdf:parseType="Collection">
@@ -5329,6 +5385,27 @@ Note that the infected and susceptible organisms may be of different species.</o
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000007"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                                <owl:someValuesFrom>
+                                    <owl:Restriction>
+                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
+                                        <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000090"/>
+                                    </owl:Restriction>
+                                </owl:someValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000112 xml:lang="en">vaccination control strategy, antiviral control strategy</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">An infectious disease control strategy that immediately targets individuals.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
@@ -5364,7 +5441,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000197">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000188"/>
-        <rdfs:comment xml:lang="en">An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. </rdfs:comment>
+        <rdfs:comment xml:lang="en">An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved.</rdfs:comment>
         <rdfs:label xml:lang="en">agent level population and environment census</rdfs:label>
     </owl:Class>
     
@@ -5374,7 +5451,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000198">
         <rdfs:comment xml:lang="en">At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics.</rdfs:comment>
-        <rdfs:label xml:lang="en">agent model ecosystem census description</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete agent model ecosystem census description</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -5384,7 +5461,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000199">
         <rdfs:comment xml:lang="en">The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census).</rdfs:comment>
-        <rdfs:label xml:lang="en">compartment model population and environment census</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete compartment model population and environment census</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -5417,7 +5494,7 @@ Note that the infected and susceptible organisms may be of different species.</o
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000202">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
         <apollo_sv:APOLLO_SV_0000040>ApolloIndexableItem</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:comment xml:lang="en">A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. </rdfs:comment>
+        <rdfs:comment xml:lang="en">A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved.</rdfs:comment>
         <rdfs:label xml:lang="en">indexable Apollo item</rdfs:label>
     </owl:Class>
     
@@ -5665,9 +5742,9 @@ Note that the infected and sucseptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000215">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
-        <obo:IAO_0000115 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.</obo:IAO_0000115>
         <obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Probability_distribution</obo:IAO_0000119>
-        <obo:IAO_0000600 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ProbabilityDistribution</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">probability distribution</rdfs:label>
     </owl:Class>
@@ -6251,7 +6328,7 @@ can&apos;t recall whether we should use process or processual_entity for future
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0100001>http://purl.obolibrary.org/obo/STATO_0000321</obo:IAO_0100001>
         <apollo_sv:APOLLO_SV_0000040>NonparametricProbabilityDistribution</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">nonparametric probability distribution</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete nonparametric probability distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -6545,8 +6622,7 @@ For example, it may take time to communicate to workers to stop vaccinating and
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An infection acquisition from an individual who is infectious.
 
-The individual acquiring the infection can be of a different species than the one who is infectious.
-</obo:IAO_0000600>
+The individual acquiring the infection can be of a different species than the one who is infectious.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>InfectionAcquisitionFromInfectedHost</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">infection acquisition from infectious host</rdfs:label>
     </owl:Class>
@@ -6588,8 +6664,7 @@ The individual acquiring the infection can be of a different species than the on
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.
 
-In epidemic simulation, it can be &apos;simulator time&apos; where time zero is the starting point of an infectious disease scenario, or it can be &apos;control strategy time&apos; where time zero is the time at which the control strategy is initiated.
-</obo:IAO_0000600>
+In epidemic simulation, it can be &apos;simulator time&apos; where time zero is the starting point of an infectious disease scenario, or it can be &apos;control strategy time&apos; where time zero is the time at which the control strategy is initiated.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>timeScale</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">time scale name</rdfs:label>
     </owl:Class>
@@ -6906,8 +6981,7 @@ For example, the trigger could occur once the incidence or prevalence of the inf
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">The unit of measure for the supply schedule of an individual treatment.
 
-For example, &apos;daily dose&apos;.
-</obo:IAO_0000600>
+For example, &apos;daily dose&apos;.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>supplyScheduleUnits</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">individual treatment strategy supply schedule unit of measure</rdfs:label>
     </owl:Class>
@@ -6960,8 +7034,7 @@ For example, &apos;daily dose&apos;.</obo:IAO_0000600>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A specification of the criteria an organism must meet to be considered to be in some abnormal state.
 
-The abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.
-</obo:IAO_0000600>
+The abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>CaseDefinition</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">case definition</rdfs:label>
     </owl:Class>
@@ -7291,7 +7364,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000651"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0032504"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0048609"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
@@ -7988,7 +8061,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -8011,7 +8084,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -8663,7 +8736,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -8686,7 +8759,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -8736,7 +8809,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:someValuesFrom>
                                             <owl:Class>
                                                 <owl:intersectionOf rdf:parseType="Collection">
-                                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                                     <owl:Restriction>
                                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
                                                         <owl:someValuesFrom>
@@ -8775,7 +8848,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:someValuesFrom>
                                     <owl:Class>
                                         <owl:intersectionOf rdf:parseType="Collection">
-                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
                                                 <owl:someValuesFrom>
@@ -8826,7 +8899,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -8849,7 +8922,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -9011,7 +9084,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000371"/>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:intersectionOf>
                             </owl:Class>
@@ -9030,7 +9103,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000371"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -9522,7 +9595,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated homeostasis</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete homeostasis</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9936,7 +10009,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A count of individuals in a population who meet an infection case definition during a particular time interval.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated infection case count</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete infection case count</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -10492,7 +10565,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A one-dimensional temporal region occupied by a place closure control strategy.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">closure period</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete closure period</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -11054,7 +11127,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A time measurement datum of the length of the temporal interval occupied by a gonotropic period.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">gonotrophic period duration</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete gonotrophic period duration</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -11327,7 +11400,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000600 xml:lang="en">An identifier curated by ORCID, Inc. to denote some academic author.</obo:IAO_0000600>
         <obo:IAO_0100001 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/IAO_0000708</obo:IAO_0100001>
         <apollo_sv:APOLLO_SV_0000040>orcId</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">ORCID</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete ORCID</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -12922,7 +12995,6 @@ has specified input some case definition.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">census of treatment facilities</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">treatment facilities census</obo:IAO_0000118>
-        <obo:IAO_0000118 xml:lang="en">treatment facility census</obo:IAO_0000118>
         <obo:IAO_0000600 xml:lang="en">A census that counts the number of treatment facilities of some kind in a particular geographical region.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">NOTE: this class counts the facilities themselves, not patients (people) in those facilities.  For example, how many hospitals in a state.  Not how many patients are in a hospital or hospitals in a state.</rdfs:comment>
         <rdfs:label xml:lang="en">treatment facility census</rdfs:label>
@@ -14046,6 +14118,7 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -14077,6 +14150,7 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -14241,6 +14315,12 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
     
 
 
+    <!-- http://purl.obolibrary.org/obo/COB_0000035 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000035"/>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/DOID_3292 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_3292"/>
@@ -14319,12 +14399,6 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
     
 
 
-    <!-- http://purl.obolibrary.org/obo/GO_0032504 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0032504"/>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/GO_0044409 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044409"/>
@@ -14337,6 +14411,12 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
     
 
 
+    <!-- http://purl.obolibrary.org/obo/GO_0048609 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0048609"/>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/GO_0051701 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0051701"/>
@@ -14751,21 +14831,21 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
     
 
 
-    <!-- http://purl.obolibrary.org/obo/UBERON_0000479 -->
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000071 -->
 
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000479"/>
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071"/>
     
 
 
-    <!-- http://purl.obolibrary.org/obo/UBERON_0002405 -->
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000479 -->
 
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002405"/>
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000479"/>
     
 
 
-    <!-- http://purl.obolibrary.org/obo/UBERON_0035944 -->
+    <!-- http://purl.obolibrary.org/obo/UBERON_0002405 -->
 
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002405"/>
     
 
 
diff --git a/apollo_sv-full.json b/apollo_sv-full.json
index e2ca93e..ef02b3a 100644
--- a/apollo_sv-full.json
+++ b/apollo_sv-full.json
@@ -49,9 +49,9 @@
         "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl.  When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)."
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2024-12-24"
+        "val" : "2026-03-13"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv-full.json"
+      "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv-full.json"
     },
     "nodes" : [ {
       "id" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160",
@@ -248,7 +248,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000011",
-      "lbl" : "control strategy reactive start time information",
+      "lbl" : "obsolete control strategy reactive start time information",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -273,7 +273,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A number of time step units in a time step of a simulation.  \n\nFor example, if the time step is 6 hours, then this value is 6.\n"
+          "val" : "A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "numberOfUnitsOfTimeInOneSimulatorStep"
@@ -318,7 +318,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The number of time steps in a simulator run.\n\nFor example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.\n"
+          "val" : "The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "runLength"
@@ -358,7 +358,7 @@
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  \n\nNote that the susceptible and infected organisms can be of different species.\n\n"
+          "val" : "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "latentPeriodDuration"
@@ -412,13 +412,13 @@
         "definition" : {
           "val" : "The count of (simulated organisms) in a simulated population."
         },
-        "comments" : [ "MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n" ],
+        "comments" : [ "MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The number of simulated organisms in a simulated population.  The number does not have to be an integer.  "
+          "val" : "The number of simulated organisms in a simulated population.  The number does not have to be an integer."
         } ]
       }
     }, {
@@ -431,7 +431,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. "
+          "val" : "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism."
         } ]
       }
     }, {
@@ -442,7 +442,7 @@
         "definition" : {
           "val" : "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination."
         },
-        "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.\n" ],
+        "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint."
@@ -495,11 +495,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  "
+          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  "
+          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease."
         } ]
       }
     }, {
@@ -641,11 +641,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A simulated organism in a simulated population that is not susceptible. "
+          "val" : "A simulated organism in a simulated population that is not susceptible."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.\n"
+          "val" : "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage."
         } ]
       }
     }, {
@@ -673,7 +673,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. "
+          "val" : "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
@@ -763,11 +763,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. "
+          "val" : "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. "
+          "val" : "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection."
         } ]
       }
     }, {
@@ -781,7 +781,7 @@
         "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2.  If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. "
+          "val" : "The fraction of individuals in a simulated population that will accept antiviral treatment if offered."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "antiviral cm compliance"
@@ -793,7 +793,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "An action specification giving the number of doses of an antiviral to be made available during a specific time interval. "
+          "val" : "An action specification giving the number of doses of an antiviral to be made available during a specific time interval."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
@@ -907,9 +907,9 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The simulation of an antiviral control measure. "
+          "val" : "The simulation of an antiviral control measure."
         },
-        "comments" : [ "MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.\n" ],
+        "comments" : [ "MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism."
@@ -962,7 +962,7 @@
         "definition" : {
           "val" : "A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation."
         },
-        "comments" : [ "MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.\n" ],
+        "comments" : [ "MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation."
@@ -1037,11 +1037,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A purely intentional entity that simulates an entity and its properties.\n\n"
+          "val" : "A purely intentional entity that simulates an entity and its properties."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A purely intentional entity that simulates an entity and its properties.\n\n"
+          "val" : "A purely intentional entity that simulates an entity and its properties."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "simulation"
@@ -1119,7 +1119,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000076",
-      "lbl" : "μ",
+      "lbl" : "obsolete μ",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1133,7 +1133,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000077",
-      "lbl" : "σ",
+      "lbl" : "obsolete σ",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1160,7 +1160,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000079",
-      "lbl" : "deprecated log normal distribution",
+      "lbl" : "obsolete log normal distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1231,7 +1231,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. "
+          "val" : "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism."
         } ]
       }
     }, {
@@ -1301,7 +1301,7 @@
         "definition" : {
           "val" : "A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study."
         },
-        "comments" : [ "1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.\n" ],
+        "comments" : [ "1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A vaccination efficacy that results from a vaccination efficacy study."
@@ -1387,7 +1387,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000095",
-      "lbl" : "deprecated discrete probability distribution",
+      "lbl" : "obsolete discrete probability distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1416,11 +1416,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The sum of all biotic and abiotic entities in a geographical region. "
+          "val" : "The sum of all biotic and abiotic entities in a geographical region."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The sum of all biotic and abiotic entities in a geographical region. "
+          "val" : "The sum of all biotic and abiotic entities in a geographical region."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "Ecosystem"
@@ -1672,15 +1672,15 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources"
+          "val" : "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources."
         },
-        "comments" : [ "Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing. \n", "Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing" ],
+        "comments" : [ "Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing.", "Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species.\n\n"
+          "val" : "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "InfectionAcquisition"
@@ -1795,7 +1795,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000125",
-      "lbl" : "school calendar",
+      "lbl" : "obsolete school calendar",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1881,7 +1881,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc.\n"
+          "val" : "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "reactiveControlMeasureThreshold"
@@ -1955,7 +1955,7 @@
       "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "the number of distinct antigenic strains in a vaccine product "
+          "val" : "The number of distinct antigenic strains in a vaccine product."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "valence"
@@ -2035,7 +2035,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000143",
-      "lbl" : "vaccine disposition",
+      "lbl" : "obsolete vaccine disposition",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "replaced with VO 'vaccine function'" ],
@@ -2079,7 +2079,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000146",
-      "lbl" : "beta",
+      "lbl" : "obsolete beta",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "it is the same thing as transmission coefficient" ],
@@ -2104,7 +2104,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000148",
-      "lbl" : "random number seed",
+      "lbl" : "obsolete random number seed",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -2282,7 +2282,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000161",
-      "lbl" : "MIDAS scenario",
+      "lbl" : "obsolete MIDAS scenario",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -2382,7 +2382,7 @@
         "definition" : {
           "val" : "An independent continuant that is the localization of a pathogen, but is not undergoing an infection."
         },
-        "comments" : [ "A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    " ],
+        "comments" : [ "A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
@@ -2701,7 +2701,7 @@
         "definition" : {
           "val" : "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero."
         },
-        "comments" : [ "Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.", "This census should exclude infection, immunity, treatment, or contamination.  " ],
+        "comments" : [ "Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.", "This census should exclude infection, immunity, treatment, or contamination." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero."
@@ -2829,11 +2829,11 @@
       "lbl" : "agent level population and environment census",
       "type" : "CLASS",
       "meta" : {
-        "comments" : [ "An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. " ]
+        "comments" : [ "An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved." ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000198",
-      "lbl" : "agent model ecosystem census description",
+      "lbl" : "obsolete agent model ecosystem census description",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics." ],
@@ -2841,7 +2841,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000199",
-      "lbl" : "compartment model population and environment census",
+      "lbl" : "obsolete compartment model population and environment census",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census)." ],
@@ -2878,7 +2878,7 @@
       "lbl" : "indexable Apollo item",
       "type" : "CLASS",
       "meta" : {
-        "comments" : [ "A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. " ],
+        "comments" : [ "A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "ApolloIndexableItem"
@@ -3110,14 +3110,14 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. "
+          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://en.wikipedia.org/wiki/Probability_distribution"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. "
+          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "ProbabilityDistribution"
@@ -3696,7 +3696,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000249",
-      "lbl" : "nonparametric probability distribution",
+      "lbl" : "obsolete nonparametric probability distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -3988,7 +3988,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious.\n"
+          "val" : "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "InfectionAcquisitionFromInfectedHost"
@@ -4046,7 +4046,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated.\n"
+          "val" : "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "timeScale"
@@ -4439,7 +4439,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'.\n"
+          "val" : "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "supplyScheduleUnits"
@@ -4506,7 +4506,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.\n"
+          "val" : "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "CaseDefinition"
@@ -5877,7 +5877,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000370",
-      "lbl" : "deprecated homeostasis",
+      "lbl" : "obsolete homeostasis",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -6436,7 +6436,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000399",
-      "lbl" : "deprecated infection case count",
+      "lbl" : "obsolete infection case count",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -7211,7 +7211,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000435",
-      "lbl" : "closure period",
+      "lbl" : "obsolete closure period",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -8080,7 +8080,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000475",
-      "lbl" : "gonotrophic period duration",
+      "lbl" : "obsolete gonotrophic period duration",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -8492,7 +8492,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000496",
-      "lbl" : "ORCID",
+      "lbl" : "obsolete ORCID",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -10390,9 +10390,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "treatment facilities census"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "treatment facility census"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A census that counts the number of treatment facilities of some kind in a particular geographical region."
@@ -12159,21 +12156,12 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000602",
-          "val" : "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] "
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000602",
           "val" : "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] "
         }, {
           "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
           "val" : "http://purl.obolibrary.org/obo/bfo.owl"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://github.com/OBOFoundry/COB/issues/65"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://github.com/oborel/obo-relations/pull/284"
         } ]
       }
     }, {
@@ -12356,6 +12344,9 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects "
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects "
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."
@@ -12722,6 +12713,9 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"
@@ -13025,6 +13019,26 @@
       "meta" : {
         "comments" : [ "The usage or intended usage of a drug product to act against a viral infection of a host." ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/COB_0000022",
+      "lbl" : "organism",
+      "type" : "CLASS",
+      "meta" : {
+        "definition" : {
+          "val" : "A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome"
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "Includes virus - we will later have a class for cellular organisms."
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/COB_0000035",
+      "lbl" : "completely executed planned process",
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/DOID_0060478",
       "lbl" : "Zika fever",
@@ -13238,21 +13252,36 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/DRON_00000005",
-      "lbl" : "drug product",
+      "lbl" : "clinical drug product",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role"
+          "val" : "A drug product that is bearer of a clinical drug role."
         },
+        "comments" : [ "We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a \"clinical drug role\" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf \"drug product\", which also required changing the definition here." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "William Hogan"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/DRON_00000074",
+      "lbl" : "drug product",
+      "type" : "CLASS",
+      "meta" : {
+        "definition" : {
+          "val" : "A material entity that (1) contains at least one scattered molecular aggregate as part and (2) is intended, when administered to an organism, to produce some therapeutic and/or psychoactive effect."
+        },
+        "comments" : [ "The \"intention\" part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered.", "The psychoactive effect is added for illicit drugs such as crack cocaine.", "We are including prophylactic and diagnostic effects / usage under the more general heading of 'therapeutic'." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
+          "val" : "William R. Hogan"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/dron.owl"
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0001-6378-1703"
         }, {
-          "pred" : "http://purl.org/dc/elements/1.1/creator",
-          "val" : "William Hogan"
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0002-5039-2052"
         } ]
       }
     }, {
@@ -14121,10 +14150,14 @@
           "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.",
           "xrefs" : [ "GOC:pdt" ]
         },
-        "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ],
+        "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "molecular function"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This is the same as GO molecular function"
         } ]
       }
     }, {
@@ -14198,7 +14231,7 @@
         "definition" : {
           "val" : "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end."
         },
-        "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ],
+        "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -14217,9 +14250,6 @@
           "val" : "Wikipedia:Biological_process"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/24968"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/go.owl"
         }, {
@@ -14265,6 +14295,8 @@
           "val" : "virulence"
         } ],
         "xrefs" : [ {
+          "val" : "Reactome:R-HSA-162906"
+        }, {
           "val" : "Wikipedia:Viral_life_cycle"
         } ],
         "basicPropertyValues" : [ {
@@ -14321,6 +14353,13 @@
           "val" : "viral replication",
           "xrefs" : [ "GOC:bf", "GOC:jl" ]
         } ],
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-162588"
+        }, {
+          "val" : "Reactome:R-HSA-168255"
+        }, {
+          "val" : "Reactome:R-HSA-9609646"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "GO:0019067"
@@ -14355,9 +14394,6 @@
           "val" : "single-organism reproductive behavior"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/23491"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/go.owl"
         }, {
@@ -14390,13 +14426,11 @@
           "xrefs" : [ "Wikipedia:Sexual_reproduction" ]
         },
         "comments" : [ "Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ],
         "xrefs" : [ {
           "val" : "Wikipedia:Sexual_reproduction"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/22929"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
         } ]
@@ -14419,9 +14453,6 @@
           "val" : "Wikipedia:Asexual_reproduction"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/22929"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
         } ]
@@ -14444,17 +14475,20 @@
           "val" : "Wikipedia:Reproduction"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/27054"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "jl"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-09-19T15:56:06Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "GO:0019952"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "GO:0044702"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "GO:0050876"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
@@ -14479,9 +14513,6 @@
           "val" : "single-multicellular organism process"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/27189"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "jl"
         }, {
@@ -14498,28 +14529,6 @@
           "val" : "biological_process"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/GO_0032504",
-      "lbl" : "obsolete multicellular organism reproduction",
-      "type" : "CLASS",
-      "meta" : {
-        "definition" : {
-          "val" : "OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.",
-          "xrefs" : [ "GOC:isa_complete", "GOC:jid" ]
-        },
-        "comments" : [ "The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process." ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/27054"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "GO:0048609"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "biological_process"
-        } ],
-        "deprecated" : true
-      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/GO_0044403",
       "lbl" : "biological process involved in symbiotic interaction",
@@ -14562,12 +14571,6 @@
           "val" : "symbiotic process"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/14807"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/20191"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "GO:0043298"
         }, {
@@ -14663,10 +14666,10 @@
           "pred" : "hasRelatedSynonym",
           "val" : "other organism invasion"
         } ],
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-173107"
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/18563"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/go.owl"
         }, {
@@ -14721,10 +14724,10 @@
           "pred" : "hasExactSynonym",
           "val" : "interspecies interaction with other organisms"
         } ],
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-9824443"
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/20191"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
         } ]
@@ -14746,10 +14749,10 @@
           "pred" : "hasExactSynonym",
           "val" : "reproductive process in a multicellular organism"
         } ],
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-1474165"
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/27054"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
         } ]
@@ -14795,10 +14798,12 @@
           "pred" : "hasNarrowSynonym",
           "val" : "growth of symbiont in host vacuole"
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/20191"
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-9635486"
         }, {
+          "val" : "Reactome:R-HSA-9658195"
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "GO:0044112"
         }, {
@@ -19946,9 +19951,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "proper name"
@@ -19992,7 +19994,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."
+          "val" : "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
@@ -20000,9 +20002,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "dubbing process"
@@ -20032,9 +20031,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://en.wikipedia.org/wiki/Personal_name"
@@ -20114,9 +20110,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "code map"
@@ -23331,6 +23324,15 @@
           "val" : "Micrococcus pneumoniae"
         } ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/NCBITaxon_131567",
+      "lbl" : "cellular organisms",
+      "type" : "CLASS",
+      "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        } ]
+      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1329799",
       "lbl" : "Archelosauria",
@@ -25324,6 +25326,13 @@
       "lbl" : "Eukaryota",
       "type" : "CLASS",
       "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        }, {
+          "val" : "PMID:23020233"
+        }, {
+          "val" : "PMID:30257078"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl"
@@ -26723,6 +26732,9 @@
       "lbl" : "Mammalia",
       "type" : "CLASS",
       "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "mammals"
@@ -30550,6 +30562,9 @@
       "lbl" : "Primates",
       "type" : "CLASS",
       "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "Primata"
@@ -30782,13 +30797,10 @@
       "lbl" : "Homo sapiens",
       "type" : "CLASS",
       "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "Homo sapiens"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "human being"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl"
         } ]
@@ -31353,9 +31365,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "planned process"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "planned process"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "Injecting mice with a vaccine in order to test its efficacy"
@@ -31368,21 +31377,12 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \n  objectives is a planned process."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Bjoern Peters"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "branch derived"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "6/11/9: Edited at workshop. Used to include: is initiated by an agent"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/obi.owl"
@@ -31751,7 +31751,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent."
+          "val" : "A device is a processed material which is designed to perform some function or functions"
         },
         "comments" : [ "would include reagents" ],
         "basicPropertyValues" : [ {
@@ -31760,18 +31760,9 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "A voltmeter is a measurement device which is intended to perform some measure function."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
-          "val" : "http://purl.obolibrary.org/obo/IAO_0000122"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
           "val" : "http://purl.obolibrary.org/obo/IAO_0000123"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions.  Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear.  For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component.  This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running  box  is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it.  This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation).  In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only"
@@ -31787,9 +31778,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "OBI Vancouver workshop 2010"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
-          "val" : "OBI development call 2012-12-17."
         } ]
       }
     }, {
@@ -32270,36 +32258,9 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "organism"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "animal"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "fungus"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "plant"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "virus"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
           "val" : "http://purl.obolibrary.org/obo/IAO_0000121"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
-          "val" : "http://purl.obolibrary.org/obo/IAO_0000122"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "13-02-2009:\nOBI doesn't take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "GROUP: OBI Biomaterial Branch"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
-          "val" : "WEB: http://en.wikipedia.org/wiki/Organism"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/obi.owl"
@@ -32658,9 +32619,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2010-07-19T10:18:02Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32680,12 +32638,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2009-06-23T10:21:58Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "result"
         } ]
       }
     }, {
@@ -32705,9 +32657,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2010-07-19T11:13:49Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32727,9 +32676,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2009-06-23T11:18:05Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32752,9 +32698,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "disease"
         } ]
       }
     }, {
@@ -32762,30 +32705,12 @@
       "lbl" : "homeostasis",
       "type" : "CLASS",
       "meta" : {
-        "definition" : {
-          "val" : "A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning."
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Barry Smith"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Richard H. Scheuermann"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Werner Ceusters"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
-          "val" : "Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. \n\nLink: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2009-06-23T11:22:01Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32808,9 +32733,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32836,9 +32758,6 @@
           "val" : "The totality of all processes through which a given disease instance is realized."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "disease course"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
         }, {
@@ -32850,12 +32769,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ido.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32879,9 +32792,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32890,9 +32800,8 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder"
+          "val" : "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process"
         },
-        "comments" : [ "Apollo-SV currently defines two subclasses of treatment.\nSee vaccination and antiviral treatment.  \n" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -32902,12 +32811,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2010-03-31T04:51:11Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "Treatment"
         } ]
       }
     }, {
@@ -32916,26 +32819,17 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A processual entity which has as parts all the processes in which a given organism is participant."
+          "val" : "A process which has as parts all the processes in which a given organism is participant."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Albert Goldfain"
+          "val" : "Albert Goldfain\nRichard Scheuermann\nSagar Jain"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://code.google.com/p/ogms/issues/detail?id=38"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "creation date: 2010-03-31T04:51:11Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A processual entity which has as parts all the processes in which a given organism is participant."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "LifeCycle"
+          "val" : "creation date: 2010-03-31T04:51:11Z\n\nEDIT: 10 NOV 2015"
         } ]
       }
     }, {
@@ -32944,20 +32838,17 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process"
+          "val" : "A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient"
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Albert Goldfain"
+          "val" : "Albert Goldfain\nSagar Jain"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
+          "val" : "creation date: 2011-02-21T09:57:44Z\neditor date: 2017-04-18"
         } ]
       }
     }, {
@@ -32968,6 +32859,10 @@
         "definition" : {
           "val" : "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role.  The health care provider role and patient are realized during the health care encounter"
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "healthcare encounter"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -32977,9 +32872,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32987,6 +32879,10 @@
       "lbl" : "hospitalization",
       "type" : "CLASS",
       "meta" : {
+        "definition" : {
+          "val" : "TODO"
+        },
+        "comments" : [ "09/16/2020\nIs this same as admission? \nIs this the same as inpatient encounter?" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -32996,12 +32892,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "hospitalization"
         } ]
       }
     }, {
@@ -33009,6 +32899,9 @@
       "lbl" : "outpatient encounter",
       "type" : "CLASS",
       "meta" : {
+        "definition" : {
+          "val" : "TODO"
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -33018,9 +32911,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -33040,16 +32930,16 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OGMS_0000101",
-      "lbl" : "ED encounter",
+      "lbl" : "emergency department encounter",
       "type" : "CLASS",
       "meta" : {
+        "definition" : {
+          "val" : "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -33059,9 +32949,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -33070,17 +32957,23 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course."
+          "val" : "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease."
         },
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course."
+        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Albert Goldfain"
+          "val" : "Albert Goldfain\nRichard Scheuermann\nSagar Jain"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
+          "val" : "recurrent"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://code.google.com/p/ogms/issues/detail?id=73"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
+          "pred" : "http://purl.org/dc/elements/1.1/date",
+          "val" : "10 NOV 2015"
         } ]
       }
     }, {
@@ -33126,21 +33019,22 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00000010",
-      "lbl" : "human health care role",
+      "lbl" : "health care role",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
           "val" : "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis."
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "healthcare role"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "William R. Hogan"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "health care role"
         } ]
       }
     }, {
@@ -33149,7 +33043,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter."
+          "val" : "A health care role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter."
         },
         "comments" : [ "In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications." ],
         "basicPropertyValues" : [ {
@@ -33174,6 +33068,10 @@
         "definition" : {
           "val" : "A role that inheres in an organization and that is realized by the providing of services in a health care encounter."
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "healthcare provider organization role"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.org/dc/elements/1.1/contributor",
           "val" : "Mathias Brochhausen"
@@ -33237,7 +33135,11 @@
         "definition" : {
           "val" : "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process"
         },
-        "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ]
+        "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "organization healthcare role"
+        } ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00000030",
@@ -33262,18 +33164,6 @@
           "val" : "William R. Hogan\nAmanda Hicks"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/OMRSE_00000048",
-      "lbl" : "material entity role",
-      "type" : "CLASS"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/OMRSE_00000049",
-      "lbl" : "organism role",
-      "type" : "CLASS"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/OMRSE_00000050",
-      "lbl" : "Homo sapiens role",
-      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00000051",
       "lbl" : "organization role",
@@ -33467,7 +33357,13 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00000172",
       "lbl" : "health care function",
-      "type" : "CLASS"
+      "type" : "CLASS",
+      "meta" : {
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "healthcare function"
+        } ]
+      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00002072",
       "lbl" : "role in human social processes",
@@ -34272,7 +34168,7 @@
           "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.",
           "xrefs" : [ "CARO:0000003" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "biological structure"
@@ -34294,7 +34190,7 @@
         }, {
           "val" : "EMAPA:0"
         }, {
-          "val" : "FBbt:00007001"
+          "val" : "FAO:0000001"
         }, {
           "val" : "FMA:305751"
         }, {
@@ -34305,8 +34201,6 @@
           "val" : "HAO:0000003"
         }, {
           "val" : "MA:0003000"
-        }, {
-          "val" : "MESH:A13"
         }, {
           "val" : "MESH:D000825"
         }, {
@@ -34317,27 +34211,77 @@
           "val" : "TGMA:0001823"
         }, {
           "val" : "VHOG:0001759"
-        }, {
-          "val" : "WBbt:0000100"
         }, {
           "val" : "XAO:0003000"
         }, {
           "val" : "ZFA:0000037"
         }, {
           "val" : "http://dbpedia.org/ontology/AnatomicalStructure"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0000071",
+      "lbl" : "death stage",
+      "type" : "CLASS",
+      "meta" : {
+        "definition" : {
+          "val" : "End of the life of an organism.",
+          "xrefs" : [ "XAO:0000437" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset" ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "death"
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
+        "xrefs" : [ {
+          "val" : "XAO:0000437"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
+          "val" : "XtroDO:0000085"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0000105",
+      "lbl" : "life cycle stage",
+      "type" : "CLASS",
+      "meta" : {
+        "definition" : {
+          "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism.",
+          "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "synonyms" : [ {
+          "pred" : "hasNarrowSynonym",
+          "val" : "developmental stage"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751"
+          "pred" : "hasNarrowSynonym",
+          "val" : "stage"
+        } ],
+        "xrefs" : [ {
+          "val" : "BILS:0000105"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
+          "val" : "EFO:0000399"
+        }, {
+          "val" : "FBdv:00007012"
+        }, {
+          "val" : "FMA:24120"
+        }, {
+          "val" : "MESH:D008018"
+        }, {
+          "val" : "PdumDv:0000090"
+        }, {
+          "val" : "WBls:0000002"
+        }, {
+          "val" : "XAO:1000000"
+        }, {
+          "val" : "ZFS:0000000"
+        }, {
+          "val" : "ZFS:0100000"
+        }, {
+          "val" : "ncithesaurus:Developmental_Stage"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here"
         } ]
       }
     }, {
@@ -34349,7 +34293,7 @@
           "val" : "Anatomical entity that has mass.",
           "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "xrefs" : [ {
           "val" : "AAO:0010264"
         }, {
@@ -34360,8 +34304,6 @@
           "val" : "CARO:0000006"
         }, {
           "val" : "EHDAA2:0003006"
-        }, {
-          "val" : "FBbt:00007016"
         }, {
           "val" : "FMA:67165"
         }, {
@@ -34372,19 +34314,6 @@
           "val" : "TGMA:0001826"
         }, {
           "val" : "VHOG:0001721"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
         } ]
       }
     }, {
@@ -34393,18 +34322,30 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]."
+          "val" : "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.",
+          "xrefs" : [ "CARO:0000011" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "synonyms" : [ {
           "pred" : "hasBroadSynonym",
-          "val" : "system"
+          "val" : "system",
+          "xrefs" : [ "GO:0048731" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "body system",
+          "xrefs" : [ "BIRNLEX:14" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "body system"
+          "val" : "connected anatomical system",
+          "xrefs" : [ "CARO:0000011" ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "organ system"
+        }, {
+          "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004",
+          "pred" : "hasRelatedSynonym",
+          "val" : "anatomical systems",
+          "xrefs" : [ "ZFA:0001439" ]
         } ],
         "xrefs" : [ {
           "val" : "AAO:0000007"
@@ -34412,6 +34353,8 @@
           "val" : "AEO:0000011"
         }, {
           "val" : "BILA:0000011"
+        }, {
+          "val" : "BIRNLEX:14"
         }, {
           "val" : "BSA:0000049"
         }, {
@@ -34426,8 +34369,6 @@
           "val" : "EMAPA:16103"
         }, {
           "val" : "EV:0100000"
-        }, {
-          "val" : "FBbt:00004856"
         }, {
           "val" : "FMA:7149"
         }, {
@@ -34435,17 +34376,13 @@
         }, {
           "val" : "MA:0000003"
         }, {
-          "val" : "NIF_GrossAnatomy:birnlex_14"
-        }, {
-          "val" : "OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ"
+          "val" : "NCIT:C12919"
         }, {
           "val" : "SCTID:278195005"
         }, {
           "val" : "TAO:0001439"
         }, {
           "val" : "TGMA:0001831"
-        }, {
-          "val" : "UMLS:C0460002"
         }, {
           "val" : "VHOG:0001725"
         }, {
@@ -34460,27 +34397,6 @@
           "val" : "ZFA:0001439"
         }, {
           "val" : "galen:AnatomicalSystem"
-        }, {
-          "val" : "ncithesaurus:Organ_System"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
-          "val" : "Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
-          "val" : "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
-          "val" : "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/EHDAA2_0001330"
         } ]
       }
     }, {
@@ -34489,19 +34405,21 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation."
+          "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.",
+          "xrefs" : [ "CARO:0000043" ]
         },
-        "comments" : [ "Editor note: changed label and definition to reflect CARO2" ],
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "portion of tissue"
+          "val" : "portion of tissue",
+          "xrefs" : [ "CARO:0000043" ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "tissue portion"
         }, {
           "pred" : "hasNarrowSynonym",
-          "val" : "simple tissue"
+          "val" : "simple tissue",
+          "xrefs" : [ "AEO:0000043" ]
         } ],
         "xrefs" : [ {
           "val" : "AAO:0000607"
@@ -34511,6 +34429,8 @@
           "val" : "AEO:0000043"
         }, {
           "val" : "BILA:0000043"
+        }, {
+          "val" : "BIRNLEX:19"
         }, {
           "val" : "CALOHA:TS-2090"
         }, {
@@ -34518,7 +34438,7 @@
         }, {
           "val" : "EHDAA2:0003043"
         }, {
-          "val" : "FBbt:00007003"
+          "val" : "EMAPA:35868"
         }, {
           "val" : "FMA:9637"
         }, {
@@ -34526,15 +34446,13 @@
         }, {
           "val" : "MA:0003002"
         }, {
-          "val" : "MESH:A10"
+          "val" : "MESH:D014024"
         }, {
-          "val" : "NIF_GrossAnatomy:birnlex_19"
+          "val" : "NCIT:C12801"
         }, {
           "val" : "TAO:0001477"
         }, {
           "val" : "TGMA:0001844"
-        }, {
-          "val" : "UMLS:C0040300"
         }, {
           "val" : "VHOG:0001757"
         }, {
@@ -34545,15 +34463,10 @@
           "val" : "ZFA:0001477"
         }, {
           "val" : "galen:Tissue"
-        }, {
-          "val" : "ncithesaurus:Tissue"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "changed label and definition to reflect CARO2"
         } ]
       }
     }, {
@@ -34562,9 +34475,10 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue."
+          "val" : "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.",
+          "xrefs" : [ "CARO:0000054", "http://orcid.org/0000-0001-9114-8737" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "xrefs" : [ {
           "val" : "AAO:0010008"
         }, {
@@ -34589,11 +34503,8 @@
           "val" : "ZFA:0001512"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]"
         } ]
       }
     }, {
@@ -34605,7 +34516,7 @@
           "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.",
           "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "xrefs" : [ {
           "val" : "AAO:0010841"
         }, {
@@ -34632,21 +34543,12 @@
           "val" : "TAO:0100000"
         }, {
           "val" : "TGMA:0001822"
-        }, {
-          "val" : "UMLS:C1515976"
         }, {
           "val" : "WBbt:0000100"
         }, {
           "val" : "XAO:0000000"
         }, {
           "val" : "ZFA:0100000"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751"
         } ]
       }
     }, {
@@ -34655,14 +34557,16 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies."
+          "val" : "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.",
+          "xrefs" : [ "Wikipedia:Immune_system" ]
         },
-        "comments" : [ "This class was created automatically from a combination of ontologies" ],
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ],
         "xrefs" : [ {
           "val" : "AAO:0011003"
         }, {
           "val" : "BILA:0000104"
+        }, {
+          "val" : "BTO:0005810"
         }, {
           "val" : "FMA:9825"
         }, {
@@ -34670,15 +34574,13 @@
         }, {
           "val" : "MA:0002711"
         }, {
-          "val" : "MESH:A15.382"
+          "val" : "MESH:D007107"
         }, {
-          "val" : "OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA"
+          "val" : "NCIT:C12735"
         }, {
           "val" : "SCTID:362590003"
         }, {
           "val" : "TAO:0001159"
-        }, {
-          "val" : "UMLS:C0020962"
         }, {
           "val" : "VHOG:0001247"
         }, {
@@ -34687,18 +34589,6 @@
           "val" : "XAO:0003152"
         }, {
           "val" : "ZFA:0001159"
-        }, {
-          "val" : "ncithesaurus:Immune_System"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003",
-          "val" : "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
         } ]
       }
     }, {
@@ -34710,7 +34600,7 @@
           "val" : "An anatomical structure that has more than one cell as a part.",
           "xrefs" : [ "CARO:0010000" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "multicellular structure",
@@ -34718,21 +34608,6 @@
         } ],
         "xrefs" : [ {
           "val" : "CARO:0010000"
-        }, {
-          "val" : "FBbt:00100313"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
         } ]
       }
     }, {
@@ -34741,51 +34616,10 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity."
+          "val" : "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.",
+          "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
-        } ]
-      }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/UBERON_0035944",
-      "lbl" : "life-death temporal boundary",
-      "type" : "CLASS",
-      "meta" : {
-        "definition" : {
-          "val" : "A life cycle temporal boundary that marks the end of the life cycle of the organism."
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "end of life cycle"
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "moment of death"
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "time of death"
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "death"
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "end of life"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
-        } ]
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/UO_0000000",
@@ -35168,7 +35002,7 @@
           "val" : "http://www.geneontology.org/formats/oboInOwl"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition",
-          "val" : "_:genid2147487128"
+          "val" : "_:genid2147487145"
         } ]
       }
     }, {
@@ -35176,7 +35010,7 @@
       "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000004",
-      "lbl" : "basis of",
+      "lbl" : "obsolete basis of",
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
@@ -35188,7 +35022,7 @@
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
-        "comments" : [ "p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. " ],
+        "comments" : [ "p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption." ],
         "deprecated" : true
       }
     }, {
@@ -35215,7 +35049,7 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "definition" : {
-          "val" : "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. "
+          "val" : "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times."
         },
         "comments" : [ "Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222." ]
       }
@@ -35231,7 +35065,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000116",
-      "lbl" : "causally_precedes",
+      "lbl" : "obsolete causally_precedes",
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
@@ -35310,45 +35144,15 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000002"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000003"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000004"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000017"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000019"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000020"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000031"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "external"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
           "val" : "part_of"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf"
         }, {
           "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Part_of"
         } ]
       }
     }, {
@@ -35413,15 +35217,6 @@
         },
         "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000054"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000054s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000054ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "obsolete_is_realized_by"
         }, {
@@ -35489,17 +35284,11 @@
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
+        "definition" : {
+          "val" : "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process"
+        },
         "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000055"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000055s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000055ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "realizes"
         }, {
@@ -35547,9 +35336,6 @@
         }, {
           "pred" : "http://purl.org/dc/elements/1.1/source",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by"
-        }, {
-          "pred" : "http://purl.org/dc/terms/source",
-          "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by"
         } ]
       }
     }, {
@@ -35614,9 +35400,6 @@
         }, {
           "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
           "val" : "http://purl.obolibrary.org/obo/bfo.owl"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Occurs_in"
         } ]
       }
     }, {
@@ -35728,15 +35511,6 @@
           "val" : "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000110"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000110s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000110ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "c-has-part_at"
         }, {
@@ -35769,15 +35543,6 @@
           "val" : "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000111"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000111s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000111ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "c-has-ppart_at"
         }, {
@@ -35839,15 +35604,6 @@
           "val" : "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000117"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000117s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000117ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "o-has-part"
         }, {
@@ -35892,15 +35648,6 @@
           "val" : "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000118"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000118s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000118ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "o-has-ppart"
         }, {
@@ -35979,15 +35726,6 @@
           "val" : "[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000132"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000132s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000132ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "o-part-of"
         }, {
@@ -36223,19 +35961,7 @@
       "id" : "http://purl.obolibrary.org/obo/BFO_0000167",
       "lbl" : "has participant at all times",
       "type" : "PROPERTY",
-      "propertyType" : "OBJECT",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000167"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000167s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000167ed"
-        } ]
-      }
+      "propertyType" : "OBJECT"
     }, {
       "id" : "http://purl.obolibrary.org/obo/BFO_0000169",
       "lbl" : "specifically depends on at some time",
@@ -36915,6 +36641,9 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/source",
+          "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204."
         } ]
       }
     }, {
@@ -37011,6 +36740,9 @@
           "val" : "The inverse property of is_specified_output_of"
         },
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
+          "val" : "has specified output"
+        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "has_specified_output"
         }, {
@@ -37056,6 +36788,9 @@
           "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."
         },
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
+          "val" : "is specified output of"
+        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "is_specified_output_of"
         }, {
@@ -37154,8 +36889,7 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "http://purl.obolibrary.org/obo/OBIB_0000732"
-        } ],
-        "deprecated" : true
+        } ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000048",
@@ -37349,17 +37083,11 @@
           "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "is concretized as"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/obi.owl"
         } ]
       }
     }, {
@@ -37369,12 +37097,9 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "definition" : {
-          "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."
+          "val" : "A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "concretizes"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "is_concretization_of"
         }, {
@@ -37383,9 +37108,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/obi.owl"
         } ]
       }
     }, {
@@ -37666,9 +37388,6 @@
         }, {
           "pred" : "http://purl.org/dc/terms/source",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Located_in"
         } ]
       }
     }, {
@@ -37900,7 +37619,7 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "David Osumi-Sutherland"
+          "val" : "https://orcid.org/0000-0002-7073-9172"
         } ]
       }
     }, {
@@ -37913,7 +37632,7 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "David Osumi-Sutherland"
+          "val" : "https://orcid.org/0000-0002-7073-9172"
         } ]
       }
     }, {
@@ -37946,7 +37665,7 @@
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "David Osumi-Sutherland"
+          "val" : "https://orcid.org/0000-0002-7073-9172"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "starts_at_end_of"
@@ -37975,18 +37694,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-7073-9172"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "David Osumi-Sutherland"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "ends_at_start_of"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "meets"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002575",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000063"
         } ]
       }
     }, {
@@ -38001,6 +37714,9 @@
           "val" : "RO:0002093"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
+          "val" : "https://orcid.org/0000-0002-7073-9172"
+        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "David Osumi-Sutherland"
         }, {
@@ -38075,9 +37791,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"
         }, {
           "pred" : "http://xmlns.com/foaf/0.1/page",
           "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"
@@ -38105,9 +37818,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency"
         } ]
       }
     }, {
@@ -38201,9 +37911,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "negatively regulates (process to process)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002211"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "external"
@@ -38234,9 +37941,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "positively regulates (process to process)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002211"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "external"
@@ -38293,9 +37997,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "has function in"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/"
         } ]
       }
     }, {
@@ -38332,8 +38033,7 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "http://purl.obolibrary.org/obo/RO_0002500"
-        } ],
-        "deprecated" : true
+        } ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002220",
@@ -38409,9 +38109,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/obi.owl"
-        }, {
-          "pred" : "http://purl.org/dc/terms/source",
-          "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"
         } ]
       }
     }, {
@@ -38430,9 +38127,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "Allen"
@@ -38457,9 +38151,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "started by"
@@ -38484,9 +38175,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.org/dc/elements/1.1/source",
           "val" : "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl"
@@ -38508,9 +38196,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "finished by"
@@ -38583,9 +38268,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "consumes"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Has_input"
         } ]
       }
     }, {
@@ -38610,9 +38292,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "produces"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Has_output"
         } ]
       }
     }, {
@@ -38628,9 +38307,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision."
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of"
         } ]
       }
     }, {
@@ -38650,9 +38326,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway."
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within"
         } ]
       }
     }, {
@@ -38691,17 +38364,7 @@
           "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q."
         },
         "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ],
-        "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002411"
-        }, {
-          "pred" : "http://purl.org/dc/terms/creator",
-          "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect"
-        } ]
+        "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002305",
@@ -38712,17 +38375,7 @@
         "definition" : {
           "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q."
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002411"
-        }, {
-          "pred" : "http://purl.org/dc/terms/creator",
-          "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect"
-        } ]
+        "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002314",
@@ -38748,9 +38401,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/"
         } ]
       }
     }, {
@@ -38840,9 +38490,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized."
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Enables"
         } ]
       }
     }, {
@@ -38897,9 +38544,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "enables part of"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Involved_in"
         } ]
       }
     }, {
@@ -38915,9 +38559,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Enabled_by"
         } ]
       }
     }, {
@@ -39113,12 +38754,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "indirectly activates"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002579",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002213"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates"
         } ]
       }
     }, {
@@ -39136,12 +38771,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "indirectly inhibits"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002579",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002212"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates"
         } ]
       }
     }, {
@@ -39201,9 +38830,52 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/RO_0002413",
+      "lbl" : "provides input for",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT",
+      "meta" : {
+        "definition" : {
+          "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c."
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
+          "val" : "https://orcid.org/0000-0002-6601-2165"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
+          "val" : "directly provides input for"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
+          "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
+          "val" : "directly provides input for (process to process)"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/RO_0002414",
+      "lbl" : "transitively provides input for",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT",
+      "meta" : {
+        "definition" : {
+          "val" : "transitive form of directly_provides_input_for"
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000428"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
+          "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002575",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002411"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
+          "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
+          "val" : "transitively provides input for (process to process)"
         } ]
       }
     }, {
@@ -39274,9 +38946,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002428"
         } ]
       }
     }, {
@@ -39291,9 +38960,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002428"
         } ]
       }
     }, {
@@ -39326,7 +38992,6 @@
           "val" : "c executes activity in d if and only if c enables p and p occurs_in d.  Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.",
           "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ]
         },
-        "comments" : [ "" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "enables activity in"
@@ -39340,9 +39005,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "executes activity in"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Is_active_in"
         } ]
       }
     }, {
@@ -39371,12 +39033,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules."
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"
-        }, {
-          "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch",
-          "val" : "http://purl.obolibrary.org/obo/MI_0914"
         } ]
       }
     }, {
@@ -39397,12 +39053,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "molecularly binds with"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ECO_0000353"
-        }, {
-          "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch",
-          "val" : "http://purl.obolibrary.org/obo/MI_0915"
         } ]
       }
     }, {
@@ -39580,9 +39230,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000169"
         } ]
       }
     }, {
@@ -39631,12 +39278,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"
         } ]
       }
     }, {
@@ -39692,9 +39333,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "directly regulates (processual)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002575",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002211"
         } ]
       }
     }, {
@@ -39812,12 +39450,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "directly positively regulates (process to process)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002578"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Directly_positively_regulates"
         } ]
       }
     }, {
@@ -39836,12 +39468,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "directly negatively regulates (process to process)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002578"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Directly_negatively_regulates"
         } ]
       }
     }, {
@@ -39923,17 +39549,11 @@
       "meta" : {
         "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002264"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-26T23:49:30Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"
         } ]
       }
     }, {
@@ -39944,17 +39564,11 @@
       "meta" : {
         "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002264"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-26T23:49:51Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"
         } ]
       }
     }, {
@@ -39968,17 +39582,11 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002263"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-26T23:53:14Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"
         } ]
       }
     }, {
@@ -39992,17 +39600,11 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002263"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-26T23:53:22Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"
         } ]
       }
     }, {
@@ -40012,17 +39614,11 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002418"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-03-13T23:55:05Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"
         } ]
       }
     }, {
@@ -40032,17 +39628,11 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002418"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-03-13T23:55:19Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect"
         } ]
       }
     }, {
@@ -40097,9 +39687,6 @@
         }, {
           "pred" : "http://purl.org/dc/terms/contributor",
           "val" : "https://orcid.org/0000-0002-8461-9745"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"
         } ]
       }
     }, {
@@ -40281,6 +39868,20 @@
           "val" : "https://orcid.org/0000-0002-8688-6599"
         } ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/RO_0020105",
+      "lbl" : "is anatomical entity",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT",
+      "meta" : {
+        "definition" : {
+          "val" : "This property only applies to anatomical entities."
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0001-6677-8489"
+        } ]
+      }
     }, {
       "id" : "http://purl.org/obo/owl/OBO_REL#has_disposition",
       "lbl" : "obsolete has_disposition",
@@ -40506,12 +40107,21 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "failed exploratory term"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "Terms created as placeholders with the expectation of being permanent should instead be deprecated using the \"placeholder removed\" (obo:IAO_0000226) justification."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Person:Alan Ruttenberg"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Person:Alan Ruttenberg"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40623,9 +40233,21 @@
       "lbl" : "placeholder removed",
       "type" : "INDIVIDUAL",
       "meta" : {
+        "definition" : {
+          "val" : "The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "placeholder removed"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40633,12 +40255,24 @@
       "lbl" : "terms merged",
       "type" : "INDIVIDUAL",
       "meta" : {
+        "definition" : {
+          "val" : "The term has been combined with one or more other terms to create a more encompassing (merged) term."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "terms merged"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "An editor note should explain what were the merged terms and the reason for the merge."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40646,12 +40280,24 @@
       "lbl" : "term imported",
       "type" : "INDIVIDUAL",
       "meta" : {
+        "definition" : {
+          "val" : "The term has been replaced by a term imported from another ontology."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "term imported"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40659,12 +40305,24 @@
       "lbl" : "term split",
       "type" : "INDIVIDUAL",
       "meta" : {
+        "definition" : {
+          "val" : "The term has been split into two or more new terms."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "term split"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40811,6 +40469,9 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "http://orcid.org/0000-0001-5208-3432"
@@ -40820,6 +40481,12 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000234",
           "val" : "https://orcid.org/0000-0001-5208-3432"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40836,18 +40503,6 @@
       "meta" : {
         "comments" : [ "\"An area unit which is equal to an area enclosed by a square with sides each 1 meter long.\" [NIST:NIST]" ]
       }
-    }, {
-      "id" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://protege.stanford.edu/plugins/owl/protege#defaultLanguage",
       "type" : "PROPERTY",
@@ -40861,7 +40516,7 @@
         "comments" : [ "This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "National Library of Medicine Identifier\n"
+          "val" : "National Library of Medicine Identifier"
         } ]
       }
     }, {
@@ -41320,9 +40975,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
-          "val" : "http://purl.obolibrary.org/obo/iao.owl"
         } ]
       }
     }, {
@@ -41966,6 +41618,10 @@
           "val" : "https://orcid.org/0000-0002-8688-6599"
         } ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/OMO_0003004",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0001900",
       "lbl" : "temporal interpretation",
@@ -41976,61 +41632,14 @@
           "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"
-        }, {
           "pred" : "http://xmlns.com/foaf/0.1/page",
           "val" : "https://github.com/oborel/obo-relations/wiki/ROAndTime"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002175",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002259",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002575",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002579",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002581",
-      "lbl" : "is a defining property chain axiom",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION",
-      "meta" : {
-        "definition" : {
-          "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL"
-        }
-      }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002582",
-      "lbl" : "is a defining property chain axiom where second argument is reflexive",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION",
-      "meta" : {
-        "definition" : {
-          "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R."
-        }
-      }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0004049",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0004050",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0040042",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/STATO_0000032",
       "lbl" : "STATO alternative term",
@@ -42202,17 +41811,31 @@
       "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco",
       "lbl" : "eco subset",
       "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/"
-        } ]
-      }
+      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#human_subset",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#mouse_subset",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim",
       "type" : "PROPERTY",
@@ -42322,10 +41945,6 @@
       "id" : "http://purl.org/dc/terms/contributor",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.org/dc/terms/creator",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.org/dc/terms/description",
       "type" : "PROPERTY",
@@ -42342,10 +41961,6 @@
       "id" : "http://purl.org/dc/terms/title",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://usefulinc.com/ns/doap#bug-database",
       "type" : "PROPERTY",
@@ -42355,15 +41970,17 @@
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+      "lbl" : "created by",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#default-namespace",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+      "lbl" : "creation date",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
@@ -42393,9 +42010,21 @@
       }
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
-      "lbl" : "database_cross_reference",
+      "lbl" : "has cross-reference",
       "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
+      "propertyType" : "ANNOTATION",
+      "meta" : {
+        "definition" : {
+          "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI."
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
+          "val" : "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string"
+        }, {
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
+        } ]
+      }
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition",
       "lbl" : "has_definition",
@@ -42441,10 +42070,6 @@
           "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19"
         } ]
       }
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
       "lbl" : "has_obo_namespace",
@@ -42490,10 +42115,6 @@
       "lbl" : "shorthand",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#source",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://www.referent-tracking.com/RTS_00000001",
       "lbl" : "ontology IUI",
@@ -42533,10 +42154,6 @@
       "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://www.w3.org/2004/02/skos/core#closeMatch",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://xmlns.com/foaf/0.1/homepage",
       "type" : "PROPERTY",
@@ -42588,6 +42205,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000007",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000594"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008",
       "pred" : "is_a",
@@ -42712,6 +42333,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032",
       "pred" : "http://purl.obolibrary.org/obo/OBI_0000312",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033",
       "pred" : "is_a",
@@ -42848,6 +42473,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000066",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000070"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000066",
+      "pred" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000067",
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000038"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000068",
       "pred" : "is_a",
@@ -42956,6 +42585,14 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000109"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089",
+      "pred" : "http://purl.obolibrary.org/obo/IAO_0000136",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000025"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090",
       "pred" : "is_a",
@@ -42984,6 +42621,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000094",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000027"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000094",
+      "pred" : "http://purl.obolibrary.org/obo/RO_0002351",
+      "obj" : "http://purl.obolibrary.org/obo/PCO_0000001"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000095",
       "pred" : "is_a",
@@ -43404,6 +43045,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000183",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000183",
+      "pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000015"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184",
       "pred" : "is_a",
@@ -43448,6 +43093,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000193",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000027"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000086"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000195",
       "pred" : "is_a",
@@ -43955,7 +43604,7 @@
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000312",
       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/GO_0032504"
+      "obj" : "http://purl.obolibrary.org/obo/GO_0048609"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000312",
       "pred" : "http://purl.obolibrary.org/obo/RO_0002218",
@@ -45380,6 +45029,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000795",
       "pred" : "is_a",
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       "pred" : "http://purl.obolibrary.org/obo/OBI_0000299",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000100"
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       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000023"
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       "pred" : "is_a",
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       "pred" : "http://purl.obolibrary.org/obo/IAO_0000219",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000018"
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       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000023"
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       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000310"
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       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000038"
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       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0020020"
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       "pred" : "is_a",
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       "pred" : "is_a",
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       "obj" : "http://purl.obolibrary.org/obo/BFO_0000016"
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       "pred" : "is_a",
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       "pred" : "is_a",
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       "pred" : "is_a",
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+      "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
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-      "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048"
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000023"
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@@ -49927,13 +49628,7 @@
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-          "val" : "09/09/2017"
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@@ -49969,7 +49664,11 @@
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+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000023"
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       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465"
+    }, {
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@@ -50534,10 +50237,6 @@
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-      "sub" : "http://purl.obolibrary.org/obo/OBI_0000299",
-      "pred" : "subPropertyOf",
-      "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/OBI_0000308",
       "pred" : "subPropertyOf",
@@ -50586,14 +50285,6 @@
       "sub" : "http://purl.obolibrary.org/obo/RO_0000057",
       "pred" : "subPropertyOf",
       "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty"
-    }, {
-      "sub" : "http://purl.obolibrary.org/obo/RO_0000058",
-      "pred" : "subPropertyOf",
-      "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty"
-    }, {
-      "sub" : "http://purl.obolibrary.org/obo/RO_0000059",
-      "pred" : "subPropertyOf",
-      "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/RO_0000079",
       "pred" : "subPropertyOf",
@@ -50966,6 +50657,18 @@
       "sub" : "http://purl.obolibrary.org/obo/RO_0002412",
       "pred" : "subPropertyOf",
       "obj" : "http://purl.obolibrary.org/obo/RO_0002411"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/RO_0002413",
+      "pred" : "subPropertyOf",
+      "obj" : "http://purl.obolibrary.org/obo/RO_0002412"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/RO_0002413",
+      "pred" : "subPropertyOf",
+      "obj" : "http://purl.obolibrary.org/obo/RO_0002414"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/RO_0002414",
+      "pred" : "subPropertyOf",
+      "obj" : "http://purl.obolibrary.org/obo/RO_0004047"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/RO_0002418",
       "pred" : "subPropertyOf",
@@ -52006,27 +51709,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052",
         "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000048",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052",
-        "fillerId" : "http://purl.obolibrary.org/obo/BFO_0000040"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000049",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000048" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052",
-        "fillerId" : "http://purl.obolibrary.org/obo/OBI_0100026"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000050",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000049" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052",
-        "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000051",
       "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ],
@@ -52110,7 +51792,7 @@
       } ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000312",
-      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ],
+      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035", "http://purl.obolibrary.org/obo/OBI_0000011" ],
       "allValuesFromEdges" : [ {
         "sub" : "http://purl.obolibrary.org/obo/IAO_0000013",
         "pred" : "http://purl.obolibrary.org/obo/OBI_0000312",
@@ -52126,18 +51808,6 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0000052",
       "allValuesFromEdges" : [ {
-        "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048",
-        "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
-        "obj" : "http://purl.obolibrary.org/obo/BFO_0000040"
-      }, {
-        "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049",
-        "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
-        "obj" : "http://purl.obolibrary.org/obo/OBI_0100026"
-      }, {
-        "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050",
-        "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
-        "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606"
-      }, {
         "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051",
         "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
         "obj" : "http://purl.obolibrary.org/obo/OBI_0000245"
@@ -52244,7 +51914,7 @@
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000299",
-      "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ]
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035", "http://purl.obolibrary.org/obo/OBI_0000011" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056",
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ],
@@ -52323,6 +51993,10 @@
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002334",
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ],
       "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414",
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ],
+      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002434",
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ],
@@ -52391,6 +52065,9 @@
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000",
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ],
       "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/RO_0020105",
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000039",
       "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000003" ]
@@ -52419,18 +52096,9 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000066" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000055", "http://purl.obolibrary.org/obo/RO_0000052" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ]
@@ -52446,9 +52114,6 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ]
@@ -52482,9 +52147,6 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002596",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002211" ]
@@ -52524,6 +52186,9 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002234",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002230", "http://purl.obolibrary.org/obo/RO_0002234" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002413",
+      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002234", "http://purl.obolibrary.org/obo/RO_0002233" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002314", "http://purl.obolibrary.org/obo/BFO_0000050" ]
@@ -52536,9 +52201,6 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ]
@@ -52605,6 +52267,9 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002418",
+      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002418", "http://purl.obolibrary.org/obo/BFO_0000050" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ]
diff --git a/apollo_sv-full.obo b/apollo_sv-full.obo
index abcf89b..193322a 100644
--- a/apollo_sv-full.obo
+++ b/apollo_sv-full.obo
@@ -1,7 +1,8 @@
 format-version: 1.2
-data-version: apollo_sv/releases/2024-12-24/apollo_sv-full.owl
+data-version: apollo_sv/releases/2026-03-13/apollo_sv-full.owl
 subsetdef: attribute_slim ""
 subsetdef: common_anatomy ""
+subsetdef: efo_slim ""
 subsetdef: gocheck_do_not_annotate ""
 subsetdef: goslim_agr ""
 subsetdef: goslim_candida ""
@@ -20,12 +21,19 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
+subsetdef: human_reference_atlas ""
+subsetdef: human_subset ""
+subsetdef: mouse_subset ""
 subsetdef: mpath_slim ""
+subsetdef: pheno_slim ""
 subsetdef: ro-eco ""
 subsetdef: RO:0002259 ""
 subsetdef: scalar_slim ""
+subsetdef: uberon_slim ""
 subsetdef: unit_group_slim ""
 subsetdef: upper_level ""
+subsetdef: vertebrate_core ""
+synonymtypedef: OMO:0003004 ""
 idspace: ace_lexicon http://attempto.ifi.uzh.ch/ace_lexicon# 
 idspace: dc http://purl.org/dc/elements/1.1/ 
 idspace: doap http://usefulinc.com/ns/doap# 
@@ -48,7 +56,7 @@ property_value: dc:contributor "Mike Wagner" xsd:string
 property_value: dc:contributor "Shawn T. Brown" xsd:string
 property_value: dc:contributor "William R. Hogan" xsd:string
 property_value: dc:creator "Mathias Brochhausen" xsd:string
-property_value: owl:versionInfo "2024-12-24" xsd:string
+property_value: owl:versionInfo "2026-03-13" xsd:string
 property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI
 property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string
 property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string
@@ -125,6 +133,7 @@ property_value: IAO:0000600 "A software application that provides a model of a r
 id: APOLLO_SV:00000008
 name: software development
 def: "A planned process that has specified output a software product and that involves the creation of source code." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -151,7 +160,7 @@ property_value: IAO:0000600 "An identifier that refers to all versions of a spec
 
 [Term]
 id: APOLLO_SV:00000011
-name: control strategy reactive start time information
+name: obsolete control strategy reactive start time information
 def: "A control strategy start time information item that is based on a condition that triggers the control strategy." []
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A control strategy start time information item that is based on a condition that triggers the control strategy." xsd:string
@@ -163,7 +172,7 @@ name: simulation time step value
 def: "A numeral that is part of a simulation time step action specification." []
 is_a: IAO:0000029 ! numeral
 property_value: APOLLO_SV:0000040 "numberOfUnitsOfTimeInOneSimulatorStep" xsd:string
-property_value: IAO:0000600 "A number of time step units in a time step of a simulation.  \n\nFor example, if the time step is 6 hours, then this value is 6.\n" xsd:string
+property_value: IAO:0000600 "A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6." xsd:string
 
 [Term]
 id: APOLLO_SV:00000013
@@ -188,7 +197,7 @@ def: "The action specification that specifies the number of time steps a simulat
 is_a: APOLLO_SV:00000793 ! epidemic simulator action specification
 relationship: has_part APOLLO_SV:00000068 ! simulation time step action specification
 property_value: APOLLO_SV:0000040 "runLength" xsd:string
-property_value: IAO:0000600 "The number of time steps in a simulator run.\n\nFor example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.\n" xsd:string
+property_value: IAO:0000600 "The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero." xsd:string
 
 [Term]
 id: APOLLO_SV:00000016
@@ -205,11 +214,10 @@ id: APOLLO_SV:00000017
 name: latent period duration
 def: "A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts." []
 comment: MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs
-comment: The duration of the period between when an organism becomes infected and when it becomes infectious.
 is_a: APOLLO_SV:00000243 ! duration
 property_value: APOLLO_SV:0000040 "latentPeriodDuration" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  \n\nNote that the susceptible and infected organisms can be of different species.\n\n" xsd:string
+property_value: IAO:0000600 "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species." xsd:string
 
 [Term]
 id: APOLLO_SV:00000018
@@ -239,31 +247,29 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 id: APOLLO_SV:00000022
 name: count of simulated population
 def: "The count of (simulated organisms) in a simulated population." []
-comment: MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n
+comment: MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "The number of simulated organisms in a simulated population.  The number does not have to be an integer.  " xsd:string
+property_value: IAO:0000600 "The number of simulated organisms in a simulated population.  The number does not have to be an integer." xsd:string
 
 [Term]
 id: APOLLO_SV:00000023
 name: vaccination dose schedule
 def: "An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent." []
 is_a: APOLLO_SV:00000084 ! control strategy dose schedule
-property_value: IAO:0000600 "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. " xsd:string
+property_value: IAO:0000600 "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism." xsd:string
 
 [Term]
 id: APOLLO_SV:00000024
 name: vaccination compliance
 def: "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination." []
 comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
-comment: MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.\n
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: IAO:0000600 "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint." xsd:string
 
 [Term]
 id: APOLLO_SV:00000025
 name: vaccination efficacy
 def: "The infectious disease treatment efficacy of a vaccine." []
-comment: need to generate class restriction.  Something like:\n\n'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance'))\n\nwe'd also like to say that the protective resistance disposition began to exist during the process.  \n\ncan't recall whether we should use process or processual_entity for future BFO compatibility.
 comment: Notes: \n1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer
 is_a: APOLLO_SV:00000227 ! infectious disease treatment efficacy
 property_value: APOLLO_SV:0000040 "vaccinationEfficacies" xsd:string
@@ -283,18 +289,18 @@ comment: Motivating use case is Synthia synthetic population data.
 is_a: APOLLO_SV:00000173 ! census
 intersection_of: APOLLO_SV:00000173 ! census
 intersection_of: IAO:0000136 OMRSE:00000064 ! is about school facility
-intersection_of: OBI:0000312 APOLLO_SV:00000026 ! is_specified_output_of facility survey
-intersection_of: OBI:0000312 APOLLO_SV:00000026 {all_only="true"} ! is_specified_output_of facility survey
+intersection_of: OBI:0000312 APOLLO_SV:00000026 ! is specified output of facility survey
+intersection_of: OBI:0000312 APOLLO_SV:00000026 {all_only="true"} ! is specified output of facility survey
 relationship: IAO:0000136 OMRSE:00000064 ! is about school facility
-relationship: OBI:0000312 APOLLO_SV:00000026 ! is_specified_output_of facility survey
+relationship: OBI:0000312 APOLLO_SV:00000026 ! is specified output of facility survey
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
 id: APOLLO_SV:00000029
 name: infectious disease control strategy execution
-def: "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  " []
+def: "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease." []
 is_a: OBI:0000011 ! planned process
-property_value: IAO:0000600 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  " xsd:string
+property_value: IAO:0000600 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease." xsd:string
 
 [Term]
 id: APOLLO_SV:00000030
@@ -322,8 +328,8 @@ name: count
 def: "A measurement datum that is the output of counting." []
 is_a: IAO:0000109 ! measurement datum
 intersection_of: IAO:0000027 ! data item
-intersection_of: OBI:0000312 APOLLO_SV:00000033 ! is_specified_output_of counting
-relationship: OBI:0000312 APOLLO_SV:00000033 ! is_specified_output_of counting
+intersection_of: OBI:0000312 APOLLO_SV:00000033 ! is specified output of counting
+relationship: OBI:0000312 APOLLO_SV:00000033 ! is specified output of counting
 property_value: APOLLO_SV:0000040 "count" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A measurement datum that is the output of counting." xsd:string
@@ -332,10 +338,11 @@ property_value: IAO:0000600 "A measurement datum that is the output of counting.
 id: APOLLO_SV:00000033
 name: counting
 def: "The planned process of finding the number of elements in a finite set of objects." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 intersection_of: OBI:0000011 ! planned process
-intersection_of: OBI:0000299 APOLLO_SV:00000032 ! has_specified_output count
-relationship: OBI:0000299 APOLLO_SV:00000032 ! has_specified_output count
+intersection_of: OBI:0000299 APOLLO_SV:00000032 ! has specified output count
+relationship: OBI:0000299 APOLLO_SV:00000032 ! has specified output count
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Counting" xsd:string
 property_value: IAO:0000600 "The planned process of finding the number of elements in a finite set of objects." xsd:string
@@ -383,9 +390,9 @@ property_value: IAO:0000600 "A simulated organism in a simulated population that
 [Term]
 id: APOLLO_SV:00000041
 name: simulation of recovered organism
-def: "A simulated organism in a simulated population that is not susceptible. " []
+def: "A simulated organism in a simulated population that is not susceptible." []
 is_a: APOLLO_SV:00000034 ! simulation of organism
-property_value: IAO:0000600 "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.\n" xsd:string
+property_value: IAO:0000600 "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage." xsd:string
 
 [Term]
 id: APOLLO_SV:00000042
@@ -399,7 +406,7 @@ property_value: IAO:0000600 "The disease being simulated." xsd:string
 [Term]
 id: APOLLO_SV:00000043
 name: reproduction number
-def: "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. " []
+def: "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection." []
 property_value: APOLLO_SV:0000040 "ReproductionNumber" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "The number of susceptible organisms that each infected organism infects.  ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation." xsd:string
@@ -446,24 +453,23 @@ property_value: IAO:0000600 "The degree to which a particular antiviral drug red
 [Term]
 id: APOLLO_SV:00000049
 name: antiviral efficacy delay
-def: "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. " []
+def: "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role." []
 is_a: APOLLO_SV:00000243 ! duration
-property_value: IAO:0000600 "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. " xsd:string
+property_value: IAO:0000600 "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection." xsd:string
 
 [Term]
 id: APOLLO_SV:00000050
 name: antiviral compliance
 def: "The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible." []
 comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
-comment: MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2.  If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: APOLLO_SV:0000040 "antiviral cm compliance" xsd:string
-property_value: IAO:0000600 "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. " xsd:string
+property_value: IAO:0000600 "The fraction of individuals in a simulated population that will accept antiviral treatment if offered." xsd:string
 
 [Term]
 id: APOLLO_SV:00000051
 name: antiviral supply schedule
-def: "An action specification giving the number of doses of an antiviral to be made available during a specific time interval. " []
+def: "An action specification giving the number of doses of an antiviral to be made available during a specific time interval." []
 is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
 property_value: IAO:0000600 "Counts of antiviral doses that become available in a specific location per time step unit." xsd:string
 
@@ -479,7 +485,6 @@ id: APOLLO_SV:00000053
 name: simulation of organism awaiting control measure
 def: "A simulated organism that is assumed “eligible, willing and able” to participate with a particular control measure." []
 comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
-comment: This class will need more ontological reasoning, since the "willing" part of the definition is not representable in BFO to date.
 is_a: APOLLO_SV:00000034 ! simulation of organism
 disjoint_from: APOLLO_SV:00000058 ! simulation of organism not awaiting control measure
 property_value: IAO:0000600 "A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure." xsd:string
@@ -519,7 +524,6 @@ id: APOLLO_SV:00000058
 name: simulation of organism not awaiting control measure
 def: "A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular control measure." []
 comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
-comment: This class will need more ontological reasoning, since the "unwilling" part of the definition is not representable in BFO to date.
 property_value: IAO:0000600 "A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure." xsd:string
 
 [Term]
@@ -532,8 +536,8 @@ property_value: IAO:0000600 "This concept represents a simulated organism that h
 [Term]
 id: APOLLO_SV:00000060
 name: simulation of antiviral control measure
-def: "The simulation of an antiviral control measure. " []
-comment: MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.\n
+def: "The simulation of an antiviral control measure." []
+comment: MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.
 is_a: APOLLO_SV:00000070 ! simulation
 property_value: APOLLO_SV:0000040 "antiviral control measure" xsd:string
 property_value: IAO:0000600 "A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism." xsd:string
@@ -563,7 +567,7 @@ property_value: IAO:0000600 "A simulated organism in a simulated population has
 id: APOLLO_SV:00000064
 name: simulation time series
 def: "A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation." []
-comment: MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.\n
+comment: MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.
 is_a: IAO:0000584 ! time sampled measurement data set
 property_value: IAO:0000600 "A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation." xsd:string
 
@@ -575,7 +579,7 @@ comment: Class was originally created to correspond with an element from Apollo
 is_a: IAO:0000029 ! numeral
 intersection_of: IAO:0000029 ! numeral
 intersection_of: IAO:0000219 APOLLO_SV:00000005 ! denotes simulating of process of type X
-intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output_of identifier creating process
+intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is specified output of identifier creating process
 relationship: IAO:0000219 APOLLO_SV:00000005 ! denotes simulating of process of type X
 property_value: IAO:0000600 "The run id indexes a run of a specific simulator version on a specific simulated population, disease(s), and optionally control measures.  The simulator is responsible for generating a run id and ensuring its uniqueness." xsd:string
 
@@ -584,6 +588,7 @@ id: APOLLO_SV:00000066
 name: simulation of time step
 def: "A purely intentional entity that simulates a temporal interval of pre-specified length." []
 is_a: APOLLO_SV:00000070 ! simulation
+relationship: APOLLO_SV:00000067 BFO:0000038 ! simulates one-dimensional temporal region
 property_value: APOLLO_SV:0000040 "simulation time step" xsd:string
 property_value: IAO:0000600 "A purely intentional entity that simulates a temporal interval of pre-specified length." xsd:string
 
@@ -606,7 +611,7 @@ def: "A numeral that indexes a specific time step of a simulation." []
 is_a: IAO:0000029 ! numeral
 intersection_of: IAO:0000029 ! numeral
 intersection_of: IAO:0000219 APOLLO_SV:00000066 ! denotes simulation of time step
-intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output_of identifier creating process
+intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is specified output of identifier creating process
 relationship: IAO:0000219 APOLLO_SV:00000066 ! denotes simulation of time step
 property_value: APOLLO_SV:0000040 "simulatorTime" xsd:string
 property_value: IAO:0000600 "The time step number of a simulation." xsd:string
@@ -614,13 +619,13 @@ property_value: IAO:0000600 "The time step number of a simulation." xsd:string
 [Term]
 id: APOLLO_SV:00000070
 name: simulation
-def: "A purely intentional entity that simulates an entity and its properties.\n\n" []
+def: "A purely intentional entity that simulates an entity and its properties." []
 is_a: APOLLO_SV:00000000 ! purely intentional entity
 intersection_of: APOLLO_SV:00000000 ! purely intentional entity
 intersection_of: APOLLO_SV:00000067 BFO:0000001 ! simulates entity
 relationship: APOLLO_SV:00000067 BFO:0000001 ! simulates entity
 property_value: APOLLO_SV:0000040 "simulation" xsd:string
-property_value: IAO:0000600 "A purely intentional entity that simulates an entity and its properties.\n\n" xsd:string
+property_value: IAO:0000600 "A purely intentional entity that simulates an entity and its properties." xsd:string
 
 [Term]
 id: APOLLO_SV:00000071
@@ -665,7 +670,7 @@ property_value: IAO:0000600 "an objective of achieving satisfactory control of e
 
 [Term]
 id: APOLLO_SV:00000076
-name: μ
+name: obsolete μ
 is_a: oboInOwl:ObsoleteClass ! Obsolete Class
 property_value: APOLLO_SV:0000040 "μ" xsd:string
 property_value: IAO:0000600 "the mean or expectation of a distribution" xsd:string
@@ -673,7 +678,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000077
-name: σ
+name: obsolete σ
 is_a: oboInOwl:ObsoleteClass ! Obsolete Class
 property_value: APOLLO_SV:0000040 "sigma" xsd:string
 property_value: IAO:0000600 "standard deviation" xsd:string
@@ -688,7 +693,7 @@ property_value: IAO:0000600 "A continuous probability distribution whose charact
 
 [Term]
 id: APOLLO_SV:00000079
-name: deprecated log normal distribution
+name: obsolete log normal distribution
 is_a: oboInOwl:ObsoleteClass ! Obsolete Class
 property_value: IAO:0000600 "a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm" xsd:string
 is_obsolete: true
@@ -727,7 +732,7 @@ name: control strategy dose schedule
 def: "An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism." []
 is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
 relationship: part_of APOLLO_SV:00000086 ! infectious disease control strategy
-property_value: IAO:0000600 "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. " xsd:string
+property_value: IAO:0000600 "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism." xsd:string
 
 [Term]
 id: APOLLO_SV:00000085
@@ -767,8 +772,9 @@ property_value: IAO:0000600 "The count of individuals in an exposed population (
 id: APOLLO_SV:00000089
 name: measured vaccination efficacy
 def: "A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study." []
-comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.\n
+comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.
 is_a: IAO:0000109 ! measurement datum
+relationship: IAO:0000136 APOLLO_SV:00000025 ! is about vaccination efficacy
 property_value: APOLLO_SV:0000040 "VaccinationEfficacyMeasured" xsd:string
 property_value: IAO:0000600 "A vaccination efficacy that results from a vaccination efficacy study." xsd:string
 
@@ -776,12 +782,13 @@ property_value: IAO:0000600 "A vaccination efficacy that results from a vaccinat
 id: APOLLO_SV:00000090
 name: vaccination efficacy study design execution
 def: "a study design execution that has as its specified output one or more measured vaccination efficacy data items" []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000471 ! study design execution
 intersection_of: OBI:0000471 ! study design execution
 intersection_of: has_part APOLLO_SV:00000142 ! vaccination
-intersection_of: OBI:0000299 APOLLO_SV:00000089 ! has_specified_output measured vaccination efficacy
+intersection_of: OBI:0000299 APOLLO_SV:00000089 ! has specified output measured vaccination efficacy
 relationship: has_part APOLLO_SV:00000142 ! vaccination
-relationship: OBI:0000299 APOLLO_SV:00000089 ! has_specified_output measured vaccination efficacy
+relationship: OBI:0000299 APOLLO_SV:00000089 ! has specified output measured vaccination efficacy
 property_value: APOLLO_SV:0000040 "VaccinationEfficacyStudy" xsd:string
 property_value: IAO:0000600 "an experiment that measures vaccination efficacy from a sample of vaccinated and possibly unvaccinated individuals" xsd:string
 
@@ -811,14 +818,15 @@ property_value: IAO:0000600 "a type of interval estimate of a population paramet
 id: APOLLO_SV:00000094
 name: community
 def: "Two or more distinct populations that are part of the same biotic ecosystem." []
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
+relationship: RO:0002351 PCO:0000001 ! has member population
 property_value: APOLLO_SV:0000040 "community" xsd:string
 property_value: dc:creator "William R. Hogan" xsd:string
 property_value: IAO:0000600 "Two or more distinct populations that are part of the same biotic ecosystem." xsd:string
 
 [Term]
 id: APOLLO_SV:00000095
-name: deprecated discrete probability distribution
+name: obsolete discrete probability distribution
 is_a: oboInOwl:ObsoleteClass ! Obsolete Class
 property_value: APOLLO_SV:0000040 "discrete probability distribution" xsd:string
 property_value: IAO:0000600 "a probability distribution over a discrete random variable" xsd:string
@@ -833,11 +841,11 @@ is_obsolete: true
 [Term]
 id: APOLLO_SV:00000097
 name: ecosystem
-def: "The sum of all biotic and abiotic entities in a geographical region. " []
+def: "The sum of all biotic and abiotic entities in a geographical region." []
 is_a: BFO:0000040 ! material entity
 property_value: APOLLO_SV:0000040 "Ecosystem" xsd:string
 property_value: dc:creator "William R. Hogan" xsd:string
-property_value: IAO:0000600 "The sum of all biotic and abiotic entities in a geographical region. " xsd:string
+property_value: IAO:0000600 "The sum of all biotic and abiotic entities in a geographical region." xsd:string
 
 [Term]
 id: APOLLO_SV:00000098
@@ -912,8 +920,7 @@ id: APOLLO_SV:00000107
 name: atmosphere
 def: "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force" []
 comment: atmosphere of Earth, Earth's moon, Saturn, Titan, etc.
-comment: outer, gaseous layers of exoplanets are called extraterrestrial atmosphere.
-is_a: BFO:0000024 ! fiat object part
+is_a: BFO:0000024 ! fiat object
 property_value: dc:creator "William R. Hogan" xsd:string
 property_value: IAO:0000600 "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force" xsd:string
 
@@ -975,14 +982,13 @@ property_value: IAO:0000600 "A process of reproduction of a particular pathogen
 [Term]
 id: APOLLO_SV:00000115
 name: infection acquisition
-def: "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources" []
-comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing. \n
-comment: Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing
+def: "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources." []
+comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing.
 is_a: GO:0044409 ! entry into host
 relationship: RO:0002411 APOLLO_SV:00000114 ! causally upstream of infection
 property_value: APOLLO_SV:0000040 "InfectionAcquisition" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species.\n\n" xsd:string
+property_value: IAO:0000600 "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species." xsd:string
 
 [Term]
 id: APOLLO_SV:00000117
@@ -1047,7 +1053,7 @@ property_value: IAO:0000600 "The number of time steps that a school closure cont
 
 [Term]
 id: APOLLO_SV:00000125
-name: school calendar
+name: obsolete school calendar
 property_value: IAO:0000600 "The time steps that a school will be in session." xsd:string
 is_obsolete: true
 
@@ -1094,7 +1100,7 @@ name: reactive control strategy threshold
 def: "A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy." []
 is_a: IAO:0000027 ! data item
 property_value: APOLLO_SV:0000040 "reactiveControlMeasureThreshold" xsd:string
-property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc.\n" xsd:string
+property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc." xsd:string
 
 [Term]
 id: APOLLO_SV:00000132
@@ -1137,7 +1143,7 @@ id: APOLLO_SV:00000137
 name: vaccine valence
 is_a: APOLLO_SV:00000032 ! count
 property_value: APOLLO_SV:0000040 "valence" xsd:string
-property_value: IAO:0000600 "the number of distinct antigenic strains in a vaccine product " xsd:string
+property_value: IAO:0000600 "The number of distinct antigenic strains in a vaccine product." xsd:string
 
 [Term]
 id: APOLLO_SV:00000138
@@ -1151,7 +1157,6 @@ id: APOLLO_SV:00000139
 name: control strategy compliance
 def: "A measurement datum about the fraction of individuals in a population that elect to participate in a control strategy when offered." []
 comment: the class restriction can be made more precise AH
-comment: the fraction of some population that is targeted for a control strategy that accepts it.  It can obviously also be interpreted as a probability that the average individual in the targeted population accepts/complies with the control strategy.  It is not simulated
 property_value: APOLLO_SV:0000040 "compliance" xsd:string
 property_value: IAO:0000600 "A fraction of eligible individuals in a population who receive an intervention or participate in a control strategy." xsd:string
 
@@ -1181,7 +1186,7 @@ property_value: IAO:0000600 "A treatment of an individual with antigenic materia
 
 [Term]
 id: APOLLO_SV:00000143
-name: vaccine disposition
+name: obsolete vaccine disposition
 comment: replaced with VO 'vaccine function'
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_obsolete: true
@@ -1192,7 +1197,7 @@ name: disposition to become contaminated with a pathogen
 is_a: BFO:0000016 ! disposition
 intersection_of: BFO:0000016 ! disposition
 intersection_of: BFO:0000054 APOLLO_SV:00000167 {all_some="true", all_only="true"} ! is realized by contamination acquisition
-relationship: RO:0000052 BFO:0000040 ! inheres in material entity
+relationship: RO:0000052 BFO:0000040 ! characteristic of material entity
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -1207,7 +1212,7 @@ property_value: IAO:0000600 "The dispostion of an organism of a particular biolo
 
 [Term]
 id: APOLLO_SV:00000146
-name: beta
+name: obsolete beta
 comment: it is the same thing as transmission coefficient
 property_value: IAO:0000600 "Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons." xsd:string
 is_obsolete: true
@@ -1221,7 +1226,7 @@ property_value: IAO:0000600 "Transmission parameter" xsd:string
 
 [Term]
 id: APOLLO_SV:00000148
-name: random number seed
+name: obsolete random number seed
 property_value: IAO:0000600 "random number seed" xsd:string
 is_obsolete: true
 
@@ -1261,10 +1266,10 @@ def: "A census that is the outcome of a population survey." []
 is_a: APOLLO_SV:00000173 ! census
 intersection_of: APOLLO_SV:00000173 ! census
 intersection_of: IAO:0000136 PCO:0000001 ! is about population
-intersection_of: OBI:0000312 APOLLO_SV:00000152 ! is_specified_output_of population survey
-intersection_of: OBI:0000312 APOLLO_SV:00000152 {all_only="true"} ! is_specified_output_of population survey
+intersection_of: OBI:0000312 APOLLO_SV:00000152 ! is specified output of population survey
+intersection_of: OBI:0000312 APOLLO_SV:00000152 {all_only="true"} ! is specified output of population survey
 relationship: IAO:0000136 PCO:0000001 ! is about population
-relationship: OBI:0000312 APOLLO_SV:00000152 ! is_specified_output_of population survey
+relationship: OBI:0000312 APOLLO_SV:00000152 ! is specified output of population survey
 property_value: IAO:0000600 "A census that is the outcome of a population survey." xsd:string
 
 [Term]
@@ -1280,7 +1285,6 @@ id: APOLLO_SV:00000155
 name: population infection survey
 def: "A population survey that counts the number of individuals in the population who are infected with a particular pathogen." []
 comment: Comment from Mike (to do!):\nI checked because an infection and immunity census would involve two different census methods.   One would be some kind of disease surveillance that counts infections.  The other is some kind of immunity census process based on seroprevalence studies or vaccination registries.
-comment: Equivalent class was:\n'population survey' and (has_part some \n(counting and (has_specified_output some \n(count and ('is about' some 'exposed population'))) and (has_specified_output some \n(count and ('is about' some 'infectious population'))) and (has_specified_output some \n(count and ('is about' some 'susceptible population'))) and (has_specified_output some \n(count and ('is about' some 'immune population')))))
 is_a: APOLLO_SV:00000152 ! population survey
 property_value: APOLLO_SV:0000040 "PopulationInfectionSurvey" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1299,10 +1303,10 @@ name: population infection and immunity census
 def: "A census that is the result of a population infection survey and a population immunity survey." []
 is_a: APOLLO_SV:00000173 ! census
 intersection_of: APOLLO_SV:00000173 ! census
-intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true"} ! is_specified_output_of population infection survey
-intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true", all_only="true"} ! is_specified_output_of population infection survey
-relationship: OBI:0000312 APOLLO_SV:00000003 ! is_specified_output_of population immunity survey
-relationship: OBI:0000312 APOLLO_SV:00000155 ! is_specified_output_of population infection survey
+intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true"} ! is specified output of population infection survey
+intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true", all_only="true"} ! is specified output of population infection survey
+relationship: OBI:0000312 APOLLO_SV:00000003 ! is specified output of population immunity survey
+relationship: OBI:0000312 APOLLO_SV:00000155 ! is specified output of population infection survey
 property_value: APOLLO_SV:0000040 "PopulationInfectionAndImmunityCensus" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "PII Census" xsd:string
@@ -1319,9 +1323,9 @@ name: population demographic census
 def: "A census that is the specific outcome of a population demographic survey." []
 is_a: APOLLO_SV:00000173 ! census
 intersection_of: APOLLO_SV:00000173 ! census
-intersection_of: OBI:0000312 APOLLO_SV:00000158 ! is_specified_output_of population demographic survey
-intersection_of: OBI:0000312 APOLLO_SV:00000158 {all_only="true"} ! is_specified_output_of population demographic survey
-relationship: OBI:0000312 APOLLO_SV:00000158 ! is_specified_output_of population demographic survey
+intersection_of: OBI:0000312 APOLLO_SV:00000158 ! is specified output of population demographic survey
+intersection_of: OBI:0000312 APOLLO_SV:00000158 {all_only="true"} ! is specified output of population demographic survey
+relationship: OBI:0000312 APOLLO_SV:00000158 ! is specified output of population demographic survey
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A census that is the specific outcome of a population demographic survey." xsd:string
 
@@ -1334,7 +1338,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000161
-name: MIDAS scenario
+name: obsolete MIDAS scenario
 def: "An ecosystem in which a population of hosts is undergoing at least one infection." []
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "An ecosystem in which a population of hosts is undergoing at least one infection." xsd:string
@@ -1381,7 +1385,7 @@ property_value: IAO:0000600 "A census that is the specified output of a agent-le
 id: APOLLO_SV:00000166
 name: contaminated thing
 def: "An independent continuant that is the localization of a pathogen, but is not undergoing an infection." []
-comment: A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    
+comment: A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.
 is_a: BFO:0000004 ! independent continuant
 property_value: APOLLO_SV:0000040 "ContaminatedThing" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1526,6 +1530,7 @@ name: simulator time specification
 def: "An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps)." []
 is_a: APOLLO_SV:00000793 ! epidemic simulator action specification
 relationship: has_part APOLLO_SV:00000015 ! simulation run length
+relationship: has_part APOLLO_SV:00000015 ! simulation run length
 relationship: has_part APOLLO_SV:00000068 ! simulation time step action specification
 property_value: APOLLO_SV:0000040 "SimulatorTimeSpecification" xsd:string
 property_value: IAO:0000600 "An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps)." xsd:string
@@ -1554,7 +1559,7 @@ id: APOLLO_SV:00000186
 name: contamination
 def: "The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism." []
 comment: the preferred term is biological contamination to distinguish from things like radiological contamination, contamination of the Gulf of Mexico with oil, the contamination of air with pollution, etc.
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: APOLLO_SV:0000040 "Contamination" xsd:string
 property_value: IAO:0000111 "biological contamination" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -1573,7 +1578,6 @@ id: APOLLO_SV:00000188
 name: population and environment census
 def: "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero." []
 comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.
-comment: This census should exclude infection, immunity, treatment, or contamination.  
 is_a: APOLLO_SV:00000173 ! census
 property_value: IAO:0000600 "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero." xsd:string
 
@@ -1590,8 +1594,8 @@ name: contagious organism
 def: "A host who is able to transmit some infection to another organism." []
 is_a: APOLLO_SV:00000238 ! host organism
 intersection_of: APOLLO_SV:00000238 ! host organism
-intersection_of: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness
-relationship: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness
+intersection_of: RO:0000053 APOLLO_SV:00000182 ! bearer of contagiousness
+relationship: RO:0000053 APOLLO_SV:00000182 ! bearer of contagiousness
 property_value: APOLLO_SV:0000040 "infectious" xsd:string
 property_value: IAO:0000600 "An infected organism of a particular species who is able to transmit the infection to a susceptible organism of a particular species.\n\nNote that the infected and susceptible organisms may be of different species." xsd:string
 
@@ -1622,6 +1626,7 @@ property_value: IAO:0000600 "A data item inferring a vaccination efficacy based
 id: APOLLO_SV:00000194
 name: individual treatment control strategy
 def: "An infectious disease control strategy that immediately targets individuals." []
+is_a: APOLLO_SV:00000086 ! infectious disease control strategy
 property_value: APOLLO_SV:0000040 "IndividualTreatmentControlMeasure" xsd:string
 property_value: IAO:0000112 "vaccination control strategy, antiviral control strategy" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1643,18 +1648,18 @@ is_a: APOLLO_SV:00000136 ! vaccination control strategy
 [Term]
 id: APOLLO_SV:00000197
 name: agent level population and environment census
-comment: An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. 
+comment: An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved.
 is_a: APOLLO_SV:00000188 ! population and environment census
 
 [Term]
 id: APOLLO_SV:00000198
-name: agent model ecosystem census description
+name: obsolete agent model ecosystem census description
 comment: At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics.
 is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000199
-name: compartment model population and environment census
+name: obsolete compartment model population and environment census
 comment: The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census).
 is_obsolete: true
 
@@ -1675,7 +1680,7 @@ property_value: IAO:0000600 "A census about contaminated things of a given type
 [Term]
 id: APOLLO_SV:00000202
 name: indexable Apollo item
-comment: A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. 
+comment: A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved.
 is_a: IAO:0000030 ! information content entity
 property_value: APOLLO_SV:0000040 "ApolloIndexableItem" xsd:string
 
@@ -1703,8 +1708,8 @@ name: susceptible organism
 def: "An organism that is the bearer of a susceptibility disposition." []
 is_a: OBI:0100026 ! organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000172 ! is bearer of susceptibility
-relationship: RO:0000053 APOLLO_SV:00000172 ! is bearer of susceptibility
+intersection_of: RO:0000053 APOLLO_SV:00000172 ! bearer of susceptibility
+relationship: RO:0000053 APOLLO_SV:00000172 ! bearer of susceptibility
 property_value: APOLLO_SV:0000040 "susceptible" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism of a particular species that can undergo infection with a particular pathogen." xsd:string
@@ -1715,8 +1720,8 @@ name: immune organism
 def: "An organism that is the bearer of an immune resistance disposition." []
 is_a: APOLLO_SV:00000207 ! resistant organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000151 ! is bearer of immune resistance to infection
-relationship: RO:0000053 APOLLO_SV:00000151 ! is bearer of immune resistance to infection
+intersection_of: RO:0000053 APOLLO_SV:00000151 ! bearer of immune resistance to infection
+relationship: RO:0000053 APOLLO_SV:00000151 ! bearer of immune resistance to infection
 property_value: APOLLO_SV:0000040 "immune" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species." xsd:string
@@ -1727,8 +1732,8 @@ name: resistant organism
 def: "an organism that is the bearer of resistance to infection" []
 is_a: OBI:0100026 ! organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000145 ! is bearer of resistance to infection
-relationship: RO:0000053 APOLLO_SV:00000145 ! is bearer of resistance to infection
+intersection_of: RO:0000053 APOLLO_SV:00000145 ! bearer of resistance to infection
+relationship: RO:0000053 APOLLO_SV:00000145 ! bearer of resistance to infection
 property_value: APOLLO_SV:0000040 "resistant" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism of a particular species that is unable to undergo infection with a particular pathogen." xsd:string
@@ -1797,11 +1802,11 @@ property_value: IAO:0000600 "An information content entity that specifies the va
 [Term]
 id: APOLLO_SV:00000215
 name: probability distribution
-def: "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. " []
+def: "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference." []
 is_a: IAO:0000030 ! information content entity
 property_value: APOLLO_SV:0000040 "ProbabilityDistribution" xsd:string
 property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Probability_distribution" xsd:string
-property_value: IAO:0000600 "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. " xsd:string
+property_value: IAO:0000600 "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference." xsd:string
 
 [Term]
 id: APOLLO_SV:00000216
@@ -1988,8 +1993,8 @@ name: pathogen
 def: "An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon." []
 is_a: OBI:0100026 ! organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000404 ! is bearer of infectiousness
-relationship: RO:0000053 APOLLO_SV:00000404 ! is bearer of infectiousness
+intersection_of: RO:0000053 APOLLO_SV:00000404 ! bearer of infectiousness
+relationship: RO:0000053 APOLLO_SV:00000404 ! bearer of infectiousness
 property_value: APOLLO_SV:0000040 "pathogen" xsd:string
 property_value: IAO:0000600 "An organism, virus, or prion that can infect another organism." xsd:string
 
@@ -2055,7 +2060,6 @@ id: APOLLO_SV:00000244
 name: disease unique identifier
 def: "a unique identifier that refers to a disease." []
 comment: This class is different from its superclass, in that the identifier is non-redundant with other identifiers in its context (such as a coding system or terminology or ontology).  The superclass admits of natural langugage names of diseases, whereas this one typically does not.
-comment: We still need to decide which coding schema to adopt.-MB
 is_a: APOLLO_SV:00000598 ! disease identifier
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A unique identifier that refers to a particular type of disease." xsd:string
@@ -2097,7 +2101,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000249
-name: nonparametric probability distribution
+name: obsolete nonparametric probability distribution
 property_value: APOLLO_SV:0000040 "NonparametricProbabilityDistribution" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_obsolete: true
@@ -2227,7 +2231,7 @@ id: APOLLO_SV:00000264
 name: infection acquisition from contaminated thing
 def: "An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing." []
 is_a: APOLLO_SV:00000115 ! infection acquisition
-relationship: RO:0000057 APOLLO_SV:00000166 ! has_participant contaminated thing
+relationship: RO:0000057 APOLLO_SV:00000166 ! has participant contaminated thing
 property_value: APOLLO_SV:0000040 "InfectionAcquisitionFromContaminatedAbioticThing" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An infection acquisition from a contaminated thing." xsd:string
@@ -2239,7 +2243,7 @@ def: "An infection acquisition whereby a susceptible host acquires an infection
 is_a: APOLLO_SV:00000115 ! infection acquisition
 property_value: APOLLO_SV:0000040 "InfectionAcquisitionFromInfectedHost" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious.\n" xsd:string
+property_value: IAO:0000600 "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious." xsd:string
 
 [Term]
 id: APOLLO_SV:00000266
@@ -2267,7 +2271,7 @@ def: "An identifier that designates a scale according to which time is measured
 is_a: IAO:0020000 ! identifier
 property_value: APOLLO_SV:0000040 "timeScale" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated.\n" xsd:string
+property_value: IAO:0000600 "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated." xsd:string
 
 [Term]
 id: APOLLO_SV:00000269
@@ -2463,7 +2467,7 @@ def: "The unit of measure for the supply schedule of an individual treatment." [
 is_a: UO:0000000 ! unit
 property_value: APOLLO_SV:0000040 "supplyScheduleUnits" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'.\n" xsd:string
+property_value: IAO:0000600 "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'." xsd:string
 
 [Term]
 id: APOLLO_SV:00000293
@@ -2496,7 +2500,7 @@ def: "An information content entity that specifies the criteria that an organism
 is_a: IAO:0000030 ! information content entity
 property_value: APOLLO_SV:0000040 "CaseDefinition" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.\n" xsd:string
+property_value: IAO:0000600 "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on." xsd:string
 
 [Term]
 id: APOLLO_SV:00000297
@@ -2548,8 +2552,8 @@ name: recovered organism
 def: "An organism that is the bearer of a naturally-acquired, active immune resistance to infection." []
 is_a: APOLLO_SV:00000206 ! immune organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000301 ! is bearer of naturally-acquired active immune resistance
-relationship: RO:0000053 APOLLO_SV:00000301 ! is bearer of naturally-acquired active immune resistance
+intersection_of: RO:0000053 APOLLO_SV:00000301 ! bearer of naturally-acquired active immune resistance
+relationship: RO:0000053 APOLLO_SV:00000301 ! bearer of naturally-acquired active immune resistance
 property_value: APOLLO_SV:0000040 "recovered" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism that has recovered from infection with a particular pathogen, is no longer infectious to other organisms of any species, and is not able to be infected again with that pathogen." xsd:string
@@ -2638,10 +2642,10 @@ id: APOLLO_SV:00000312
 name: individual mosquito reproduction
 def: "A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157)" []
 is_a: APOLLO_SV:00000651 ! reproduction
-is_a: GO:0032504 ! obsolete multicellular organism reproduction
+is_a: GO:0048609 ! multicellular organismal reproductive process
 intersection_of: APOLLO_SV:00000651 ! reproduction
-intersection_of: RO:0002218 NCBITaxon:7157 ! has active participant Culicidae
-relationship: RO:0002218 NCBITaxon:7157 ! has active participant Culicidae
+intersection_of: RO:0002218 NCBITaxon:7157 ! obsolete has active participant Culicidae
+relationship: RO:0002218 NCBITaxon:7157 ! obsolete has active participant Culicidae
 property_value: APOLLO_SV:0000040 "MosquitoReproduction" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "Reproduction of a single mosquito" xsd:string
@@ -2660,7 +2664,7 @@ property_value: IAO:0000600 "The duration of the gonotrophic cycle in a female m
 id: APOLLO_SV:00000314
 name: gonotrophic cycle
 def: "The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition)." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition)." xsd:string
 
@@ -2696,8 +2700,8 @@ name: drug treatment
 def: "A treatment with a drug product." []
 is_a: OGMS:0000090 ! treatment
 intersection_of: OGMS:0000090 ! treatment
-intersection_of: OBI:0000293 DRON:00000005 ! has_specified_input drug product
-relationship: OBI:0000293 DRON:00000005 ! has_specified_input drug product
+intersection_of: OBI:0000293 DRON:00000005 ! has_specified_input clinical drug product
+relationship: OBI:0000293 DRON:00000005 ! has_specified_input clinical drug product
 property_value: APOLLO_SV:0000040 "DrugTreatment" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "Treatment with a drug." xsd:string
@@ -2803,7 +2807,6 @@ id: APOLLO_SV:00000335
 name: chemical resistance to infection
 def: "A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism." []
 comment: As with all dispositions, chemical resistance need not be realized to exist.  The presence of cholorquine confers this disposition even if the person is never bitten by a mosquito, let alone a malaria-laden mosquito.
-comment: Examples: chemoprophylaxis of malaria with chloroquine, treatment of infections with antibiotics, antiviral treatment
 property_value: IAO:0000111 "chemical resistance to infection" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "chemoprotection" xsd:string
@@ -3177,7 +3180,7 @@ property_value: IAO:0000600 "An endosymbiotic mutualism that realizes a biologic
 
 [Term]
 id: APOLLO_SV:00000370
-name: deprecated homeostasis
+name: obsolete homeostasis
 def: "A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3442,7 +3445,7 @@ property_value: IAO:0000600 "A data set whose data items are about a host and it
 
 [Term]
 id: APOLLO_SV:00000399
-name: deprecated infection case count
+name: obsolete infection case count
 def: "A count of individuals in a population who meet an infection case definition during a particular time interval." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3484,7 +3487,6 @@ id: APOLLO_SV:00000403
 name: transmission tree
 def: "A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host." []
 comment: Because a set A is a subset of itself, we capture the possibility that all infected organisms in the epidemic are represented in the tree.
-comment: This definition allows for multiple trees in an epidemic because we did not require that the first case infected temporally be the index case, although the ideal situation is that there is one tree for the epidemic that includes the index case.
 is_a: OBI:0000658 ! data representational model
 property_value: APOLLO_SV:0000040 "TransmissionTree" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
@@ -3499,8 +3501,8 @@ comment: The disposition of Influenza A virus H3N2 subtype to infect human being
 is_a: BFO:0000016 ! disposition
 intersection_of: BFO:0000016 ! disposition
 intersection_of: BFO:0000054 APOLLO_SV:00000114 {all_only="true"} ! is realized by infection
-intersection_of: RO:0000052 OBI:0100026 ! inheres in organism
-relationship: RO:0000052 OBI:0100026 ! inheres in organism
+intersection_of: RO:0000052 OBI:0100026 ! characteristic of organism
+relationship: RO:0000052 OBI:0100026 ! characteristic of organism
 property_value: IAO:0000111 "infectious disposition" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "A disposition inhering in an organism of a particular biological taxon that is realized only by the organism participating in an infection as the reproducing organism inside another organism of a different particular biological taxon." xsd:string
@@ -3509,7 +3511,7 @@ property_value: IAO:0000600 "A disposition inhering in an organism of a particul
 id: APOLLO_SV:00000405
 name: potentially infectious contacting
 def: "A biological process that brings the organism into sufficiently close physical proximity to a pathogen population, either in or on a contaminated thing or an infectious host, such that the organism is likely but not certain to acquire an infection with the pathogen." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000111 "potentially infectious contact process" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "potentially infectious contact" xsd:string
@@ -3536,8 +3538,8 @@ name: contacted organism
 def: "An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process." []
 is_a: OBI:0100026 ! organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000406 ! is bearer of potentially infectious contact role
-relationship: RO:0000053 APOLLO_SV:00000406 ! is bearer of potentially infectious contact role
+intersection_of: RO:0000053 APOLLO_SV:00000406 ! bearer of potentially infectious contact role
+relationship: RO:0000053 APOLLO_SV:00000406 ! bearer of potentially infectious contact role
 property_value: IAO:0000111 "potentially infectious contact organism" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism that has been exposed to a pathogen by coming into close physical proximity with either an infectious host or a contaminated thing." xsd:string
@@ -3741,7 +3743,7 @@ property_value: IAO:0000600 "An epidemic simulator action specification that whe
 id: APOLLO_SV:00000428
 name: disease outcome with probability
 def: "A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism." []
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: APOLLO_SV:0000040 "DiseaseOutcomeWithProbability" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3801,7 +3803,7 @@ property_value: IAO:0000600 "A data item that specifies the largest numerical va
 id: APOLLO_SV:00000434
 name: statistical confidence
 def: "A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest." []
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: APOLLO_SV:0000040 "confidence" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3809,7 +3811,7 @@ property_value: IAO:0000600 "A predicted data item that estimates how reliable s
 
 [Term]
 id: APOLLO_SV:00000435
-name: closure period
+name: obsolete closure period
 def: "A one-dimensional temporal region occupied by a place closure control strategy." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -4211,7 +4213,7 @@ property_value: IAO:0000600 "An epidemic simulator action specification that spe
 
 [Term]
 id: APOLLO_SV:00000475
-name: gonotrophic period duration
+name: obsolete gonotrophic period duration
 def: "A time measurement datum of the length of the temporal interval occupied by a gonotropic period." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -4252,7 +4254,7 @@ property_value: IAO:0000600 "A vector control strategy that has 1) an action spe
 id: APOLLO_SV:00000479
 name: ovisite carrying capacity
 def: "A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining." []
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining." xsd:string
@@ -4402,7 +4404,7 @@ property_value: IAO:0000600 "An identifier curated by the United States National
 
 [Term]
 id: APOLLO_SV:00000496
-name: ORCID
+name: obsolete ORCID
 def: "An identifier curated by ORCID, Inc. to denote some academic author." []
 property_value: APOLLO_SV:0000040 "orcId" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
@@ -4667,7 +4669,6 @@ id: APOLLO_SV:00000524
 name: compiling software
 def: "A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions." []
 comment: It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code".  Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
-comment: Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
 is_a: APOLLO_SV:00000008 ! software development
 property_value: IAO:0000111 "process of compiling software" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -4935,7 +4936,7 @@ id: APOLLO_SV:00000554
 name: disease surveillance data
 def: "A data set that is about some disease surveillance." []
 is_a: IAO:0000100 ! data set
-relationship: OBI:0000312 APOLLO_SV:00000545 ! is_specified_output_of disease surveillance
+relationship: OBI:0000312 APOLLO_SV:00000545 ! is specified output of disease surveillance
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "A data set that is about some disease surveillance." xsd:string
@@ -4985,7 +4986,7 @@ id: APOLLO_SV:00000559
 name: case series data set
 def: "A data set that is the output of a case series investigation." []
 is_a: IAO:0000100 ! data set
-relationship: OBI:0000312 APOLLO_SV:00000558 ! is_specified_output_of case series
+relationship: OBI:0000312 APOLLO_SV:00000558 ! is specified output of case series
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "A data set that is the output of a case series investigation." xsd:string
@@ -5077,7 +5078,7 @@ id: APOLLO_SV:00000569
 name: total disease cases
 def: "A count of the total number of diseased indivduals in a population during a particular time interval." []
 is_a: APOLLO_SV:00000617 ! population count
-relationship: OBI:0000312 APOLLO_SV:00000155 ! is_specified_output_of population infection survey
+relationship: OBI:0000312 APOLLO_SV:00000155 ! is specified output of population infection survey
 property_value: APOLLO_SV:0000040 "totalCaseCount" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5153,7 +5154,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string
 id: APOLLO_SV:00000577
 name: epidemic peak intensity
 def: "A predicted data item that is about some aggregate of cases in an epidemic and whose value specification contains the maximum value in a data set that is about the epidemic." []
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: IAO:0000117 "Amanda Hicks" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5313,7 +5314,6 @@ property_value: IAO:0000111 "census of treatment facility" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "census of treatment facilities" xsd:string
 property_value: IAO:0000118 "treatment facilities census" xsd:string
-property_value: IAO:0000118 "treatment facility census" xsd:string
 property_value: IAO:0000600 "A census that counts the number of treatment facilities of some kind in a particular geographical region." xsd:string
 
 [Term]
@@ -5548,8 +5548,8 @@ def: "A monkeypox disease inhering in a human being." []
 comment: requested by MIDAS CC
 is_a: DOID:3292 ! monkeypox
 intersection_of: DOID:3292 ! monkeypox
-intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
-relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
+intersection_of: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
+relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
 property_value: dc:date "2022-09-18T18:51:00" xsd:dateTime
 property_value: IAO:0000111 "monkeypox disease inhering in a human being" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5620,7 +5620,6 @@ id: APOLLO_SV:00000623
 name: incident epidemic case count
 def: "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." []
 comment: Incident case counts are measured according to regular intervals, typically day or week.
-comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin.
 is_a: APOLLO_SV:00000498 ! count of cases in an epidemic
 is_a: APOLLO_SV:00000649 ! incident case count
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5843,7 +5842,7 @@ property_value: IAO:0000600 "The intent of a guardian to have a ward under their
 id: APOLLO_SV:00000651
 name: reproduction
 def: "The process by which new organisms are created from existing ones." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 union_of: GO:0019058 ! viral life cycle
 union_of: GO:0019953 ! sexual reproduction
 union_of: GO:0019954 ! asexual reproduction
@@ -5885,10 +5884,11 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string
 id: APOLLO_SV:00000796
 name: dataset creating
 def: "A planned process that has a data set as its specified output." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 intersection_of: OBI:0000011 ! planned process
-intersection_of: OBI:0000299 IAO:0000100 ! has_specified_output data set
-relationship: OBI:0000299 IAO:0000100 ! has_specified_output data set
+intersection_of: OBI:0000299 IAO:0000100 ! has specified output data set
+relationship: OBI:0000299 IAO:0000100 ! has specified output data set
 property_value: IAO:0000111 "creating a data set" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "data set creation" xsd:string
@@ -5899,10 +5899,11 @@ id: APOLLO_SV:00000797
 name: creating a copyright license
 def: "A planned process that has a copyright license as its specified output." []
 comment: Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time.
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 intersection_of: OBI:0000011 ! planned process
-intersection_of: OBI:0000299 APOLLO_SV:00000798 ! has_specified_output copyright license
-relationship: OBI:0000299 APOLLO_SV:00000798 ! has_specified_output copyright license
+intersection_of: OBI:0000299 APOLLO_SV:00000798 ! has specified output copyright license
+relationship: OBI:0000299 APOLLO_SV:00000798 ! has specified output copyright license
 property_value: IAO:0000111 "creating a copyright license" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "copyright license creation" xsd:string
@@ -6024,11 +6025,10 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 id: BFO:0000004
 name: independent continuant
 def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
-def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
 comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
 is_a: BFO:0000002 ! continuant
-disjoint_from: BFO:0000020 ! characteristic
-disjoint_from: BFO:0000020 ! characteristic
+disjoint_from: BFO:0000020 ! specifically dependent continuant
+disjoint_from: BFO:0000020 ! specifically dependent continuant
 disjoint_from: BFO:0000031 ! generically dependent continuant
 relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant
 property_value: BFO:0000179 "ic" xsd:string
@@ -6125,7 +6125,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 id: BFO:0000015
 name: process
 def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
-def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
 comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
 is_a: BFO:0000003 ! occurrent
 property_value: BFO:0000179 "process" xsd:string
@@ -6161,10 +6160,9 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 
 [Term]
 id: BFO:0000017
-name: realizable
 name: realizable entity
 def: "A specifically dependent continuant  that inheres in continuant  entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." []
-is_a: BFO:0000020 ! characteristic
+is_a: BFO:0000020 ! specifically dependent continuant
 disjoint_from: BFO:0000019 ! quality
 relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity
 property_value: BFO:0000179 "realizable" xsd:string
@@ -6194,7 +6192,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 [Term]
 id: BFO:0000019
 name: quality
-is_a: BFO:0000020 ! characteristic
+is_a: BFO:0000020 ! specifically dependent continuant
 relationship: part_of BFO:0000019 {all_only="true"} ! quality
 property_value: BFO:0000179 "quality" xsd:string
 property_value: BFO:0000180 "Quality" xsd:string
@@ -6212,15 +6210,12 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 
 [Term]
 id: BFO:0000020
-name: characteristic
 name: specifically dependent continuant
 def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
-def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1  i &lt; j  n, ci  and cj share no common parts, are such that for each 1  i  n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"}
-def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
 comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
 is_a: BFO:0000002 ! continuant
 disjoint_from: BFO:0000031 ! generically dependent continuant
-relationship: part_of BFO:0000020 {all_only="true"} ! characteristic
+relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant
 property_value: BFO:0000179 "sdc" xsd:string
 property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string
 property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string
@@ -6235,11 +6230,8 @@ property_value: IAO:0000112 "the role of being a doctor" xsd:string
 property_value: IAO:0000112 "the shape of this hole." xsd:string
 property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string
 property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"}
-property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"}
 property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
 property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
-property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string
-property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string
 
 [Term]
 id: BFO:0000023
@@ -6263,7 +6255,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 [Term]
 id: BFO:0000024
 name: fiat object
-name: fiat object part
 is_a: BFO:0000040 ! material entity
 property_value: BFO:0000179 "fiat-object" xsd:string
 property_value: BFO:0000179 "fiat-object-part" xsd:string
@@ -6294,11 +6285,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 
 [Term]
 id: BFO:0000027
-name: object aggregate
 name: object_aggregate
 comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
-comment: Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
-comment: Synonyms: substance aggregate
 is_a: BFO:0000040 ! material entity
 property_value: BFO:0000179 "object-aggregate" xsd:string
 property_value: BFO:0000180 "ObjectAggregate" xsd:string
@@ -6316,6 +6304,7 @@ property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string
 property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string
 property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string
 property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"}
+property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011", IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"}
 property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"}
 property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string
 property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"}
@@ -6389,7 +6378,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 id: BFO:0000031
 name: generically dependent continuant
 def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." []
-def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
 comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
 is_a: BFO:0000002 ! continuant
 relationship: part_of BFO:0000031 {all_only="true"} ! generically dependent continuant
@@ -6465,6 +6453,7 @@ property_value: IAO:0000112 "the undetached arm of a human being" xsd:string
 property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string
 property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string
 property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string
+property_value: IAO:0000116 "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." xsd:string
 property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
 property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
 property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
@@ -6597,6 +6586,20 @@ name: antiviral drug
 comment: The usage or intended usage of a drug product to act against a viral infection of a host.
 is_a: BFO:0000023 ! role
 
+[Term]
+id: COB:0000022
+name: organism
+def: "A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome" []
+is_a: UBERON:0000465 ! material anatomical entity
+property_value: IAO:0000116 "'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'." xsd:string
+property_value: IAO:0000116 "Includes virus - we will later have a class for cellular organisms." xsd:string
+
+[Term]
+id: COB:0000035
+name: completely executed planned process
+is_a: BFO:0000015 ! process
+disjoint_from: GO:0008150 ! biological_process
+
 [Term]
 id: DOID:0060478
 name: Zika fever
@@ -6695,12 +6698,21 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/doid.owl" xsd:string
 
 [Term]
 id: DRON:00000005
-name: drug product
-def: "a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role" []
-is_a: BFO:0000030 ! object
-property_value: dc:creator "William Hogan" xsd:string
+name: clinical drug product
+def: "A drug product that is bearer of a clinical drug role." []
+comment: We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a "clinical drug role" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf "drug product", which also required changing the definition here.
+is_a: DRON:00000074 ! drug product
 property_value: IAO:0000117 "William Hogan" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/dron.owl" xsd:string
+
+[Term]
+id: DRON:00000074
+name: drug product
+def: "A material entity that (1) contains at least one scattered molecular aggregate as part and (2) is intended, when administered to an organism, to produce some therapeutic and/or psychoactive effect." []
+comment: The "intention" part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered.
+is_a: BFO:0000040 ! material entity
+property_value: IAO:0000117 "William R. Hogan" xsd:string
+property_value: terms:contributor https://orcid.org/0000-0001-6378-1703
+property_value: terms:contributor https://orcid.org/0000-0002-5039-2052
 
 [Term]
 id: EFO:0004600
@@ -6936,7 +6948,6 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string
 [Term]
 id: GEO:000000007
 name: aggregate of major administrative subdivisions
-name: group of major administrative subdivisions
 def: "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common." []
 comment: Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc.
 is_a: GEO:000000337 ! aggregate of governmental organizations
@@ -6946,7 +6957,6 @@ property_value: IAO:0000117 "Amanda Hicks" xsd:string
 [Term]
 id: GEO:000000008
 name: aggregate of dependencies
-name: group of dependencies
 def: "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." []
 comment: Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies.
 is_a: GEO:000000337 ! aggregate of governmental organizations
@@ -6994,9 +7004,6 @@ id: GEO:000000370
 name: geographical entity
 def: "A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface)." []
 comment: Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc.\n\nGenerally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought.  But the intent is definitely for this class to NOT subsume organism universally.  Human beings are contained within, but not part of, the Earth, for example.
-comment: Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc.
-comment: We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn).  So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities.
-comment: We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond.  \n\nThus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc.
 is_a: BFO:0000040 ! material entity
 property_value: IAO:0000111 "geographical entity of astronomical body" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -7013,7 +7020,6 @@ is_a: GEO:000000370 ! geographical entity
 id: GEO:000000372
 name: geographical region
 def: "A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface." []
-def: "A site designated by some relative spatial orientation." []
 is_a: GEO:000000370 ! geographical entity
 property_value: APOLLO_SV:0000040 "Location" xsd:string
 property_value: IAO:0000117 "François Modave" xsd:string
@@ -7048,7 +7054,7 @@ is_a: GEO:000000334 ! subcontinental land mass
 id: GEO:000000377
 name: aggregate of geographical entities
 def: "An object aggregate of geographical entities" []
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 relationship: BFO:0000075 GEO:000000370 ! is aggregate of geographical entity
 
 [Term]
@@ -7204,20 +7210,18 @@ property_value: IAO:0000118 "de jure state" xsd:string
 
 [Term]
 id: GO:0003674
-name: gene product or complex activity
 name: molecular_function
 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt]
-comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
-comment: This is the same as GO molecular function
+comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
 synonym: "molecular function" EXACT []
 is_a: BFO:0000015 ! process
-disjoint_from: GO:0008150 ! biological process
+property_value: IAO:0000116 "This is the same as GO molecular function" xsd:string
 
 [Term]
 id: GO:0006955
 name: immune response
 def: "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 
 [Term]
@@ -7245,18 +7249,13 @@ creation_date: 2012-09-20T14:06:08Z
 
 [Term]
 id: GO:0008150
-name: biological process
 name: biological_process
 namespace: biological_process
 alt_id: GO:0000004
 alt_id: GO:0007582
 alt_id: GO:0044699
 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
-def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." []
-def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." []
-comment: A biological process is an evolved process
 comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
-comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
 subset: goslim_candida
 subset: goslim_chembl
 subset: goslim_metagenomics
@@ -7270,8 +7269,6 @@ synonym: "single organism process" RELATED []
 synonym: "single-organism process" RELATED []
 xref: Wikipedia:Biological_process
 is_a: BFO:0000015 ! process
-disjoint_from: OBI:0000011 ! planned process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 created_by: jl
 creation_date: 2012-09-19T15:05:24Z
@@ -7289,8 +7286,9 @@ subset: goslim_virus
 synonym: "viral infection" RELATED []
 synonym: "virulence" RELATED []
 synonym: "virus process" EXACT [GOC:bf, GOC:jl]
+xref: Reactome:R-HSA-162906 "HIV Infection"
 xref: Wikipedia:Viral_life_cycle
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 
 [Term]
 id: GO:0016301
@@ -7313,6 +7311,9 @@ synonym: "lytic viral life cycle" RELATED []
 synonym: "viral assembly, maturation, egress, and release" NARROW [GOC:bf, GOC:jl]
 synonym: "viral infectious cycle" RELATED [GOC:bf, GOC:jl]
 synonym: "viral replication" RELATED [GOC:bf, GOC:jl]
+xref: Reactome:R-HSA-162588 "Budding and maturation of HIV virion"
+xref: Reactome:R-HSA-168255 "Influenza Infection"
+xref: Reactome:R-HSA-9609646 "HCMV Infection"
 is_a: APOLLO_SV:00000651 ! reproduction
 is_a: GO:0016032 ! viral process
 
@@ -7333,7 +7334,6 @@ is_a: GO:0007610 ! behavior
 is_a: GO:0048609 ! multicellular organismal reproductive process
 intersection_of: GO:0007610 ! behavior
 intersection_of: GO:0048609 ! multicellular organismal reproductive process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23491" xsd:anyURI
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 created_by: jl
 creation_date: 2012-09-19T16:01:37Z
@@ -7344,10 +7344,10 @@ name: sexual reproduction
 namespace: biological_process
 def: "A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid)." [Wikipedia:Sexual_reproduction]
 comment: Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
+subset: gocheck_do_not_annotate
 xref: Wikipedia:Sexual_reproduction
 is_a: APOLLO_SV:00000651 ! reproduction
 is_a: GO:0022414 ! reproductive process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI
 
 [Term]
 id: GO:0019954
@@ -7358,13 +7358,14 @@ synonym: "parthenogenesis" RELATED [Wikipedia:Parthenogenesis]
 xref: Wikipedia:Asexual_reproduction
 is_a: APOLLO_SV:00000651 ! reproduction
 is_a: GO:0022414 ! reproductive process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI
 
 [Term]
 id: GO:0022414
 name: reproductive process
 namespace: biological_process
+alt_id: GO:0019952
 alt_id: GO:0044702
+alt_id: GO:0050876
 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete]
 subset: gocheck_do_not_annotate
 subset: goslim_agr
@@ -7376,8 +7377,7 @@ subset: goslim_plant
 subset: goslim_plant_ribbon
 synonym: "single organism reproductive process" RELATED []
 xref: Wikipedia:Reproduction
-is_a: GO:0008150 ! biological process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI
+is_a: GO:0008150 ! biological_process
 created_by: jl
 creation_date: 2012-09-19T15:56:06Z
 
@@ -7393,21 +7393,10 @@ subset: gocheck_do_not_annotate
 subset: goslim_pir
 synonym: "organismal physiological process" EXACT []
 synonym: "single-multicellular organism process" RELATED []
-is_a: GO:0008150 ! biological process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI
+is_a: GO:0008150 ! biological_process
 created_by: jl
 creation_date: 2012-09-19T16:07:47Z
 
-[Term]
-id: GO:0032504
-name: obsolete multicellular organism reproduction
-namespace: biological_process
-def: "OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:isa_complete, GOC:jid]
-comment: The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process.
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI
-is_obsolete: true
-replaced_by: GO:0048609
-
 [Term]
 id: GO:0044403
 name: biological process involved in symbiotic interaction
@@ -7429,13 +7418,10 @@ synonym: "symbiotic interaction between organisms" RELATED []
 synonym: "symbiotic interaction between species" RELATED []
 synonym: "symbiotic process" RELATED []
 is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14807" xsd:anyURI
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI
 
 [Term]
 id: GO:0044409
 name: entry into host
-name: symbiont entry into host
 namespace: biological_process
 alt_id: GO:0030260
 alt_id: GO:0044411
@@ -7446,7 +7432,6 @@ alt_id: GO:0075052
 alt_id: GO:0085027
 alt_id: GO:0085028
 def: "Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:vw]
-def: "Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." []
 subset: goslim_virus
 synonym: "entry into cell of other organism during symbiotic interaction" NARROW [GOC:tb]
 synonym: "entry into cell of other organism involved in symbiotic interaction" RELATED []
@@ -7469,9 +7454,9 @@ synonym: "other organism invasion" RELATED []
 synonym: "penetration into host" EXACT [GOC:vw]
 synonym: "penetration into host via a specialized structure" NARROW [GOC:vw]
 synonym: "penetration into host via a specialized structure during symbiotic interaction" NARROW [GOC:vw]
+xref: Reactome:R-HSA-173107 "Binding and entry of HIV virion"
 is_a: GO:0051701 ! biological process involved in interaction with host
 is_a: GO:0051704 ! multi-organism process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/18563" xsd:anyURI
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 
 [Term]
@@ -7486,8 +7471,8 @@ synonym: "interaction with another species" EXACT []
 synonym: "interspecies interaction" EXACT []
 synonym: "interspecies interaction between organisms" EXACT []
 synonym: "interspecies interaction with other organisms" EXACT []
-is_a: GO:0008150 ! biological process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI
+xref: Reactome:R-HSA-9824443 "Parasitic Infection Pathways"
+is_a: GO:0008150 ! biological_process
 
 [Term]
 id: GO:0048609
@@ -7498,14 +7483,14 @@ subset: gocheck_do_not_annotate
 subset: goslim_drosophila
 synonym: "organismal reproductive process" BROAD []
 synonym: "reproductive process in a multicellular organism" EXACT []
+xref: Reactome:R-HSA-1474165 "Reproduction"
 is_a: GO:0022414 ! reproductive process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI
 
 [Term]
 id: GO:0051234
 name: establishment of localization
 def: "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000412 "Gene Ontology: http://purl.obolibrary.org/obo/go.owl" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 
@@ -7526,14 +7511,15 @@ synonym: "growth of symbiont in host cell" NARROW []
 synonym: "growth of symbiont in host organelle" NARROW []
 synonym: "growth of symbiont in host vacuole" NARROW []
 synonym: "interaction with host" EXACT []
+xref: Reactome:R-HSA-9635486 "Infection with Mycobacterium tuberculosis"
+xref: Reactome:R-HSA-9658195 "Leishmania infection"
 is_a: GO:0044403 ! biological process involved in symbiotic interaction
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI
 
 [Term]
 id: GO:0051704
 name: multi-organism process
 def: "A biological process which involves another organism of the same or different species." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 
 [Term]
@@ -7551,8 +7537,7 @@ property_value: IAO:0000119 "OBI_0000349" xsd:string
 id: IAO:0000003
 name: measurement unit label
 def: "A data item label that denotes a unit of measure." []
-def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." []
-is_a: IAO:0000009 ! datum label
+is_a: IAO:0000009 ! data item label
 property_value: IAO:0000111 "measurement unit label" xsd:string
 property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string
 property_value: IAO:0000114 IAO:0000122
@@ -7616,9 +7601,7 @@ is_obsolete: true
 [Term]
 id: IAO:0000009
 name: data item label
-name: datum label
 def: "A label is a symbol that is part of some other datum and is used to either partially define  the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" []
-def: "An information content entity that is part of some data item and is used to partially define the denotation of that data item." []
 is_a: IAO:0000030 ! information content entity
 property_value: IAO:0000111 "data item label" xsd:string
 property_value: IAO:0000111 "datum label" xsd:string
@@ -7663,8 +7646,8 @@ name: journal article
 def: "A report that is published in a journal." []
 is_a: IAO:0000088 ! report
 is_a: IAO:0000311 ! publication
-relationship: OBI:0000312 IAO:0000444 {all_only="true"} ! is_specified_output_of publishing process
-relationship: OBI:0000312 IAO:0000444 ! is_specified_output_of publishing process
+relationship: OBI:0000312 IAO:0000444 {all_only="true"} ! is specified output of publishing process
+relationship: OBI:0000312 IAO:0000444 ! is specified output of publishing process
 property_value: IAO:0000111 "journal article" xsd:string
 property_value: IAO:0000112 "Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g.  Authors, Title of article, Journal name, date or year of publication, volume and page number." xsd:string
 property_value: IAO:0000114 IAO:0000120
@@ -7815,7 +7798,6 @@ property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
 id: IAO:0000032
 name: scalar measurement datum
 def: "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." []
-def: "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." []
 is_a: IAO:0000109 ! measurement datum
 property_value: IAO:0000111 "scalar measurement datum" xsd:string
 property_value: IAO:0000112 "10 feet. 3 ml." xsd:string
@@ -8128,7 +8110,6 @@ property_value: IAO:0000119 "OBI_0000030" xsd:string
 id: IAO:0000102
 name: data about an ontology part
 def: "Data about an ontology part is a data item about a part of an ontology, for example a term" []
-def: "data about an ontology part is a data item about a part of an ontology, for example a term" []
 is_a: IAO:0000027 ! data item
 property_value: IAO:0000111 "data about an ontology part" xsd:string
 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
@@ -8494,7 +8475,7 @@ def: "A document that is the output of a publishing process." []
 comment: Revisit the term in Octorber 2020. Improve the defintion.
 is_a: IAO:0000310 ! document
 intersection_of: IAO:0000310 ! document
-intersection_of: OBI:0000312 IAO:0000444 {all_only="true"} ! is_specified_output_of publishing process
+intersection_of: OBI:0000312 IAO:0000444 {all_only="true"} ! is specified output of publishing process
 property_value: IAO:0000111 "publication" xsd:string
 property_value: IAO:0000112 "journal article, newspaper story, book, etc." xsd:string
 property_value: IAO:0000114 IAO:0000120
@@ -8879,9 +8860,10 @@ property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
 id: IAO:0000443
 name: data item extraction from journal article
 def: "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000013 ! has_specified_input journal article
-relationship: OBI:0000299 IAO:0000027 ! has_specified_output data item
+relationship: OBI:0000299 IAO:0000027 ! has specified output data item
 property_value: IAO:0000114 IAO:0000120
 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
 
@@ -8911,9 +8893,10 @@ property_value: IAO:0000234 "VEuPathDB" xsd:string
 id: IAO:0000572
 name: documenting
 def: "A planned process in which a document is created or added to by including the specified input in it." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity
-relationship: OBI:0000299 IAO:0000310 ! has_specified_output document
+relationship: OBI:0000299 IAO:0000310 ! has specified output document
 property_value: IAO:0000112 "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database." xsd:string
 property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000116 "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape" xsd:string
@@ -8937,9 +8920,10 @@ property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Line_chart" xsd:s
 id: IAO:0000574
 name: assigning a centrally registered identifier
 def: "A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity" []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
-relationship: OBI:0000299 IAO:0000577 ! has_specified_output centrally registered identifier symbol
-relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
+relationship: OBI:0000299 IAO:0000577 ! has specified output centrally registered identifier symbol
+relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry
 property_value: IAO:0000112 "A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned." xsd:string
 property_value: IAO:0000114 IAO:0000120
 property_value: IAO:0000116 "2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry." xsd:string
@@ -8954,7 +8938,7 @@ name: associating information with a centrally registered identifier in its regi
 def: "A planned process in which a CRID registry associates an information content entity with a CRID symbol" []
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol
-relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
+relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry
 property_value: IAO:0000112 "Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. " xsd:string
 property_value: IAO:0000114 IAO:0000120
 property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string
@@ -9022,10 +9006,11 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 id: IAO:0000580
 name: looking up a centrally registered identifier
 def: "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol
-relationship: OBI:0000299 IAO:0000030 ! has_specified_output information content entity
-relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
+relationship: OBI:0000299 IAO:0000030 ! has specified output information content entity
+relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry
 property_value: IAO:0000112 "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. " xsd:string
 property_value: IAO:0000114 IAO:0000120
 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
@@ -9677,9 +9662,10 @@ property_value: IAO:0000118 "ZIP code" xsd:string
 id: IAO:0000650
 name: database extract, transform, and load process
 def: "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity
-relationship: OBI:0000299 IAO:0000030 ! has_specified_output information content entity
+relationship: OBI:0000299 IAO:0000030 ! has specified output information content entity
 property_value: foaf:page https://en.wikipedia.org/wiki/Extract,_transform,_load
 property_value: IAO:0000111 "database extract, transform, and load process" xsd:string
 property_value: IAO:0000116 "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second" xsd:string
@@ -9805,22 +9791,18 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 [Term]
 id: IAO:0020000
 name: identifier
-def: "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." []
 def: "An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." []
 comment: Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
 is_a: IAO:0000030 ! information content entity
 intersection_of: IAO:0000030 ! information content entity
 intersection_of: IAO:0000219 BFO:0000001 ! denotes entity
-intersection_of: IAO:0000219 BFO:0000001 ! denotes entity
-intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output_of identifier creating process
-intersection_of: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process
+intersection_of: OBI:0000312 IAO:0020010 ! is specified output of identifier creating process
 relationship: IAO:0000219 BFO:0000001 ! denotes entity
-relationship: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process
+relationship: OBI:0000312 IAO:0020010 ! is specified output of identifier creating process
 property_value: dc:creator "Mathias Brochhausen" xsd:string
 property_value: IAO:0000111 "identifier" xsd:string
 property_value: IAO:0000117 "Justin Whorton" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "proper name" xsd:string
 property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string
 
@@ -9840,15 +9822,14 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 id: IAO:0020010
 name: identifier creating process
 def: "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." []
-def: "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 intersection_of: OBI:0000011 ! planned process
-intersection_of: OBI:0000299 IAO:0020000 ! has_specified_output identifier
-relationship: OBI:0000299 IAO:0020000 ! has_specified_output identifier
+intersection_of: OBI:0000299 IAO:0020000 ! has specified output identifier
+relationship: OBI:0000299 IAO:0020000 ! has specified output identifier
 property_value: dc:creator "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "Justin Whorton" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "dubbing process" xsd:string
 property_value: IAO:0000118 "naming" xsd:string
 property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string
@@ -9856,17 +9837,11 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 [Term]
 id: IAO:0020015
 name: personal name
-def: "A personal name is a proper name identifying an individual person." []
 def: "An identifier referring to an individual entity that is ascribed personhood by the user of the identifier." []
 comment: Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
-comment: Personal names to not include names of fictional characters, e.g. Sherlock Holmes.
-comment: Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)
 is_a: IAO:0020000 ! identifier
-intersection_of: IAO:0020000 ! identifier
-intersection_of: IAO:0000219 NCBITaxon:9606 {all_only="true"} ! denotes Homo sapiens
 property_value: IAO:0000117 "Justin Whorton" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Personal_name" xsd:string
 property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string
 
@@ -9896,16 +9871,8 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 [Term]
 id: IAO:0020020
 name: code set
-def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate." []
 def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things." []
 comment: Code sets might include non-entities/things (e.g. missing thumbs).
-comment: Does not imply absence vs. presence of any taxonomy.
-comment: Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
-comment: Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
-comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
-comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
-comment: Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
-comment: The information content entities do not denote each other.
 is_a: IAO:0000030 ! information content entity
 relationship: has_part IAO:0020000 ! identifier
 property_value: dc:contributor "Alan Ruttenberg" xsd:string
@@ -9916,7 +9883,6 @@ property_value: dc:contributor "William R. Hogan" xsd:string
 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
 property_value: IAO:0000117 "Justin Whorton" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "code map" xsd:string
 property_value: IAO:0000118 "code system" xsd:string
 property_value: IAO:0000118 "codeset" xsd:string
@@ -9929,7 +9895,7 @@ id: IAO:0021003
 name: social act
 def: "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived." []
 comment: The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).\nReinach clearly does not imply that a command that does not fulfill its prupose would not be a command.\nThanks to W.R. Hogan for finding the Reinach quote.
-is_a: OBI:0000011 ! planned process
+is_a: COB:0000035 ! completely executed planned process
 property_value: IAO:0000112 "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
@@ -10112,7 +10078,6 @@ id: IDO:0000406
 name: opportunistic infectious disposition
 def: "An infectious disposition to become part of a disorder only in organisms whose defenses are compromised." []
 comment: The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.
-comment: This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin).
 is_a: IDO:0000452 ! infectious disposition
 disjoint_from: IDO:0000407 ! primary infectious disposition
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
@@ -10125,7 +10090,6 @@ id: IDO:0000407
 name: primary infectious disposition
 def: "An infectious disposition to become part of a disorder in organisms that have intact defenses." []
 comment: A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
-comment: A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms.  ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease.  ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease."
 is_a: IDO:0000452 ! infectious disposition
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
@@ -10136,10 +10100,10 @@ id: IDO:0000450
 name: pathogenic disposition
 def: "A disposition to initiate processes that result in a disorder." []
 comment: A pathogenic disposition is realized in processes that create a disorder.
-comment: The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition.  By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.
 is_a: BFO:0000016 ! disposition
 disjoint_from: IDO:0000618 ! immunocompetence
 disjoint_from: OGMS:0000031 ! disease
+relationship: RO:0000052 BFO:0000040 ! characteristic of material entity
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10151,6 +10115,7 @@ name: infectious disposition
 def: "A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder." []
 comment: The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder.  The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder.
 is_a: IDO:0000450 ! pathogenic disposition
+relationship: RO:0000052 OBI:0100026 ! characteristic of organism
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10194,7 +10159,7 @@ def: "A quality that inheres in an infectious agent and is the likelihood that t
 comment: The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.
 is_a: BFO:0000019 ! quality
 disjoint_from: IDO:0000464 ! infectivity
-relationship: RO:0000052 IDO:0000596 ! inheres in infectious agent
+relationship: RO:0000052 IDO:0000596 ! characteristic of infectious agent
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10205,7 +10170,7 @@ name: infectivity
 def: "A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism." []
 comment: This quality is measured by the proportion of exposed who become infected.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10216,7 +10181,7 @@ name: virulence
 def: "A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal. " []
 comment: This quality is measured by the proportion of clinically apparent cases that are severe or fatal.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000596 ! inheres in infectious agent
+relationship: RO:0000052 IDO:0000596 ! characteristic of infectious agent
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10227,7 +10192,7 @@ name: susceptibility
 def: "A quality that inheres in an entity and is the degree to which it can be harmed by another entity." []
 comment: Low susceptibility is often referred to as resistance.  In this sense, resistance is a quality.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 BFO:0000040 ! inheres in material entity
+relationship: RO:0000052 BFO:0000040 ! characteristic of material entity
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10238,7 +10203,7 @@ name: infectious disease incidence
 def: "A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time." []
 comment: A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time.  Incidence is used as a measure of risk.  Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location.  Other constraints may include population demographics.  These constraints will vary with the context of the incidence measure.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10249,7 +10214,7 @@ name: infection incidence
 def: "A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time." []
 comment: A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time.  Incidence is used as a measure of risk.  Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location.  Other constraints may include population demographics.  These constraints will vary with the context of the incidence measure.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10260,7 +10225,7 @@ name: infectious disease incidence proportion
 def: "A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time. " []
 comment: An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10272,7 +10237,7 @@ name: infection incidence proportion
 def: "A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. " []
 comment: An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10284,7 +10249,7 @@ name: infectious disease incidence rate
 def: "A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time." []
 comment: An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10295,7 +10260,7 @@ name: infection incidence rate
 def: "A quality that inheres in an organism population and is the infection incidence proportion per unit time." []
 comment: An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10306,7 +10271,7 @@ name: infectious disease prevalence
 def: "A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time." []
 comment: Prevalence is sometimes defined as a proportion with total population size in the denominator.  A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time.  Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location.  Other constraints may include population demographics.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10317,7 +10282,7 @@ name: infection prevalence
 def: "A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time." []
 comment: Prevalence is sometimes defined as a proportion with total population size in the denominator.  A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time.  Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location.  Other constraints may include population demographics.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10328,7 +10293,7 @@ name: infectious disease lifetime prevalence
 def: "A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease." []
 comment: Prevalence is sometimes defined as a proportion with total population size in the denominator.  A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population.  Actual measures of prevalence are based only on reported cases and usually specify a geographic location.  Other constraints may include population demographics.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10339,7 +10304,7 @@ name: infectious agent seroprevalence
 def: "A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time." []
 comment: Prevalence is sometimes defined as a proportion with total population size in the denominator.  A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population.  Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location.  Other constraints may include population demographics.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10350,7 +10315,7 @@ name: infectious disease mortality rate
 def: "A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time." []
 comment: A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population.  Actual measures of mortality rate are based only on reported cases and usually specify a geographic location.  Other constraints may include population demographics.  Mortality rate is typically expressed in units of deaths per 1000 individuals per year.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10361,7 +10326,7 @@ name: infectious disease endemicity
 def: "A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir." []
 comment: A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population.  The population may be specified by temporal, geographic, or demographic constraints.  Infectious diseases that are typical or common to a particular population are referred to as endemic.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10372,7 +10337,7 @@ name: infectious disease sporadicity
 def: "A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence." []
 comment: Sporadic quality of infectious disease is relational to previous prevalence of the disease.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10382,7 +10347,7 @@ id: IDO:0000509
 name: organism population
 def: "An aggregate of organisms of the same Species." []
 comment: The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10457,7 +10422,8 @@ comment: The disposition inheres in a bearer in virtue of the fact that the bear
 is_a: BFO:0000016 ! disposition
 disjoint_from: OGMS:0000031 ! disease
 relationship: BFO:0000054 GO:0006955 ! is realized by immune response
-relationship: RO:0000052 OBI:0100026 ! inheres in organism
+relationship: RO:0000052 OBI:0100026 ! characteristic of organism
+relationship: RO:0000052 OBI:0100026 ! characteristic of organism
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10498,7 +10464,7 @@ property_value: IAO:0000117 "Lindsay Cowell" xsd:string
 id: IDO:0000629
 name: host role
 def: "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." []
-is_a: OMRSE:00000049 ! organism role
+is_a: BFO:0000023 ! role
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10561,7 +10527,6 @@ property_value: IAO:0000118 "House mouse" xsd:string
 
 [Term]
 id: NCBITaxon:10239
-name: Virus
 name: Viruses
 is_a: OBI:0100026 ! organism
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl
@@ -10569,7 +10534,7 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl
 [Term]
 id: NCBITaxon:10240
 name: Poxviridae
-is_a: NCBITaxon:35237 ! dsDNA virus, no RNA stage
+is_a: NCBITaxon:35237 ! dsDNA viruses, no RNA stage
 
 [Term]
 id: NCBITaxon:10241
@@ -11547,6 +11512,12 @@ property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string
 property_value: IAO:0000118 "Diplococcus pneumoniae" xsd:string
 property_value: IAO:0000118 "Micrococcus pneumoniae" xsd:string
 
+[Term]
+id: NCBITaxon:131567
+name: cellular organisms
+xref: GC_ID:1
+is_a: COB:0000022 ! organism
+
 [Term]
 id: NCBITaxon:1329799
 name: Archelosauria
@@ -12493,6 +12464,10 @@ property_value: has_rank NCBITaxon:family
 [Term]
 id: NCBITaxon:2759
 name: Eukaryota
+xref: GC_ID:1
+xref: PMID:23020233
+xref: PMID:30257078
+is_a: NCBITaxon:131567 ! cellular organisms
 is_a: OBI:0100026 ! organism
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl
 
@@ -12933,16 +12908,15 @@ property_value: has_rank NCBITaxon:family
 
 [Term]
 id: NCBITaxon:35237
-name: dsDNA virus, no RNA stage
 name: dsDNA viruses, no RNA stage
 namespace: ncbi_taxonomy
 xref: GC_ID:1
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 
 [Term]
 id: NCBITaxon:35268
 name: Retro-transcribing viruses
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 property_value: IAO:0000118 "Retroid viruses" xsd:string
 
 [Term]
@@ -12972,7 +12946,7 @@ is_a: NCBITaxon:1933264 ! California encephalitis orthobunyavirus
 [Term]
 id: NCBITaxon:35325
 name: dsRNA viruses
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string
 property_value: IAO:0000118 "dsRNA nonenveloped viruses" xsd:string
 
@@ -13113,7 +13087,7 @@ property_value: has_rank NCBITaxon:genus
 [Term]
 id: NCBITaxon:39759
 name: Deltavirus
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string
 
 [Term]
@@ -13140,6 +13114,7 @@ property_value: has_rank NCBITaxon:subgenus
 [Term]
 id: NCBITaxon:40674
 name: Mammalia
+xref: GC_ID:1
 is_a: NCBITaxon:32524 ! Amniota
 property_value: IAO:0000118 "mammals" xsd:string
 
@@ -13234,7 +13209,7 @@ is_a: NCBITaxon:7157 ! Culicidae
 [Term]
 id: NCBITaxon:439488
 name: ssRNA virus
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 
 [Term]
 id: NCBITaxon:44025
@@ -13671,7 +13646,7 @@ id: NCBITaxon:548681
 name: Herpesvirales
 namespace: ncbi_taxonomy
 xref: GC_ID:1
-is_a: NCBITaxon:35237 ! dsDNA virus, no RNA stage
+is_a: NCBITaxon:35237 ! dsDNA viruses, no RNA stage
 property_value: has_rank NCBITaxon:order
 
 [Term]
@@ -14951,6 +14926,7 @@ property_value: has_rank NCBITaxon:genus
 [Term]
 id: NCBITaxon:9443
 name: Primates
+xref: GC_ID:1
 is_a: NCBITaxon:314146 ! Euarchontoglires
 property_value: IAO:0000118 "Primata" xsd:string
 property_value: IAO:0000118 "primate" xsd:string
@@ -15048,9 +15024,8 @@ property_value: IAO:0000118 "rhesus monkeys" xsd:string
 [Term]
 id: NCBITaxon:9606
 name: Homo sapiens
-is_a: NCBITaxon:2759 ! Eukaryota
-property_value: IAO:0000111 "Homo sapiens" xsd:string
-property_value: IAO:0000118 "human being" xsd:string
+xref: GC_ID:1
+is_a: NCBITaxon:9443 ! Primates
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl
 
 [Term]
@@ -15276,19 +15251,14 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/dideo/dev/dideo.owl"
 id: OBI:0000011
 name: planned process
 def: "A process that realizes a plan which is the concretization of a plan specification." []
-def: "A processual entity that realizes a plan which is the concretization of a plan specification." []
 is_a: BFO:0000015 ! process
 property_value: IAO:0000111 "planned process" xsd:string
-property_value: IAO:0000111 "planned process" xsd:string
 property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string
 property_value: IAO:0000114 IAO:0000122
 property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string
 property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \n  objectives is a planned process." xsd:string
-property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string
 property_value: IAO:0000117 "Bjoern Peters" xsd:string
 property_value: IAO:0000119 "branch derived" xsd:string
-property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string
-property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 
 [Term]
@@ -15338,7 +15308,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 id: OBI:0000245
 name: organization
 def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." []
-def: "An organization is a continuant entity which can play roles,  has members, and has a set of organization rules.  Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." []
 is_a: BFO:0000040 ! material entity
 property_value: IAO:0000111 "organization" xsd:string
 property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string
@@ -15375,7 +15344,7 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 id: OBI:0000576
 name: scattered molecular aggregate
 def: "a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates" []
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 property_value: IAO:0000111 "scattered molecular aggregate" xsd:string
 property_value: IAO:0000112 "the sodium and chloride ions in a glass of salt water" xsd:string
 property_value: IAO:0000114 IAO:0000123
@@ -15420,8 +15389,8 @@ name: average value
 def: "A  data item that is produced as the output of an averaging data transformation and represents the average value of the input data." []
 is_a: IAO:0000027 ! data item
 intersection_of: IAO:0000027 ! data item
-intersection_of: OBI:0000312 OBI:0200170 ! is_specified_output_of averaging data transformation
-relationship: OBI:0000312 OBI:0200170 ! is_specified_output_of averaging data transformation
+intersection_of: OBI:0000312 OBI:0200170 ! is specified output of averaging data transformation
+relationship: OBI:0000312 OBI:0200170 ! is specified output of averaging data transformation
 property_value: APOLLO_SV:0000040 "mean" xsd:string
 property_value: IAO:0000111 "average value" xsd:string
 property_value: IAO:0000114 IAO:0000125
@@ -15450,20 +15419,15 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 id: OBI:0000968
 name: device
 def: "A device is a processed material which is designed to perform some function or functions" []
-def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." []
 comment: would include reagents
 is_a: OBI:0000047 ! processed material
 property_value: IAO:0000111 "device" xsd:string
 property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string
-property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string
-property_value: IAO:0000114 IAO:0000122
 property_value: IAO:0000114 IAO:0000123
-property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions.  Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear.  For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component.  This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running  box  is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it.  This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation).  In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string
 property_value: IAO:0000116 "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only" xsd:string
 property_value: IAO:0000116 "if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of  the definition. device was needed, but couldn't define in Philadelphia. If we decide  that in addition to function there are also capabilities for which a device is created we will include these in the definition." xsd:string
 property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string
 property_value: IAO:0000118 "instrument" xsd:string
-property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string
 property_value: IAO:0000119 "OBI Vancouver workshop 2010" xsd:string
 
 [Term]
@@ -15670,30 +15634,21 @@ id: OBI:0100026
 name: organism
 def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." []
 is_a: BFO:0000040 ! material entity
-union_of: NCBITaxon:10239 ! Virus
+union_of: NCBITaxon:10239 ! Viruses
 union_of: NCBITaxon:2 ! Bacteria
 union_of: NCBITaxon:2157 ! Archaea
 union_of: NCBITaxon:2759 ! Eukaryota
 disjoint_from: OGMS:0000045 ! disorder
 property_value: APOLLO_SV:0000040 "Individual" xsd:string
 property_value: IAO:0000111 "organism" xsd:string
-property_value: IAO:0000112 "animal" xsd:string
-property_value: IAO:0000112 "fungus" xsd:string
-property_value: IAO:0000112 "plant" xsd:string
-property_value: IAO:0000112 "virus" xsd:string
 property_value: IAO:0000114 IAO:0000121
-property_value: IAO:0000114 IAO:0000122
-property_value: IAO:0000116 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string
-property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string
-property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string
-property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 
 [Term]
 id: OBI:0200000
 name: data transformation
-def: "A data transformation is a process which produces output data from input data" []
-def: "A planned process that produces output data from input data." []
+def: "A completely executed planned process that produces output data from input data." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective
 property_value: IAO:0000111 "data transformation" xsd:string
@@ -15752,7 +15707,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 [Term]
 id: OBI:0302867
 name: calculated datum
-name: predicted data item
 def: "A data item that was generated on the basis of a calculation or logical reasoning" []
 comment: APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class.
 is_a: IAO:0000109 ! measurement datum
@@ -15837,22 +15791,19 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/OBIws.owl" xsd:strin
 id: OGMS:0000014
 name: clinical finding
 def: "A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof." []
-is_a: IAO:0000027 ! data item
+is_a: IAO:0000030 ! information content entity
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2010-07-19T10:18:02Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000018
 name: laboratory finding
 def: "A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient." []
 is_a: OGMS:0000014 ! clinical finding
-property_value: APOLLO_SV:0000040 "result" xsd:string
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T10:21:58Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000023
@@ -15862,7 +15813,6 @@ is_a: BFO:0000019 ! quality
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2010-07-19T11:13:49Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000027
@@ -15872,14 +15822,12 @@ is_a: OGMS:0000023 ! phenotype
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:18:05Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000031
 name: disease
 def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." []
 is_a: BFO:0000016 ! disposition
-property_value: APOLLO_SV:0000040 "disease" xsd:string
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:21:20Z" xsd:string
@@ -15888,15 +15836,9 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl
 [Term]
 id: OGMS:0000032
 name: homeostasis
-def: "A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning." []
 is_a: BFO:0000016 ! disposition
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
-property_value: IAO:0000117 "Barry Smith" xsd:string
-property_value: IAO:0000117 "Richard H. Scheuermann" xsd:string
-property_value: IAO:0000117 "Werner Ceusters" xsd:string
-property_value: IAO:0000119 "Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. \n\nLink: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:22:01Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000045
@@ -15907,7 +15849,6 @@ property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:39:44Z" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000060
@@ -15923,89 +15864,78 @@ id: OGMS:0000063
 name: disease course
 def: "The totality of all processes through which a given disease instance is realized." []
 is_a: BFO:0000015 ! process
-property_value: IAO:0000111 "disease course" xsd:string
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:55:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000087
 name: extended organism
 def: "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism." []
 comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=3" xsd:string
 property_value: IAO:0000232 "creation date: 2010-01-25T04:51:11Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl
 
 [Term]
 id: OGMS:0000090
 name: treatment
-def: "A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder" []
-comment: Apollo-SV currently defines two subclasses of treatment.\nSee vaccination and antiviral treatment.  \n
-is_a: OBI:0000011 ! planned process
-property_value: APOLLO_SV:0000040 "Treatment" xsd:string
+def: "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process" []
+is_a: OGMS:0000096 ! health care process
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=35" xsd:string
 property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000092
 name: life course
-def: "A processual entity which has as parts all the processes in which a given organism is participant." []
-is_a: BFO:0000182 ! history
-property_value: APOLLO_SV:0000040 "LifeCycle" xsd:string
-property_value: IAO:0000117 "Albert Goldfain" xsd:string
+def: "A process which has as parts all the processes in which a given organism is participant." []
+is_a: BFO:0000015 ! process
+property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string
 property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=38" xsd:string
-property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
-property_value: IAO:0000600 "A processual entity which has as parts all the processes in which a given organism is participant." xsd:string
+property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z\n\nEDIT: 10 NOV 2015" xsd:string
 
 [Term]
 id: OGMS:0000096
 name: health care process
-def: "A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process" []
-is_a: BFO:0000015 ! process
-property_value: IAO:0000117 "Albert Goldfain" xsd:string
+def: "A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient" []
+is_a: COB:0000035 ! completely executed planned process
+is_a: OBI:0000011 ! planned process
+property_value: IAO:0000117 "Albert Goldfain\nSagar Jain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
-property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
+property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z\neditor date: 2017-04-18" xsd:string
 
 [Term]
 id: OGMS:0000097
 name: health care encounter
 def: "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role.  The health care provider role and patient are realized during the health care encounter" []
-is_a: OBI:0000011 ! planned process
+synonym: "healthcare encounter" EXACT []
 is_a: OGMS:0000096 ! health care process
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000098
 name: hospitalization
-is_a: OGMS:0000097 ! health care encounter
-property_value: APOLLO_SV:0000040 "hospitalization" xsd:string
+def: "TODO" []
+comment: 09/16/2020\nIs this same as admission? \nIs this the same as inpatient encounter?
+is_a: OGMS:0000096 ! health care process
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000099
 name: outpatient encounter
+def: "TODO" []
 is_a: OGMS:0000097 ! health care encounter
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000100
@@ -16015,25 +15945,26 @@ is_a: OGMS:0000097 ! health care encounter
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000101
-name: ED encounter
+name: emergency department encounter
+def: "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention." []
 is_a: OGMS:0000097 ! health care encounter
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000105
 name: relapse
-def: "A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course." []
+def: "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease." []
 is_a: BFO:0000015 ! process
-property_value: IAO:0000117 "Albert Goldfain" xsd:string
+property_value: dc:date "10 NOV 2015" xsd:string
+property_value: IAO:0000116 "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course." xsd:string
+property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string
+property_value: IAO:0000118 "recurrent" xsd:string
 property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=73" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OMIABIS:0000019
@@ -16051,27 +15982,27 @@ id: OMRSE:00000001
 name: human social role
 def: "A social role inhering in a human being." []
 is_a: OMRSE:00000026 ! organism social role
-is_a: OMRSE:00000050 ! Homo sapiens role
+relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 
 [Term]
 id: OMRSE:00000010
-name: human health care role
+name: health care role
 def: "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis." []
+synonym: "healthcare role" EXACT []
 is_a: OMRSE:00002072 ! role in human social processes
 relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000118 "health care role" xsd:string
 
 [Term]
 id: OMRSE:00000011
 name: patient role
-def: "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." []
+def: "A health care role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." []
 comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.
-is_a: OMRSE:00000010 ! human health care role
-is_a: OMRSE:00000049 ! organism role
+is_a: OMRSE:00000010 ! health care role
+relationship: RO:0000052 COB:0000022 ! characteristic of organism
 property_value: IAO:0000117 "Amanda Hicks" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "patient" xsd:string
@@ -16081,6 +16012,7 @@ property_value: IAO:0000119 "CAFE domain expert working group." xsd:string
 id: OMRSE:00000015
 name: health care provider organization role
 def: "A role that inheres in an organization and that is realized by the providing of services in a health care encounter." []
+synonym: "healthcare provider organization role" EXACT []
 is_a: OMRSE:00000027 ! organization health care role
 relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter
 property_value: dc:contributor "Mathias Brochhausen" xsd:string
@@ -16091,7 +16023,7 @@ id: OMRSE:00000022
 name: aggregate of objectual organisms
 def: "An object aggregate of objectual organisms." []
 comment: Any arbitrary collection of organisms.  They need not be of the same taxonomic class.  
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 
 [Term]
 id: OMRSE:00000023
@@ -16114,10 +16046,8 @@ id: OMRSE:00000026
 name: organism social role
 def: "A role in human social processes that inheres in an organism." []
 comment: Defined class that we will ultimately move to an application ontology.  We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants.
-comment: Includes animals as well as humans.  For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc.  Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
-comment: Previous definition: A role in human social processes played by an organism.
-is_a: OMRSE:00000049 ! organism role
 is_a: OMRSE:00002072 ! role in human social processes
+relationship: RO:0000052 COB:0000022 ! characteristic of organism
 property_value: IAO:0000117 "William R. Hogan\nMathias Brochhausen" xsd:string
 
 [Term]
@@ -16125,6 +16055,7 @@ id: OMRSE:00000027
 name: organization health care role
 def: "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process" []
 comment: Previous definition: An organization social role played by an organization in health care processes.
+synonym: "organization healthcare role" EXACT []
 is_a: OMRSE:00000025 ! organization social role
 
 [Term]
@@ -16132,9 +16063,9 @@ id: OMRSE:00000030
 name: human patient role
 def: "A patient role that inheres in a human being." []
 is_a: OMRSE:00000011 ! patient role
-is_a: OMRSE:00000050 ! Homo sapiens role
 intersection_of: OMRSE:00000011 ! patient role
-intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
+intersection_of: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
+relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
 
 [Term]
 id: OMRSE:00000033
@@ -16145,41 +16076,14 @@ is_a: BFO:0000040 ! material entity
 relationship: RO:0002351 OBI:0000245 ! has member organization
 property_value: IAO:0000117 "William R. Hogan\nAmanda Hicks" xsd:string
 
-[Term]
-id: OMRSE:00000048
-name: material entity role
-is_a: BFO:0000023 ! role
-intersection_of: BFO:0000023 ! role
-intersection_of: RO:0000052 BFO:0000040 ! inheres in material entity
-relationship: RO:0000052 BFO:0000040 {all_only="true"} ! inheres in material entity
-relationship: RO:0000052 BFO:0000040 ! inheres in material entity
-
-[Term]
-id: OMRSE:00000049
-name: organism role
-is_a: OMRSE:00000048 ! material entity role
-intersection_of: OMRSE:00000048 ! material entity role
-intersection_of: RO:0000052 OBI:0100026 ! inheres in organism
-relationship: RO:0000052 OBI:0100026 {all_only="true"} ! inheres in organism
-relationship: RO:0000052 OBI:0100026 ! inheres in organism
-
-[Term]
-id: OMRSE:00000050
-name: Homo sapiens role
-is_a: OMRSE:00000049 ! organism role
-intersection_of: OMRSE:00000049 ! organism role
-intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
-relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
-relationship: RO:0000052 NCBITaxon:9606 {all_only="true"} ! inheres in Homo sapiens
-
 [Term]
 id: OMRSE:00000051
 name: organization role
-is_a: OMRSE:00000048 ! material entity role
+is_a: BFO:0000023 ! role
 intersection_of: BFO:0000023 ! role
-intersection_of: RO:0000052 OBI:0000245 ! inheres in organization
-relationship: RO:0000052 OBI:0000245 ! inheres in organization
-relationship: RO:0000052 OBI:0000245 {all_only="true"} ! inheres in organization
+intersection_of: RO:0000052 OBI:0000245 ! characteristic of organization
+relationship: RO:0000052 OBI:0000245 ! characteristic of organization
+relationship: RO:0000052 OBI:0000245 {all_only="true"} ! characteristic of organization
 
 [Term]
 id: OMRSE:00000053
@@ -16208,8 +16112,8 @@ name: hospital organization
 def: "An organization that is the bearer of a hospital role." []
 is_a: OBI:0000245 ! organization
 intersection_of: OBI:0000245 ! organization
-intersection_of: RO:0000053 OMRSE:00000054 ! is bearer of hospital role
-relationship: RO:0000053 OMRSE:00000054 ! is bearer of hospital role
+intersection_of: RO:0000053 OMRSE:00000054 ! bearer of hospital role
+relationship: RO:0000053 OMRSE:00000054 ! bearer of hospital role
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -16218,8 +16122,8 @@ name: school organization
 def: "An organization that is the bearer of a school role." []
 is_a: OBI:0000245 ! organization
 intersection_of: OBI:0000245 ! organization
-intersection_of: RO:0000053 OMRSE:00000055 ! is bearer of school role
-relationship: RO:0000053 OMRSE:00000055 ! is bearer of school role
+intersection_of: RO:0000053 OMRSE:00000055 ! bearer of school role
+relationship: RO:0000053 OMRSE:00000055 ! bearer of school role
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -16245,7 +16149,6 @@ id: OMRSE:00000061
 name: architectural structure
 def: "A material entity that is a human made strcuture with firm connection between its foundation and the ground." []
 comment: "Building" is a subclass of this. 
-comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".
 is_a: BFO:0000040 ! material entity
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000119 "http://de.wikipedia.org/wiki/Bauwerk" xsd:string
@@ -16256,9 +16159,9 @@ name: facility
 def: "An architectural structure that bears some function." []
 is_a: OMRSE:00000061 ! architectural structure
 intersection_of: OMRSE:00000061 ! architectural structure
-intersection_of: RO:0000053 BFO:0000034 ! is bearer of function
-relationship: OMRSE:00000068 OBI:0000245 {owl:versionInfo="09/09/2017"} ! is administered by organization
-relationship: RO:0000053 BFO:0000034 ! is bearer of function
+intersection_of: RO:0000053 BFO:0000034 ! bearer of function
+relationship: OMRSE:00000068 OBI:0000245 ! is administered by organization
+relationship: RO:0000053 BFO:0000034 ! bearer of function
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -16266,7 +16169,7 @@ id: OMRSE:00000064
 name: school facility
 def: "A facility that is run by a school organization and is the bearer of a school function." []
 is_a: OMRSE:00000062 ! facility
-relationship: RO:0000053 OMRSE:00000053 ! is bearer of school function
+relationship: RO:0000053 OMRSE:00000053 ! bearer of school function
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -16297,6 +16200,7 @@ property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/issues/79" xsd:anyUR
 [Term]
 id: OMRSE:00000172
 name: health care function
+synonym: "healthcare function" EXACT []
 is_a: BFO:0000034 ! function
 intersection_of: BFO:0000034 ! function
 intersection_of: BFO:0000054 OGMS:0000097 ! is realized by health care encounter
@@ -16307,8 +16211,9 @@ id: OMRSE:00002072
 name: role in human social processes
 def: "A role that inheres in some entity that is realized in a social act." []
 comment: Previous definition: A role played by an entity in human social processes.
-is_a: OMRSE:00000048 ! material entity role
-relationship: RO:0000052 BFO:0000040 {all_only="true"} ! inheres in material entity
+is_a: BFO:0000023 ! role
+relationship: RO:0000052 BFO:0000040 ! characteristic of material entity
+relationship: RO:0000052 BFO:0000040 {all_only="true"} ! characteristic of material entity
 property_value: dc:contributor "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 
@@ -16316,7 +16221,7 @@ property_value: IAO:0000117 "Matthew Diller" xsd:string
 id: PATO:0000001
 name: quality
 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG]
-is_a: BFO:0000020 ! characteristic
+is_a: BFO:0000020 ! specifically dependent continuant
 
 [Term]
 id: PATO:0000040
@@ -16513,7 +16418,7 @@ id: PCO:0000000
 name: PCO:collection of organisms
 def: "A material entity that consists of two or more organisms, viruses, or viroids." []
 comment: May be of the same or different species.
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string
 property_value: IAO:0000118 "group of organisms" xsd:string
 property_value: IAO:0000118 "organism collection" xsd:string
@@ -16677,10 +16582,11 @@ property_value: IAO:0000412 "Transmission Ontology: http://purl.obolibrary.org/o
 [Term]
 id: UBERON:0000061
 name: anatomical structure
-namespace: uberon
-def: "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome." []
 def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003]
 subset: common_anatomy
+subset: human_reference_atlas
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 synonym: "biological structure" EXACT []
 synonym: "connected biological structure" EXACT [CARO:0000003]
@@ -16690,40 +16596,72 @@ xref: BILA:0000003
 xref: CARO:0000003
 xref: EHDAA2:0003003
 xref: EMAPA:0
-xref: FBbt:00007001
+xref: FAO:0000001
 xref: FMA:305751
 xref: FMA:67135
 xref: GAID:781
 xref: HAO:0000003
 xref: http://dbpedia.org/ontology/AnatomicalStructure
 xref: MA:0003000
-xref: MESH:A13
 xref: MESH:D000825
 xref: SCTID:362889002
 xref: TAO:0000037
 xref: TGMA:0001823
 xref: VHOG:0001759
-xref: WBbt:0000100
 xref: XAO:0003000
 xref: ZFA:0000037
 is_a: UBERON:0000465 ! material anatomical entity
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: RO:0002175 NCBITaxon:33090
-property_value: RO:0002175 NCBITaxon:4751
+
+[Term]
+id: UBERON:0000071
+name: death stage
+def: "End of the life of an organism." [XAO:0000437]
+subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
+synonym: "death" RELATED []
+xref: XAO:0000437
+xref: XtroDO:0000085
+is_a: UBERON:0000105 ! life cycle stage
+
+[Term]
+id: UBERON:0000105
+name: life cycle stage
+def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165]
+subset: common_anatomy
+subset: efo_slim
+subset: human_subset
+subset: mouse_subset
+subset: upper_level
+synonym: "developmental stage" NARROW []
+synonym: "stage" NARROW []
+xref: BILS:0000105
+xref: EFO:0000399
+xref: FBdv:00007012
+xref: FMA:24120
+xref: MESH:D008018
+xref: ncithesaurus:Developmental_Stage
+xref: PdumDv:0000090
+xref: WBls:0000002
+xref: XAO:1000000
+xref: ZFS:0000000
+xref: ZFS:0100000
+is_a: BFO:0000015 ! process
+property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string
 
 [Term]
 id: UBERON:0000465
 name: material anatomical entity
-namespace: uberon
 def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737]
 subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 xref: AAO:0010264
 xref: AEO:0000006
 xref: BILA:0000006
 xref: CARO:0000006
 xref: EHDAA2:0003006
-xref: FBbt:00007016
 xref: FMA:67165
 xref: HAO:0000006
 xref: TAO:0001836
@@ -16731,23 +16669,27 @@ xref: TGMA:0001826
 xref: VHOG:0001721
 is_a: BFO:0000040 ! material entity
 is_a: UBERON:0001062 ! anatomical entity
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: RO:0002175 NCBITaxon:33090
-property_value: RO:0002175 NCBITaxon:4751
 
 [Term]
 id: UBERON:0000467
 name: anatomical system
-namespace: uberon
-def: "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]." []
+def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [CARO:0000011]
+subset: common_anatomy
+subset: human_reference_atlas
+subset: human_subset
+subset: mouse_subset
+subset: pheno_slim
 subset: uberon_slim
 subset: upper_level
-synonym: "body system" EXACT []
+synonym: "anatomical systems" RELATED OMO:0003004 [ZFA:0001439]
+synonym: "body system" EXACT [BIRNLEX:14]
+synonym: "connected anatomical system" EXACT [CARO:0000011]
 synonym: "organ system" EXACT []
-synonym: "system" BROAD []
+synonym: "system" BROAD [GO:0048731]
 xref: AAO:0000007
 xref: AEO:0000011
 xref: BILA:0000011
+xref: BIRNLEX:14
 xref: BSA:0000049
 xref: CALOHA:TS-2088
 xref: CARO:0000011
@@ -16755,71 +16697,65 @@ xref: EHDAA2:0003011
 xref: EHDAA:392
 xref: EMAPA:16103
 xref: EV:0100000
-xref: FBbt:00004856
 xref: FMA:7149
 xref: galen:AnatomicalSystem
 xref: HAO:0000011
 xref: MA:0000003
-xref: ncithesaurus:Organ_System
-xref: NIF_GrossAnatomy:birnlex_14
-xref: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
+xref: NCIT:C12919
 xref: SCTID:278195005
 xref: TAO:0001439
 xref: TGMA:0001831
-xref: UMLS:C0460002
 xref: VHOG:0001725
 xref: WBbt:0005746
 xref: WBbt:0005763
 xref: Wikipedia:Organ_system
 xref: XAO:0003002
 xref: ZFA:0001439
-is_a: UBERON:0000480 ! anatomical group
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: seeAlso EHDAA2:0001330
-property_value: UBPROP:0000001 "Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]" xsd:string
-property_value: UBPROP:0000001 "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]" xsd:string
-property_value: UBPROP:0000001 "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]" xsd:string
+is_a: UBERON:0000061 ! anatomical structure
 
 [Term]
 id: UBERON:0000479
 name: tissue
-namespace: uberon
-def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." []
-comment: Editor note: changed label and definition to reflect CARO2
+def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [CARO:0000043]
+subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
+subset: pheno_slim
 subset: upper_level
-synonym: "portion of tissue" EXACT []
-synonym: "simple tissue" NARROW []
+synonym: "portion of tissue" EXACT [CARO:0000043]
+synonym: "simple tissue" NARROW [AEO:0000043]
 synonym: "tissue portion" EXACT []
 xref: AAO:0000607
 xref: AAO:0010054
 xref: AEO:0000043
 xref: BILA:0000043
+xref: BIRNLEX:19
 xref: CALOHA:TS-2090
 xref: CARO:0000043
 xref: EHDAA2:0003043
-xref: FBbt:00007003
+xref: EMAPA:35868
 xref: FMA:9637
 xref: galen:Tissue
 xref: HAO:0000043
 xref: MA:0003002
-xref: MESH:A10
-xref: ncithesaurus:Tissue
-xref: NIF_GrossAnatomy:birnlex_19
+xref: MESH:D014024
+xref: NCIT:C12801
 xref: TAO:0001477
 xref: TGMA:0001844
-xref: UMLS:C0040300
 xref: VHOG:0001757
 xref: WBbt:0005729
 xref: XAO:0003040
 xref: ZFA:0001477
 is_a: UBERON:0010000 ! multicellular anatomical structure
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
+property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string
 
 [Term]
 id: UBERON:0000480
 name: anatomical group
-namespace: uberon
-def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." []
+def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." [CARO:0000054, http://orcid.org/0000-0001-9114-8737]
+subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 xref: AAO:0010008
 xref: AEO:0000054
@@ -16833,13 +16769,15 @@ xref: VHOG:0001724
 xref: XAO:0003001
 xref: ZFA:0001512
 is_a: UBERON:0000061 ! anatomical structure
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
+property_value: IAO:0000116 "Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]" xsd:string
 
 [Term]
 id: UBERON:0001062
 name: anatomical entity
 def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737]
 subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 xref: AAO:0010841
 xref: AEO:0000000
@@ -16854,78 +16792,58 @@ xref: MA:0000001
 xref: NCIT:C12219
 xref: TAO:0100000
 xref: TGMA:0001822
-xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"}
 xref: WBbt:0000100
 xref: XAO:0000000
 xref: ZFA:0100000
 is_a: BFO:0000004 ! independent continuant
-property_value: RO:0002175 NCBITaxon:33090
-property_value: RO:0002175 NCBITaxon:4751
 
 [Term]
 id: UBERON:0002405
 name: immune system
-namespace: uberon
-def: "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." []
-comment: This class was created automatically from a combination of ontologies
+def: "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." [Wikipedia:Immune_system]
+subset: human_reference_atlas
+subset: human_subset
+subset: mouse_subset
+subset: pheno_slim
 subset: uberon_slim
 subset: vertebrate_core
 xref: AAO:0011003
 xref: BILA:0000104
+xref: BTO:0005810
 xref: FMA:9825
 xref: GAID:328
 xref: MA:0002711
-xref: MESH:A15.382
-xref: ncithesaurus:Immune_System
-xref: OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA
+xref: MESH:D007107
+xref: NCIT:C12735
 xref: SCTID:362590003
 xref: TAO:0001159
-xref: UMLS:C0020962
 xref: VHOG:0001247
 xref: Wikipedia:Immune_system
 xref: XAO:0003152
 xref: ZFA:0001159
-is_a: UBERON:0000467 ! anatomical system
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string
+is_a: UBERON:0000465 ! material anatomical entity
 
 [Term]
 id: UBERON:0010000
 name: multicellular anatomical structure
-namespace: uberon
 def: "An anatomical structure that has more than one cell as a part." [CARO:0010000]
 subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 synonym: "multicellular structure" EXACT [FBbt:00100313]
 xref: CARO:0010000
-xref: FBbt:00100313
 is_a: UBERON:0000061 ! anatomical structure
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: RO:0002175 NCBITaxon:33090
-property_value: RO:0002175 NCBITaxon:4751
 
 [Term]
 id: UBERON:0035943
 name: life cycle temporal boundary
-namespace: uberon
-def: "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity." []
+def: "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity." [https://orcid.org/0000-0002-6601-2165]
+subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
-is_a: BFO:0000015 ! process
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-
-[Term]
-id: UBERON:0035944
-name: life-death temporal boundary
-namespace: uberon
-def: "A life cycle temporal boundary that marks the end of the life cycle of the organism." []
-synonym: "death" RELATED []
-synonym: "end of life" RELATED []
-synonym: "end of life cycle" EXACT []
-synonym: "moment of death" EXACT []
-synonym: "time of death" EXACT []
-is_a: UBERON:0035943 ! life cycle temporal boundary
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
+is_a: BFO:0000035 ! process boundary
 
 [Term]
 id: UO:0000000
@@ -17022,7 +16940,7 @@ id: VO:0000001
 name: vaccine
 def: "A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine." []
 is_a: OBI:0000047 ! processed material
-relationship: OBI:0000312 VO:0000590 ! is_specified_output_of vaccine preparation
+relationship: OBI:0000312 VO:0000590 ! is specified output of vaccine preparation
 property_value: APOLLO_SV:0000040 "Vaccine" xsd:string
 property_value: IAO:0000116 "Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy." xsd:string
 property_value: IAO:0000117 "a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo." xsd:string
@@ -17062,7 +16980,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/vo.owl" xsd:string
 [Term]
 id: oboInOwl:ObsoleteClass
 name: Obsolete Class
-name: obsolete_class
 property_value: IAO:0000412 "http://www.geneontology.org/formats/oboInOwl" xsd:string
 
 [Term]
@@ -17071,14 +16988,14 @@ is_a: IAO:0000102 ! data about an ontology part
 
 [Typedef]
 id: APOLLO_SV:00000004
-name: basis of
+name: obsolete basis of
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
 is_obsolete: true
 
 [Typedef]
 id: APOLLO_SV:00000028
 name: obsolete is based on
-comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. 
+comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption.
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
 is_obsolete: true
 
@@ -17093,7 +17010,7 @@ is_asymmetric: true
 [Typedef]
 id: APOLLO_SV:00000057
 name: instantiates
-def: "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. " []
+def: "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times." []
 comment: Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.
 domain: BFO:0000001 ! entity
 is_asymmetric: true
@@ -17108,7 +17025,7 @@ is_asymmetric: true
 
 [Typedef]
 id: APOLLO_SV:00000116
-name: causally_precedes
+name: obsolete causally_precedes
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
 is_obsolete: true
@@ -17132,12 +17049,8 @@ range: BFO:0000019 ! quality
 [Typedef]
 id: BFO:0000054
 name: is realized by
-name: realized in
 def: "Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]" []
 comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
-property_value: ace_lexicon:TV_pl "BFO_0000054" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000054s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000054ed" xsd:string
 property_value: IAO:0000111 "obsolete_is_realized_by" xsd:string
 property_value: IAO:0000111 "realized in" xsd:string
 property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string
@@ -17165,10 +17078,8 @@ inverse_of: BFO:0000055 ! realizes
 [Typedef]
 id: BFO:0000055
 name: realizes
+def: "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" []
 comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
-property_value: ace_lexicon:TV_pl "BFO_0000055" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000055s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000055ed" xsd:string
 property_value: IAO:0000111 "realizes" xsd:string
 property_value: IAO:0000112 "this disease course realizes this disease" xsd:string
 property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string
@@ -17189,7 +17100,6 @@ property_value: IAO:0000116 "An example is: translation preceded_by transcriptio
 property_value: IAO:0000118 "is preceded by" xsd:string
 property_value: IAO:0000118 "preceded_by" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string
-property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string
 domain: BFO:0000003 ! occurrent
 range: BFO:0000003 ! occurrent
 holds_over_chain: part_of BFO:0000062
@@ -17213,7 +17123,6 @@ is_a: RO:0002222 ! temporal relation
 [Typedef]
 id: BFO:0000067
 name: contains process
-def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
 def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001" []
 comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
 property_value: BFO:0000179 "contains-process" xsd:string
@@ -17259,10 +17168,6 @@ name: exists at
 id: BFO:0000110
 name: has continuant part at all times
 def: "[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)" []
-def: "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])" []
-property_value: ace_lexicon:TV_pl "BFO_0000110" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000110s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000110ed" xsd:string
 property_value: BFO:0000179 "c-has-part_at" xsd:string
 property_value: BFO:0000180 "hasContinuantPartAt" xsd:string
 property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'" xsd:string
@@ -17276,9 +17181,6 @@ is_transitive: true
 id: BFO:0000111
 name: has proper continuant part at all times
 def: "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001" []
-property_value: ace_lexicon:TV_pl "BFO_0000111" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000111s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000111ed" xsd:string
 property_value: BFO:0000179 "c-has-ppart_at" xsd:string
 property_value: BFO:0000180 "hasProperContinuantPartAt" xsd:string
 property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'." xsd:string
@@ -17304,9 +17206,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 id: BFO:0000117
 name: has occurrent part
 def: "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" []
-property_value: ace_lexicon:TV_pl "BFO_0000117" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000117s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000117ed" xsd:string
 property_value: BFO:0000179 "o-has-part" xsd:string
 property_value: BFO:0000180 "hasOccurrentPart" xsd:string
 property_value: IAO:0000112 "[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life" xsd:string
@@ -17325,10 +17224,6 @@ inverse_of: BFO:0000132 ! part of occurrent
 id: BFO:0000118
 name: has proper occurrent part
 def: "[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])" []
-def: "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" []
-property_value: ace_lexicon:TV_pl "BFO_0000118" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000118s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000118ed" xsd:string
 property_value: BFO:0000179 "o-has-ppart" xsd:string
 property_value: BFO:0000180 "hasProperOccurrentPart" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string
@@ -17340,7 +17235,6 @@ is_a: BFO:0000117 ! has occurrent part
 id: BFO:0000121
 name: has temporal part
 def: "[copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])" []
-def: "[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t  & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" []
 property_value: BFO:0000179 "has-t-part" xsd:string
 property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" xsd:string
 property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life." xsd:string
@@ -17365,9 +17259,6 @@ range: BFO:0000004 ! independent continuant
 id: BFO:0000132
 name: part of occurrent
 def: "[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" []
-property_value: ace_lexicon:TV_pl "BFO_0000132" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000132s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000132ed" xsd:string
 property_value: BFO:0000179 "o-part-of" xsd:string
 property_value: BFO:0000180 "occurrentPartOf" xsd:string
 property_value: IAO:0000112 "Mary’s 5th birthday occurrent_part_of Mary’s life" xsd:string
@@ -17418,7 +17309,6 @@ inverse_of: BFO:0000187 ! has continuant part at all times that part exists
 id: BFO:0000138
 name: proper part of occurrent
 def: "[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" []
-def: "b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])" []
 property_value: BFO:0000179 "o-ppart-of" xsd:string
 property_value: BFO:0000180 "properOccurrentPartOf" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string
@@ -17430,7 +17320,6 @@ is_a: BFO:0000132 ! part of occurrent
 id: BFO:0000139
 name: temporal part of
 def: "b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])" []
-def: "b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t  & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" []
 property_value: BFO:0000179 "t-part-of" xsd:string
 property_value: BFO:0000180 "temporalPartOf" xsd:string
 property_value: IAO:0000112 "the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" xsd:string
@@ -17475,9 +17364,6 @@ name: during which exists
 [Typedef]
 id: BFO:0000167
 name: has participant at all times
-property_value: ace_lexicon:TV_pl "BFO_0000167" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000167s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000167ed" xsd:string
 
 [Typedef]
 id: BFO:0000169
@@ -17607,8 +17493,6 @@ range: GEO:000000400 ! governmental organization
 [Typedef]
 id: GEO:000000336
 name: has jurisdiction in
-comment: a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories.
-comment: if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b.
 comment: It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c.\n\nin other words, it is perfectly fine to say:\na disjoint b\nc has_jurisdiction_in a\nc has_jurisdiction_in b\n\notherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc.  We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc.  Seems like an unnecessary duplication of entities.
 domain: GEO:000000400 ! governmental organization
 range: GEO:000000375 ! land mass
@@ -17642,7 +17526,6 @@ is_obsolete: true
 id: IAO:0000136
 name: is about
 def: "A (currently) primitive relation that relates an information artifact to an entity." []
-def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." []
 property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string
 property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string
@@ -17816,7 +17699,7 @@ property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 domain: OBI:0000011 ! planned process
-is_a: RO:0000057 ! has_participant
+is_a: RO:0000057 ! has participant
 
 [Typedef]
 id: OBI:0000295
@@ -17831,8 +17714,9 @@ is_a: RO:0000056 ! participates in
 
 [Typedef]
 id: OBI:0000299
-name: has_specified_output
-def: "The inverse property of is_specified_output_of" []
+name: has specified output
+def: "The inverse property of is specified output of" []
+property_value: IAO:0000111 "has specified output" xsd:string
 property_value: IAO:0000111 "has_specified_output" xsd:string
 property_value: IAO:0000111 "has_specified_output" xsd:string
 property_value: IAO:0000114 IAO:0000122
@@ -17842,9 +17726,10 @@ property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string
 property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
+domain: COB:0000035 ! completely executed planned process
 domain: OBI:0000011 ! planned process
-is_a: RO:0000057 ! has_participant
-inverse_of: OBI:0000312 ! is_specified_output_of
+is_a: RO:0000057 ! has participant
+inverse_of: OBI:0000312 ! is specified output of
 
 [Typedef]
 id: OBI:0000308
@@ -17853,8 +17738,9 @@ is_obsolete: true
 
 [Typedef]
 id: OBI:0000312
-name: is_specified_output_of
-def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." []
+name: is specified output of
+def: "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." []
+property_value: IAO:0000111 "is specified output of" xsd:string
 property_value: IAO:0000111 "is_specified_output_of" xsd:string
 property_value: IAO:0000111 "is_specified_output_of" xsd:string
 property_value: IAO:0000114 IAO:0000122
@@ -17862,6 +17748,7 @@ property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
+range: COB:0000035 ! completely executed planned process
 range: OBI:0000011 ! planned process
 is_a: RO:0000056 ! participates in
 
@@ -17889,6 +17776,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 [Typedef]
 id: OBIB:0000732
 name: owns
+property_value: dc:source "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal." xsd:string
 inverse_of: OBIB:0000735 ! is owned by
@@ -17904,18 +17792,15 @@ is_asymmetric: true
 [Typedef]
 id: OMIABIS:0000008
 name: obsolete owns
-name: owns
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string
 property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. " xsd:string
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
-is_obsolete: true
 replaced_by: OBIB:0000732
 
 [Typedef]
 id: OMIABIS:0000048
-name: is owned by
 name: obsolete is owned by
 def: "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." []
 property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string
@@ -17942,9 +17827,7 @@ range: OMRSE:00000056 ! hospital organization
 [Typedef]
 id: RO:0000052
 name: characteristic of
-name: inheres in
 def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
-def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" []
 comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
 property_value: IAO:0000111 "inheres in" xsd:string
 property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string
@@ -17956,15 +17839,11 @@ property_value: IAO:0000118 "inheres_in" xsd:string
 property_value: RO:0001900 RO:0001901
 is_functional: true
 is_a: RO:0002314 ! characteristic of part of
-inverse_of: RO:0000053 ! is bearer of
+inverse_of: RO:0000053 ! bearer of
 
 [Typedef]
 id: RO:0000053
 name: bearer of
-name: bearer_of
-name: has characteristic
-name: is bearer of
-def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" []
 def: "Inverse of characteristic_of" []
 property_value: IAO:0000111 "bearer of" xsd:string
 property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
@@ -17975,7 +17854,7 @@ property_value: IAO:0000118 "bearer_of" xsd:string
 property_value: IAO:0000118 "is bearer of" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string
 property_value: RO:0001900 RO:0001901
-range: BFO:0000020 ! characteristic
+range: BFO:0000020 ! specifically dependent continuant
 is_inverse_functional: true
 
 [Typedef]
@@ -17990,12 +17869,11 @@ property_value: IAO:0000118 "participates_in" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 domain: BFO:0000002 ! continuant
 range: BFO:0000003 ! occurrent
-inverse_of: RO:0000057 ! has_participant
+inverse_of: RO:0000057 ! has participant
 
 [Typedef]
 id: RO:0000057
 name: has participant
-name: has_participant
 def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
 property_value: dc:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string
 property_value: IAO:0000111 "has participant" xsd:string
@@ -18014,25 +17892,21 @@ holds_over_chain: has_part RO:0000057
 [Typedef]
 id: RO:0000058
 name: is concretized as
-def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." []
-property_value: IAO:0000111 "is concretized as" xsd:string
+def: "A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes." []
 property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string
 property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 domain: BFO:0000031 ! generically dependent continuant
-range: BFO:0000020 ! characteristic
+range: BFO:0000020 ! specifically dependent continuant
 inverse_of: RO:0000059 ! concretizes
 
 [Typedef]
 id: RO:0000059
 name: concretizes
 def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." []
-property_value: IAO:0000111 "concretizes" xsd:string
 property_value: IAO:0000111 "is_concretization_of" xsd:string
 property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string
 property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
-domain: BFO:0000020 ! characteristic
+domain: BFO:0000020 ! specifically dependent continuant
 range: BFO:0000031 ! generically dependent continuant
 
 [Typedef]
@@ -18045,7 +17919,7 @@ property_value: IAO:0000116 "A function inheres in its bearer at all times for w
 property_value: IAO:0000118 "function_of" xsd:string
 property_value: IAO:0000118 "is function of" xsd:string
 domain: BFO:0000034 ! function
-is_a: RO:0000052 ! inheres in
+is_a: RO:0000052 ! characteristic of
 inverse_of: RO:0000085 ! has function
 
 [Typedef]
@@ -18057,7 +17931,7 @@ property_value: IAO:0000112 "this red color is a quality of this apple" xsd:stri
 property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string
 property_value: IAO:0000118 "is quality of" xsd:string
 property_value: IAO:0000118 "quality_of" xsd:string
-is_a: RO:0000052 ! inheres in
+is_a: RO:0000052 ! characteristic of
 inverse_of: RO:0000086 ! has quality
 
 [Typedef]
@@ -18069,7 +17943,7 @@ property_value: IAO:0000112 "this investigator role is a role of this person" xs
 property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string
 property_value: IAO:0000118 "is role of" xsd:string
 property_value: IAO:0000118 "role_of" xsd:string
-is_a: RO:0000052 ! inheres in
+is_a: RO:0000052 ! characteristic of
 inverse_of: RO:0000087 ! has role
 
 [Typedef]
@@ -18081,7 +17955,7 @@ property_value: IAO:0000116 "A bearer can have many functions, and its functions
 property_value: IAO:0000118 "has_function" xsd:string
 domain: BFO:0000004 ! independent continuant
 range: BFO:0000034 ! function
-is_a: RO:0000053 ! is bearer of
+is_a: RO:0000053 ! bearer of
 
 [Typedef]
 id: RO:0000086
@@ -18091,7 +17965,7 @@ property_value: IAO:0000112 "this apple has quality this red color" xsd:string
 property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
 property_value: IAO:0000118 "has_quality" xsd:string
 range: BFO:0000019 ! quality
-is_a: RO:0000053 ! is bearer of
+is_a: RO:0000053 ! bearer of
 
 [Typedef]
 id: RO:0000087
@@ -18102,7 +17976,7 @@ property_value: IAO:0000116 "A bearer can have many roles, and its roles can exi
 property_value: IAO:0000118 "has_role" xsd:string
 domain: BFO:0000004 ! independent continuant
 range: BFO:0000023 ! role
-is_a: RO:0000053 ! is bearer of
+is_a: RO:0000053 ! bearer of
 
 [Typedef]
 id: RO:0000091
@@ -18110,7 +17984,7 @@ name: has disposition
 def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" []
 domain: BFO:0000004 ! independent continuant
 range: BFO:0000016 ! disposition
-is_a: RO:0000053 ! is bearer of
+is_a: RO:0000053 ! bearer of
 inverse_of: RO:0000092 ! disposition of
 
 [Typedef]
@@ -18119,7 +17993,7 @@ name: disposition of
 def: "inverse of has disposition" []
 comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
 subset: RO:0002259
-is_a: RO:0000052 ! inheres in
+is_a: RO:0000052 ! characteristic of
 
 [Typedef]
 id: RO:0001000
@@ -18170,12 +18044,11 @@ property_value: IAO:0000116 "Most location relations will only hold at certain t
 property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
 property_value: IAO:0000118 "located_in" xsd:string
 property_value: RO:0001900 RO:0001901
-property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI
 property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string
 domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
 range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
 is_transitive: true
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 
 [Typedef]
 id: RO:0002000
@@ -18293,7 +18166,7 @@ id: RO:0002084
 name: during which ends
 comment: Previously had ID  http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point.  No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line.  Official ID now chosen from DOS ID range.
 subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
+property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 is_a: RO:0002222 ! temporal relation
 inverse_of: ends_during ! ends during
 
@@ -18302,7 +18175,7 @@ id: RO:0002086
 name: ends after
 comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
 subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
+property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 holds_over_chain: ends_during BFO:0000062
 is_transitive: true
 is_a: RO:0002222 ! temporal relation
@@ -18310,14 +18183,11 @@ is_a: RO:0002222 ! temporal relation
 [Typedef]
 id: RO:0002090
 name: immediately precedes
-name: immediately_precedes
 comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
 subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 property_value: IAO:0000118 "ends_at_start_of" xsd:string
 property_value: IAO:0000118 "meets" xsd:string
-property_value: RO:0002575 BFO:0000063
 holds_over_chain: RO:0002230 RO:0002224
 is_a: BFO:0000063 ! precedes
 
@@ -18330,12 +18200,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam
 subset: ro-eco
 property_value: IAO:0000114 IAO:0000125
 property_value: RO:0001900 RO:0001901
-holds_over_chain: has_part part_of {RO:0002582="true"}
 holds_over_chain: has_part RO:0002131
 holds_over_chain: part_of part_of
 is_symmetric: true
 is_a: RO:0002323 ! mereotopologically related to
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []
 
 [Typedef]
@@ -18352,7 +18221,6 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" xsd:string
 property_value: RO:0001900 RO:0001901
-property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI
 is_a: RO:0002323 ! mereotopologically related to
 expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" []
 
@@ -18365,7 +18233,6 @@ property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string
 property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string
 property_value: RO:0001900 RO:0001901
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency
 is_a: has_part ! has part
 
 [Typedef]
@@ -18390,17 +18257,13 @@ name: capable of part of
 def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "has function in" xsd:string
-property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
-holds_over_chain: RO:0002215 part_of {RO:0002582="true"}
 is_a: RO:0002328 ! functionally related to
 is_a: RO:0002500 ! causal agent in process
 
 [Typedef]
 id: RO:0002218
-name: has active participant
 name: obsolete has active participant
 def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" []
-def: "x has participant y if and only if x realizes some active role that inheres in y" []
 subset: ro-eco
 property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string
 property_value: IAO:0000114 IAO:0000125
@@ -18409,8 +18272,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "has agent" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string
-is_a: RO:0000057 ! has_participant
-is_obsolete: true
+is_a: RO:0000057 ! has participant
 replaced_by: RO:0002500
 
 [Typedef]
@@ -18420,7 +18282,7 @@ def: "x adjacent to y if and only if x and y share a boundary." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
-property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"}
+property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string
 property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string
 property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string
 property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string
@@ -18438,7 +18300,6 @@ is_a: RO:0002163 ! spatially disjoint from
 [Typedef]
 id: RO:0002222
 name: temporal relation
-name: temporally related to
 comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
 subset: ro-eco
 property_value: IAO:0000114 IAO:0000125
@@ -18448,7 +18309,6 @@ property_value: IAO:0000119 "Allen" xsd:string
 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
-property_value: terms:source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI
 domain: BFO:0000003 ! occurrent
 range: BFO:0000003 ! occurrent
 
@@ -18458,10 +18318,9 @@ name: starts
 def: "inverse of starts with" []
 subset: ro-eco
 property_value: IAO:0000114 IAO:0000125
-property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000119 "Allen" xsd:string
-is_a: part_of ! part_of
+is_a: part_of ! part of
 is_a: RO:0002222 ! temporal relation
 inverse_of: RO:0002224 ! starts with
 
@@ -18472,7 +18331,6 @@ def: "x starts with y if and only if x has part y and the time point at which x
 subset: ro-eco
 property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string
 property_value: IAO:0000114 IAO:0000125
-property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "started by" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
@@ -18487,9 +18345,8 @@ def: "inverse of ends with" []
 subset: ro-eco
 property_value: dc:source "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl" xsd:string
 property_value: IAO:0000114 IAO:0000125
-property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-is_a: part_of ! part_of
+is_a: part_of ! part of
 is_a: RO:0002222 ! temporal relation
 inverse_of: RO:0002230 ! ends with
 
@@ -18500,7 +18357,6 @@ def: "x ends with y if and only if x has part y and the time point at which x en
 subset: ro-eco
 property_value: dc:source "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl" xsd:string
 property_value: IAO:0000114 IAO:0000125
-property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "finished by" xsd:string
 property_value: IAO:0000118 "finished with" xsd:string
@@ -18545,17 +18401,15 @@ subset: ro-eco
 property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "consumes" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI
 domain: BFO:0000015 ! process
 holds_over_chain: RO:0002224 RO:0002233
-is_a: RO:0000057 ! has_participant
+is_a: RO:0000057 ! has participant
 inverse_of: RO:0002352 ! input of
 
 [Typedef]
 id: RO:0002234
 name: has output
 def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." []
-def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
@@ -18564,9 +18418,8 @@ property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "produces" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI
 holds_over_chain: RO:0002230 RO:0002234
-is_a: RO:0000057 ! has_participant
+is_a: RO:0000057 ! has participant
 inverse_of: RO:0002353 ! output of
 
 [Typedef]
@@ -18575,7 +18428,6 @@ name: acts upstream of
 def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
 property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
-property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
 holds_over_chain: RO:0002327 RO:0002411
 is_a: RO:0002264 ! acts upstream of or within
 
@@ -18586,7 +18438,6 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
 synonym: "affects" RELATED []
 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0002418
 is_a: RO:0002500 ! causal agent in process
 
@@ -18597,9 +18448,6 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of
 comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
-property_value: RO:0004049 RO:0002411
-property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect
-property_value: terms:creator https://orcid.org/0000-0002-6601-2165
 is_a: RO:0002411 ! causally upstream of
 is_a: RO:0004047 ! causally upstream of or within, positive effect
 
@@ -18609,9 +18457,6 @@ name: causally upstream of, negative effect
 def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
-property_value: RO:0004050 RO:0002411
-property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect
-property_value: terms:creator https://orcid.org/0000-0002-6601-2165
 is_a: RO:0002411 ! causally upstream of
 is_a: RO:0004046 ! causally upstream of or within, negative effect
 
@@ -18624,10 +18469,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "inheres in part of" xsd:string
 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
 property_value: RO:0001900 RO:0001901
-property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
-holds_over_chain: RO:0000052 part_of {RO:0002582="true"}
 is_a: RO:0002502 ! depends on
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 
 [Typedef]
 id: RO:0002323
@@ -18666,7 +18509,6 @@ property_value: IAO:0000118 "has" xsd:string
 property_value: IAO:0000118 "is catalyzing" xsd:string
 property_value: IAO:0000118 "is executing" xsd:string
 property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI
 is_a: RO:0002215 ! capable of
 inverse_of: RO:0002333 ! enabled by
 transitive_over: has_part ! has part
@@ -18685,7 +18527,6 @@ name: part of structure that is capable of
 def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "false" xsd:boolean
-holds_over_chain: part_of RO:0002215 {RO:0002581="true"}
 is_a: RO:0002328 ! functionally related to
 
 [Typedef]
@@ -18695,11 +18536,10 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "actively involved in" xsd:string
 property_value: IAO:0000118 "enables part of" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI
 holds_over_chain: RO:0002327 part_of
 is_a: RO:0000056 ! participates in
 is_a: RO:0002431 ! involved in or involved in regulation of
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 
 [Typedef]
 id: RO:0002333
@@ -18707,8 +18547,7 @@ name: enabled by
 def: "inverse of enables" []
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI
-is_a: RO:0000057 ! has_participant
+is_a: RO:0000057 ! has participant
 is_a: RO:0002328 ! functionally related to
 
 [Typedef]
@@ -18748,7 +18587,7 @@ property_value: IAO:0000118 "is member of" xsd:string
 property_value: IAO:0000118 "member part of" xsd:string
 property_value: IAO:0000119 "SIO" xsd:string
 property_value: RO:0001900 RO:0001901
-is_a: part_of ! part_of
+is_a: part_of ! part of
 inverse_of: RO:0002351 ! has member
 
 [Typedef]
@@ -18806,7 +18645,7 @@ id: RO:0002405
 name: immediately causally downstream of
 property_value: IAO:0000114 IAO:0000428
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-is_a: immediately_preceded_by ! immediately preceded by
+is_a: immediately_preceded_by ! immediately_preceded_by
 is_a: RO:0002404 ! causally downstream of
 inverse_of: RO:0002412 ! immediately causally upstream of
 
@@ -18816,8 +18655,6 @@ name: indirectly positively regulates
 def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "indirectly activates" xsd:string
-property_value: RO:0002579 RO:0002213
-property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI
 holds_over_chain: RO:0002409 RO:0002409
 holds_over_chain: RO:0002629 RO:0002407
 holds_over_chain: RO:0002629 RO:0002629
@@ -18832,8 +18669,6 @@ name: indirectly negatively regulates
 def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "indirectly inhibits" xsd:string
-property_value: RO:0002579 RO:0002212
-property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI
 holds_over_chain: RO:0002630 RO:0002409
 holds_over_chain: RO:0002630 RO:0002630
 is_transitive: true
@@ -18853,7 +18688,6 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a
 id: RO:0002411
 name: causally upstream of
 def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" []
-def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000114 IAO:0000428
@@ -18870,10 +18704,34 @@ id: RO:0002412
 name: immediately causally upstream of
 def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: RO:0002575 RO:0002411
 is_a: RO:0002090 ! immediately precedes
 is_a: RO:0002411 ! causally upstream of
 
+[Typedef]
+id: RO:0002413
+name: provides input for
+def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." []
+property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
+property_value: IAO:0000118 "directly provides input for" xsd:string
+property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
+property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string
+holds_over_chain: RO:0002234 RO:0002233
+is_a: RO:0002412 ! immediately causally upstream of
+is_a: RO:0002414 ! transitively provides input for
+
+[Typedef]
+id: RO:0002414
+name: transitively provides input for
+def: "transitive form of directly_provides_input_for" []
+property_value: IAO:0000114 IAO:0000428
+property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
+property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string
+property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string
+domain: BFO:0000015 ! process
+range: BFO:0000015 ! process
+is_transitive: true
+is_a: RO:0004047 ! causally upstream of or within, positive effect
+
 [Typedef]
 id: RO:0002418
 name: causally upstream of or within
@@ -18885,6 +18743,7 @@ property_value: IAO:0000118 "influences (processual)" xsd:string
 is_transitive: true
 is_a: RO:0002501 ! causal relation between processes
 inverse_of: RO:0002427 ! causally downstream of or within
+transitive_over: part_of ! part of
 
 [Typedef]
 id: RO:0002427
@@ -18911,7 +18770,6 @@ id: RO:0002429
 name: involved in positive regulation of
 def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: RO:0004049 RO:0002428
 holds_over_chain: RO:0002327 positively_regulates
 holds_over_chain: RO:0002331 positively_regulates
 is_a: RO:0002428 ! involved in regulation of
@@ -18921,7 +18779,6 @@ id: RO:0002430
 name: involved in negative regulation of
 def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: RO:0004050 RO:0002428
 holds_over_chain: RO:0002327 negatively_regulates
 holds_over_chain: RO:0002331 negatively_regulates
 is_a: RO:0002428 ! involved in regulation of
@@ -18945,8 +18802,6 @@ synonym: "enables activity in" EXACT []
 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "executes activity in" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI
-holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"}
 is_a: RO:0002131 ! overlaps
 is_a: RO:0002328 ! functionally related to
 
@@ -18960,8 +18815,6 @@ property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'
 property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string
-property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI
-property_value: skos:closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI
 domain: BFO:0000040 ! material entity
 range: BFO:0000040 ! material entity
 is_symmetric: true
@@ -18973,8 +18826,6 @@ def: "An interaction relationship in which the two partners are molecular entiti
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "binds" xsd:string
 property_value: IAO:0000118 "molecularly binds with" xsd:string
-property_value: seeAlso ECO:0000353
-property_value: skos:closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI
 is_symmetric: true
 is_a: RO:0002434 ! interacts with
 
@@ -19036,7 +18887,6 @@ subset: ro-eco
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 domain: BFO:0000003 ! occurrent
 range: BFO:0000004 ! independent continuant
-holds_over_chain: has_part occurs_in {RO:0002581="true"}
 
 [Typedef]
 id: RO:0002481
@@ -19056,7 +18906,6 @@ inverse_of: RO:0002608 ! process has causal agent
 id: RO:0002501
 name: causal relation between processes
 def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." []
-def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." []
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
@@ -19070,7 +18919,6 @@ is_a: RO:0002410 ! causally related to
 id: RO:0002502
 name: depends on
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: seeAlso BFO:0000169
 
 [Typedef]
 id: RO:0002506
@@ -19096,8 +18944,6 @@ inverse_of: RO:0002566 ! causally influences
 id: RO:0002563
 name: interaction relation helper property
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29
-property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI
 is_a: RO:0002464 ! helper property (not for use in curation)
 
 [Typedef]
@@ -19128,7 +18974,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
 property_value: IAO:0000589 "directly regulates (processual)" xsd:string
-property_value: RO:0002575 RO:0002211
 is_a: regulates ! regulates
 is_a: RO:0002412 ! immediately causally upstream of
 
@@ -19195,8 +19040,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
 property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string
-property_value: RO:0004049 RO:0002578
-property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI
 is_a: positively_regulates ! positively regulates
 is_a: RO:0002578 ! directly regulates
 
@@ -19209,8 +19052,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
 property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string
-property_value: RO:0004050 RO:0002578
-property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI
 is_a: negatively_regulates ! negatively regulates
 is_a: RO:0002578 ! directly regulates
 
@@ -19260,8 +19101,6 @@ creation_date: 2018-01-25T23:20:13Z
 id: RO:0004032
 name: acts upstream of or within, positive effect
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
-property_value: RO:0004049 RO:0002264
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0004047
 is_a: RO:0002264 ! acts upstream of or within
 created_by: https://orcid.org/0000-0002-6601-2165
@@ -19271,8 +19110,6 @@ creation_date: 2018-01-26T23:49:30Z
 id: RO:0004033
 name: acts upstream of or within, negative effect
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
-property_value: RO:0004050 RO:0002264
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0004046
 is_a: RO:0002264 ! acts upstream of or within
 created_by: https://orcid.org/0000-0002-6601-2165
@@ -19283,8 +19120,6 @@ id: RO:0004034
 name: acts upstream of, positive effect
 def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
-property_value: RO:0004049 RO:0002263
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0002304
 is_a: RO:0002263 ! acts upstream of
 is_a: RO:0004032 ! acts upstream of or within, positive effect
@@ -19296,8 +19131,6 @@ id: RO:0004035
 name: acts upstream of, negative effect
 def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
-property_value: RO:0004050 RO:0002263
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0002305
 is_a: RO:0002263 ! acts upstream of
 is_a: RO:0004033 ! acts upstream of or within, negative effect
@@ -19307,8 +19140,6 @@ creation_date: 2018-01-26T23:53:22Z
 [Typedef]
 id: RO:0004046
 name: causally upstream of or within, negative effect
-property_value: RO:0004050 RO:0002418
-property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI
 is_a: RO:0002418 ! causally upstream of or within
 created_by: https://orcid.org/0000-0002-6601-2165
 creation_date: 2018-03-13T23:55:05Z
@@ -19316,8 +19147,6 @@ creation_date: 2018-03-13T23:55:05Z
 [Typedef]
 id: RO:0004047
 name: causally upstream of or within, positive effect
-property_value: RO:0004049 RO:0002418
-property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect
 is_a: RO:0002418 ! causally upstream of or within
 created_by: https://orcid.org/0000-0002-6601-2165
 creation_date: 2018-03-13T23:55:19Z
@@ -19341,7 +19170,6 @@ synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165]
 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string
 property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string
 property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string
-property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI
 property_value: terms:contributor https://orcid.org/0000-0001-6996-0040
 property_value: terms:contributor https://orcid.org/0000-0002-6601-2165
 property_value: terms:contributor https://orcid.org/0000-0002-7073-9172
@@ -19445,6 +19273,13 @@ holds_over_chain: negatively_regulates RO:0019001
 holds_over_chain: positively_regulates RO:0019002
 is_a: RO:0019000 ! regulates characteristic
 
+[Typedef]
+id: RO:0020105
+name: is anatomical entity
+def: "This property only applies to anatomical entities." []
+property_value: terms:contributor https://orcid.org/0000-0001-6677-8489
+domain: UBERON:0001062 ! anatomical entity
+
 [Typedef]
 id: bearer_of
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
@@ -19458,6 +19293,7 @@ comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND
 subset: ro-eco
 xref: RO:0002093
 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
+property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 property_value: IAO:0000118 "o" xsd:string
 property_value: IAO:0000118 "overlaps" xsd:string
 is_a: RO:0002222 ! temporal relation
@@ -19501,7 +19337,6 @@ is_obsolete: true
 
 [Typedef]
 id: immediately_preceded_by
-name: immediately preceded by
 name: immediately_preceded_by
 namespace: uberon
 def: "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" []
@@ -19512,7 +19347,7 @@ synonym: "is immediately preceded by" EXACT []
 synonym: "starts_at_end_of" EXACT []
 xref: http://semanticscience.org/resource/SIO_000251
 xref: RO:0002087
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
+property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 property_value: IAO:0000118 "starts_at_end_of" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
 property_value: UBPROP:0000001 "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." xsd:string
@@ -19537,7 +19372,6 @@ name: negatively_regulates
 namespace: external
 namespace: relationship
 def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." []
-def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
@@ -19549,7 +19383,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string
 property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
-property_value: RO:0004050 RO:0002211
 holds_over_chain: RO:0002230 negatively_regulates
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
 is_a: regulates ! regulates
@@ -19564,12 +19397,10 @@ name: ObsoleteProperty
 [Typedef]
 id: occurs_in
 name: occurs in
-name: unfolds_in
 namespace: external
 namespace: relationship
 def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
 comment: Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
-comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
@@ -19581,17 +19412,15 @@ property_value: IAO:0000118 "unfolds_in" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
-property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI
 domain: BFO:0000003 ! occurrent
 range: BFO:0000004 ! independent continuant
 holds_over_chain: part_of occurs_in
 inverse_of: BFO:0000067 ! contains process
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 
 [Typedef]
 id: part_of
 name: part of
-name: part_of
 namespace: external
 def: "a core relation that holds between a part and its whole" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
@@ -19609,17 +19438,7 @@ property_value: IAO:0000116 "Occurrents are not subject to change and so parthoo
 property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
 property_value: IAO:0000118 "part_of" xsd:string
 property_value: RO:0001900 RO:0001901
-property_value: RO:0040042 BFO:0000002
-property_value: RO:0040042 BFO:0000003
-property_value: RO:0040042 BFO:0000004
-property_value: RO:0040042 BFO:0000017
-property_value: RO:0040042 BFO:0000019
-property_value: RO:0040042 BFO:0000020
-property_value: RO:0040042 BFO:0000031
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
 property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI
 is_reflexive: true
 is_transitive: true
 is_a: RO:0002131 ! overlaps
@@ -19637,7 +19456,6 @@ xref: RO:0002213
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
 property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
-property_value: RO:0004049 RO:0002211
 holds_over_chain: negatively_regulates negatively_regulates
 holds_over_chain: RO:0002230 positively_regulates
 is_transitive: true
@@ -19667,7 +19485,6 @@ name: regulates
 namespace: external
 namespace: relationship
 def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." []
-def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
diff --git a/apollo_sv-full.owl b/apollo_sv-full.owl
index 68ce4e4..5a74adf 100644
--- a/apollo_sv-full.owl
+++ b/apollo_sv-full.owl
@@ -27,7 +27,7 @@
      xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"
      xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/apollo_sv/apollo_sv-full.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv-full.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv-full.owl"/>
         <dc:contributor>Amanda Hicks</dc:contributor>
         <dc:contributor>John Levander</dc:contributor>
         <dc:contributor>Josh Hanna</dc:contributor>
@@ -43,7 +43,7 @@
         <www:RTS_00000001>C87985BA-6A8A-483A-A6B6-63975101F672</www:RTS_00000001>
         <www:RTS_00000002>082D5D78-D916-457E-B4FD-365F86F45B30</www:RTS_00000002>
         <rdfs:comment xml:lang="en">When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl.  When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component&apos;s Uniform Resource Identifier (URI).</rdfs:comment>
-        <owl:versionInfo>2024-12-24</owl:versionInfo>
+        <owl:versionInfo>2026-03-13</owl:versionInfo>
     </owl:Ontology>
     
 
@@ -59,24 +59,6 @@
     
 
 
-    <!-- http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl -->
-
-    <owl:AnnotationProperty rdf:about="http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl"/>
-    
-
-
-    <!-- http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg -->
-
-    <owl:AnnotationProperty rdf:about="http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg"/>
-    
-
-
-    <!-- http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg -->
-
-    <owl:AnnotationProperty rdf:about="http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg"/>
-    
-
-
     <!-- http://protege.stanford.edu/plugins/owl/protege#defaultLanguage -->
 
     <owl:AnnotationProperty rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
@@ -86,8 +68,7 @@
     <!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000319 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000319">
-        <obo:IAO_0000118 xml:lang="en">National Library of Medicine Identifier
-</obo:IAO_0000118>
+        <obo:IAO_0000118 xml:lang="en">National Library of Medicine Identifier</obo:IAO_0000118>
         <rdfs:comment xml:lang="en">This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed.</rdfs:comment>
         <rdfs:label xml:lang="en">NLM ID</rdfs:label>
     </owl:AnnotationProperty>
@@ -481,7 +462,6 @@ We also have the outstanding issue of how to aim different definitions to differ
         <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
         <rdfs:comment>Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).</rdfs:comment>
-        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
         <rdfs:label xml:lang="en">alternative label</rdfs:label>
         <rdfs:label xml:lang="en">alternative term</rdfs:label>
     </owl:AnnotationProperty>
@@ -913,24 +893,25 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
+    <!-- http://purl.obolibrary.org/obo/OMO_0003004 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0003004">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/RO_0001900 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001900">
         <obo:IAO_0000115>An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.</obo:IAO_0000115>
         <rdfs:label>temporal interpretation</rdfs:label>
         <rdfs:label xml:lang="en">temporal interpretation</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"/>
         <foaf:page rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/oborel/obo-relations/wiki/ROAndTime</foaf:page>
     </owl:AnnotationProperty>
     
 
 
-    <!-- http://purl.obolibrary.org/obo/RO_0002175 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002175"/>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/RO_0002259 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002259">
@@ -939,54 +920,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://purl.obolibrary.org/obo/RO_0002575 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002575"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0002579 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002579"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0002581 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002581">
-        <obo:IAO_0000115>If R &lt;- P o Q is a defining property chain axiom, then it also holds that R -&gt; P o Q. Note that this cannot be expressed directly in OWL</obo:IAO_0000115>
-        <rdfs:label>is a defining property chain axiom</rdfs:label>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0002582 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002582">
-        <obo:IAO_0000115>If R &lt;- P o Q is a defining property chain axiom, then (1) R -&gt; P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.</obo:IAO_0000115>
-        <rdfs:label>is a defining property chain axiom where second argument is reflexive</rdfs:label>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0004049 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0004049"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0004050 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0004050"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0040042 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0040042"/>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/STATO_0000032 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000032">
@@ -1245,7 +1178,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/ro/subsets#ro-eco">
         <rdfs:label>eco subset</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/subsets/"/>
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
     </owl:AnnotationProperty>
     
@@ -1259,9 +1191,51 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
+    <!-- http://purl.obolibrary.org/obo/uberon/core#efo_slim -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#efo_slim">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/uberon/core#human_subset -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#human_subset">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/uberon/core#mouse_subset -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#mouse_subset">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/uberon/core#pheno_slim -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#pheno_slim">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/uberon/core#uberon_slim -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#uberon_slim"/>
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#uberon_slim">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
     
 
 
@@ -1275,7 +1249,9 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
     <!-- http://purl.obolibrary.org/obo/uberon/core#vertebrate_core -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#vertebrate_core"/>
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#vertebrate_core">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
     
 
 
@@ -1405,12 +1381,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://purl.org/dc/terms/creator -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/creator"/>
-    
-
-
     <!-- http://purl.org/dc/terms/description -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description"/>
@@ -1435,12 +1405,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled -->
-
-    <owl:AnnotationProperty rdf:about="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled"/>
-    
-
-
     <!-- http://usefulinc.com/ns/doap#bug-database -->
 
     <owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#bug-database"/>
@@ -1453,21 +1417,25 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
+    <!-- http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by"/>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#creation_date -->
+    <!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#creation_date"/>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by">
+        <rdfs:label>created by</rdfs:label>
+    </owl:AnnotationProperty>
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#default-namespace -->
+    <!-- http://www.geneontology.org/formats/oboInOwl#creation_date -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#default-namespace"/>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#creation_date">
+        <rdfs:label>creation date</rdfs:label>
+    </owl:AnnotationProperty>
     
 
 
@@ -1496,7 +1464,11 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
+        <obo:IAO_0000112>disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) &quot;NCIT:C41009&quot;^^xsd:string</obo:IAO_0000112>
+        <obo:IAO_0000115>An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.</obo:IAO_0000115>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label>database_cross_reference</rdfs:label>
+        <rdfs:label>has cross-reference</rdfs:label>
     </owl:AnnotationProperty>
     
 
@@ -1537,12 +1509,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion -->
-
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion"/>
-    
-
-
     <!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace">
@@ -1597,12 +1563,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#source -->
-
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#source"/>
-    
-
-
     <!-- http://www.referent-tracking.com/RTS_00000001 -->
 
     <owl:AnnotationProperty rdf:about="http://www.referent-tracking.com/RTS_00000001">
@@ -1648,12 +1608,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://www.w3.org/2004/02/skos/core#closeMatch -->
-
-    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#closeMatch"/>
-    
-
-
     <!-- http://xmlns.com/foaf/0.1/homepage -->
 
     <owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
@@ -1687,7 +1641,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000004">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
-        <rdfs:label xml:lang="en">basis of</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete basis of</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
@@ -1697,7 +1651,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000028">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
-        <rdfs:comment xml:lang="en">p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. </rdfs:comment>
+        <rdfs:comment xml:lang="en">p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption.</rdfs:comment>
         <rdfs:label xml:lang="en">obsolete is based on</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
@@ -1740,7 +1694,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AsymmetricProperty"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#IrreflexiveProperty"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
-        <obo:IAO_0000115 xml:lang="en">A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times.</obo:IAO_0000115>
         <rdfs:comment>Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.</rdfs:comment>
         <rdfs:label xml:lang="en">instantiates</rdfs:label>
     </owl:ObjectProperty>
@@ -1765,7 +1719,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000116">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
-        <rdfs:label xml:lang="en">causally_precedes</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete causally_precedes</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
@@ -1820,13 +1774,6 @@ For example, the disposition of a piece of glass to bend light and the lattice s
 A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An occurrent cannot be part of a continuant: use &apos;has participant&apos;. A material entity cannot be part of an immaterial entity: use &apos;has location&apos;. A specifically dependent continuant cannot be part of an independent continuant: use &apos;inheres in&apos;. An independent continuant cannot be part of a specifically dependent continuant: use &apos;bearer of&apos;.</obo:IAO_0000116>
         <obo:IAO_0000118 xml:lang="en">part_of</obo:IAO_0000118>
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
         <oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>external</oboInOwl:hasOBONamespace>
         <oboInOwl:id>part_of</oboInOwl:id>
@@ -1838,10 +1785,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <rdfs:label>part of</rdfs:label>
         <rdfs:label xml:lang="en">part of</rdfs:label>
         <rdfs:label xml:lang="en">part_of</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections"/>
-        <rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:PartOf"/>
         <rdfs:seeAlso>http://www.obofoundry.org/ro/#OBO_REL:part_of</rdfs:seeAlso>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Part_of</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -1886,9 +1830,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <ace_lexicon:TV_pl>BFO_0000054</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000054s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000054ed</ace_lexicon:TV_vbg>
         <obo:IAO_0000111 xml:lang="en">obsolete_is_realized_by</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">realized in</obo:IAO_0000111>
         <obo:IAO_0000112 xml:lang="en">this disease is realized in this disease course</obo:IAO_0000112>
@@ -1922,13 +1863,11 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000055">
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
-        <ace_lexicon:TV_pl>BFO_0000055</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000055s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000055ed</ace_lexicon:TV_vbg>
         <obo:IAO_0000111 xml:lang="en">realizes</obo:IAO_0000111>
         <obo:IAO_0000112 xml:lang="en">this disease course realizes this disease</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">this investigation realizes this investigator role</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">this shattering realizes this fragility</obo:IAO_0000112>
+        <obo:IAO_0000115 xml:lang="en">Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">to say that b realizes c at t is to assert that there is some material entity d &amp; b is a process which has participant d at t &amp; c is a disposition or role of which d is bearer_of at t&amp; the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])</obo:IAO_0000600>
         <rdfs:comment>Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</rdfs:comment>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
@@ -1957,7 +1896,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
         <obo:IAO_0000118 xml:lang="en">preceded_by</obo:IAO_0000118>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/ro.owl</obo:IAO_0000412>
         <dc:source>http://www.obofoundry.org/ro/#OBO_REL:preceded_by</dc:source>
-        <terms:source>http://www.obofoundry.org/ro/#OBO_REL:preceded_by</terms:source>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">preceded by</rdfs:label>
     </owl:ObjectProperty>
@@ -2020,7 +1958,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
         <rdfs:label>occurs in</rdfs:label>
         <rdfs:label xml:lang="en">occurs in</rdfs:label>
         <rdfs:label xml:lang="en">unfolds_in</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Occurs_in</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -2093,9 +2030,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000110">
         <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000110</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000110s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000110ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>c-has-part_at</obo:BFO_0000179>
         <obo:BFO_0000180>hasContinuantPartAt</obo:BFO_0000180>
         <obo:IAO_0000115>[copied from inverse property &apos;part of continuant at all times that whole exists&apos;] forall(t) exists_at(y,t) -&gt; exists_at(x,t) and &apos;part of continuant&apos;(x,y,t)</obo:IAO_0000115>
@@ -2115,9 +2049,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000111">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000110"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000111</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000111s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000111ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>c-has-ppart_at</obo:BFO_0000179>
         <obo:BFO_0000180>hasProperContinuantPartAt</obo:BFO_0000180>
         <obo:IAO_0000115 xml:lang="en">b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001</obo:IAO_0000115>
@@ -2153,9 +2084,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
         <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000132"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000117</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000117s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000117ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>o-has-part</obo:BFO_0000179>
         <obo:BFO_0000180>hasOccurrentPart</obo:BFO_0000180>
         <obo:IAO_0000112>[copied from inverse property &apos;part of occurrent&apos;] Mary’s 5th birthday occurrent_part_of Mary’s life</obo:IAO_0000112>
@@ -2178,9 +2106,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000118">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000117"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000118</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000118s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000118ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>o-has-ppart</obo:BFO_0000179>
         <obo:BFO_0000180>hasProperOccurrentPart</obo:BFO_0000180>
         <obo:IAO_0000115>[copied from inverse property &apos;proper part of occurrent&apos;] b proper_occurrent_part_of c =Def. b occurrent_part_of c &amp; b and c are not identical. (axiom label in BFO2 Reference: [005-001])</obo:IAO_0000115>
@@ -2230,9 +2155,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000132">
         <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000132</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000132s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000132ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>o-part-of</obo:BFO_0000179>
         <obo:BFO_0000180>occurrentPartOf</obo:BFO_0000180>
         <obo:IAO_0000112 xml:lang="en">Mary’s 5th birthday occurrent_part_of Mary’s life</obo:IAO_0000112>
@@ -2373,9 +2295,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <!-- http://purl.obolibrary.org/obo/BFO_0000167 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000167">
-        <ace_lexicon:TV_pl>BFO_0000167</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000167s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000167ed</ace_lexicon:TV_vbg>
         <rdfs:label xml:lang="en">has participant at all times</rdfs:label>
     </owl:ObjectProperty>
     
@@ -2934,6 +2853,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AsymmetricProperty"/>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.</obo:IAO_0000600>
+        <dc:source>Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.</dc:source>
         <rdfs:label xml:lang="en">owns</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3001,12 +2921,14 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             </rdf:Description>
         </owl:equivalentProperty>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
-        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <obo:IAO_0000111>has specified output</obo:IAO_0000111>
         <obo:IAO_0000111>has_specified_output</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">has_specified_output</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115>The inverse property of is specified output of</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">The inverse property of is_specified_output_of</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000117>PERSON: Bjoern Peters</obo:IAO_0000117>
@@ -3014,6 +2936,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000117>PERSON: Melanie Courtot</obo:IAO_0000117>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
+        <rdfs:label xml:lang="en">has specified output</rdfs:label>
         <rdfs:label xml:lang="en">has_specified_output</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3032,16 +2955,19 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <obo:IAO_0000111>is specified output of</obo:IAO_0000111>
         <obo:IAO_0000111>is_specified_output_of</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">is_specified_output_of</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115 xml:lang="en">A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
-        <rdfs:label>is_specified_output_of</rdfs:label>
+        <rdfs:label xml:lang="en">is specified output of</rdfs:label>
         <rdfs:label xml:lang="en">is_specified_output_of</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3090,7 +3016,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/OBIB_0000732"/>
         <rdfs:label>obsolete owns</rdfs:label>
         <rdfs:label xml:lang="en">owns</rdfs:label>
-        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
 
@@ -3192,7 +3117,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/omrse.owl</obo:IAO_0000412>
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
         <rdfs:label xml:lang="en">bearer of</rdfs:label>
-        <rdfs:label xml:lang="en">bearer_of</rdfs:label>
         <rdfs:label xml:lang="en">has characteristic</rdfs:label>
         <rdfs:label xml:lang="en">is bearer of</rdfs:label>
     </owl:ObjectProperty>
@@ -3245,7 +3169,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <dc:source>http://www.obofoundry.org/ro/#OBO_REL:has_participant</dc:source>
         <terms:source>http://www.obofoundry.org/ro/#OBO_REL:has_participant</terms:source>
         <rdfs:label xml:lang="en">has participant</rdfs:label>
-        <rdfs:label>has_participant</rdfs:label>
         <rdfs:label xml:lang="en">has_participant</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3254,15 +3177,21 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
     <!-- http://purl.obolibrary.org/obo/RO_0000058 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
-        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <obo:IAO_0000111 xml:lang="en">is concretized as</obo:IAO_0000111>
+        <rdfs:range>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000020"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:range>
         <obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
+        <obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
         <rdfs:label xml:lang="en">is concretized as</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3271,15 +3200,21 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
     <!-- http://purl.obolibrary.org/obo/RO_0000059 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
-        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+        <rdfs:domain>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000020"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:domain>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
-        <obo:IAO_0000111 xml:lang="en">concretizes</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">is_concretization_of</obo:IAO_0000111>
         <obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
+        <obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.</obo:IAO_0000115>
         <rdfs:label xml:lang="en">concretizes</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3493,7 +3428,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <terms:source>http://www.obofoundry.org/ro/#OBO_REL:located_in</terms:source>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label xml:lang="en">located in</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Located_in</rdfs:seeAlso>
     </owl:ObjectProperty>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
@@ -3694,7 +3628,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002084">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002093"/>
-        <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:comment>Previously had ID  http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point.  No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line.  Official ID now chosen from DOS ID range.</rdfs:comment>
         <rdfs:label xml:lang="en">during which ends</rdfs:label>
@@ -3711,7 +3645,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002093"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000062"/>
         </owl:propertyChainAxiom>
-        <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:comment xml:lang="en">X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)</rdfs:comment>
         <rdfs:label xml:lang="en">ends after</rdfs:label>
@@ -3729,7 +3663,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002230"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)</obo:IAO_0000115>
-        <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
         <obo:IAO_0000118>starts_at_end_of</obo:IAO_0000118>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
         <obo:UBPROP_0000001>A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].</obo:UBPROP_0000001>
@@ -3758,10 +3692,8 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002224"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
-        <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
         <obo:IAO_0000118>ends_at_start_of</obo:IAO_0000118>
         <obo:IAO_0000118>meets</obo:IAO_0000118>
-        <obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:comment xml:lang="en">X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)</rdfs:comment>
         <rdfs:label xml:lang="en">immediately precedes</rdfs:label>
@@ -3774,6 +3706,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002093">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
         <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
         <obo:IAO_0000118>o</obo:IAO_0000118>
         <obo:IAO_0000118>overlaps</obo:IAO_0000118>
@@ -3798,10 +3731,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
         </owl:propertyChainAxiom>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:propertyChainAxiom>
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002131"/>
@@ -3819,15 +3748,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">overlaps</rdfs:label>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002582 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002582>
-    </owl:Axiom>
     
 
 
@@ -3848,7 +3768,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label>spatially disjoint from</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern</rdfs:seeAlso>
         <foaf:page rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern</foaf:page>
     </owl:ObjectProperty>
     
@@ -3865,7 +3784,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">has component</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:Componency"/>
     </owl:ObjectProperty>
     
 
@@ -3937,7 +3855,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/ro.owl</obo:IAO_0000412>
         <obo:IAO_0000589>negatively regulates (process to process)</obo:IAO_0000589>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
         <oboInOwl:hasDbXref>RO:0002212</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>external</oboInOwl:hasOBONamespace>
         <oboInOwl:id>negatively_regulates</oboInOwl:id>
@@ -3970,7 +3887,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000589>positively regulates (process to process)</obo:IAO_0000589>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
         <oboInOwl:hasDbXref>RO:0002213</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>external</oboInOwl:hasOBONamespace>
         <oboInOwl:id>positively_regulates</oboInOwl:id>
@@ -4009,25 +3925,11 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002216">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002500"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:propertyChainAxiom>
         <obo:IAO_0000115>c stands in this relationship to p if and only if there exists some p&apos; such that c is capable_of p&apos;, and p&apos; is part_of p.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118>has function in</obo:IAO_0000118>
         <rdfs:label xml:lang="en">capable of part of</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/reflexivity/"/>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002216"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002582 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002582>
-    </owl:Axiom>
     
 
 
@@ -4048,7 +3950,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">has active participant</rdfs:label>
         <rdfs:label>obsolete has active participant</rdfs:label>
-        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
 
@@ -4076,12 +3977,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdfs:label xml:lang="en">adjacent to</rdfs:label>
         <rdfs:seeAlso rdf:resource="https://github.com/jhpoelen/eol-globi-data/issues/225#issuecomment-218584934"/>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002220"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000112"/>
-        <owl:annotatedTarget>A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.</owl:annotatedTarget>
-        <rdfs:seeAlso rdf:resource="https://github.com/jhpoelen/eol-globi-data/issues/225#issuecomment-218584934"/>
-    </owl:Axiom>
     
 
 
@@ -4098,7 +3993,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000119>Allen</obo:IAO_0000119>
         <obo:IAO_0000232>Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.</obo:IAO_0000232>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
-        <terms:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1</terms:source>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:comment>A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.</rdfs:comment>
         <rdfs:label xml:lang="en">temporal relation</rdfs:label>
@@ -4116,7 +4010,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>inverse of starts with</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000119>Allen</obo:IAO_0000119>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">starts</rdfs:label>
@@ -4134,7 +4027,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) &lt; ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>started by</obo:IAO_0000118>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
@@ -4153,7 +4045,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>inverse of ends with</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">inverse of ends with</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <dc:source>http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl</dc:source>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">ends</rdfs:label>
@@ -4171,7 +4062,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) &gt; α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) &gt; α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>finished by</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">finished with</obo:IAO_0000118>
         <dc:source xml:lang="en">http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl</dc:source>
@@ -4240,7 +4130,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">has input</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Has_input</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4265,7 +4154,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">has output</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Has_output</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4282,7 +4170,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>c acts upstream of p if and only if c enables some f that is involved in p&apos; and p&apos; occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p&apos; are processes.</obo:IAO_0000115>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://wiki.geneontology.org/index.php/Acts_upstream_of"/>
     </owl:ObjectProperty>
     
 
@@ -4300,7 +4187,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:hasRelatedSynonym>affects</oboInOwl:hasRelatedSynonym>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of or within</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of_or_within</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4326,13 +4212,10 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0004047"/>
         <obo:IAO_0000115>p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.</obo:IAO_0000115>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
-        <terms:creator rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:comment>holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y</rdfs:comment>
         <rdfs:label>causally upstream of, positive effect</rdfs:label>
-        <rdfs:seeAlso rdf:resource="https://wiki.geneontology.org/Causally_upstream_of,_positive_effect"/>
     </owl:ObjectProperty>
     
 
@@ -4343,12 +4226,9 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0004046"/>
         <obo:IAO_0000115>p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.</obo:IAO_0000115>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
-        <terms:creator rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:label>causally upstream of, negative effect</rdfs:label>
-        <rdfs:seeAlso rdf:resource="https://wiki.geneontology.org/Causally_upstream_of,_negative_effect"/>
     </owl:ObjectProperty>
     
 
@@ -4357,10 +4237,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002314">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002502"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000052"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:propertyChainAxiom>
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002314"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
@@ -4372,17 +4248,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/20064205"/>
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
         <rdfs:label xml:lang="en">characteristic of part of</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/reflexivity/"/>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002314"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000052"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002582 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002582>
-    </owl:Axiom>
     
 
 
@@ -4443,7 +4309,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000232>This relation differs from the parent relation &apos;capable of&apos; in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.</obo:IAO_0000232>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label xml:lang="en">enables</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Enables</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4463,24 +4328,11 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002329">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
-        </owl:propertyChainAxiom>
         <obo:IAO_0000115>this relation holds between c and p when c is part of some c&apos;, and c&apos; is capable of p.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</obo:IAO_0000118>
         <rdfs:label xml:lang="en">part of structure that is capable of</rdfs:label>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002329"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002581 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002581>
-    </owl:Axiom>
     
 
 
@@ -4502,7 +4354,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000118>actively involved in</obo:IAO_0000118>
         <obo:IAO_0000118>enables part of</obo:IAO_0000118>
         <rdfs:label xml:lang="en">involved in</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Involved_in</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4516,7 +4367,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:label xml:lang="en">enabled by</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Enabled_by</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4692,9 +4542,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118>indirectly activates</obo:IAO_0000118>
-        <obo:RO_0002579 rdf:resource="http://purl.obolibrary.org/obo/RO_0002213"/>
         <rdfs:label xml:lang="en">indirectly positively regulates</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Indirectly_positively_regulates</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4720,9 +4568,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118>indirectly inhibits</obo:IAO_0000118>
-        <obo:RO_0002579 rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
         <rdfs:label xml:lang="en">indirectly negatively regulates</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Indirectly_negatively_regulates</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4786,18 +4632,57 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
         <obo:IAO_0000115>p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
         <rdfs:label xml:lang="en">immediately causally upstream of</rdfs:label>
     </owl:ObjectProperty>
     
 
 
+    <!-- http://purl.obolibrary.org/obo/RO_0002413 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002413">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002412"/>
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002414"/>
+        <owl:propertyChainAxiom rdf:parseType="Collection">
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002234"/>
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002233"/>
+        </owl:propertyChainAxiom>
+        <obo:IAO_0000115>p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
+        <obo:IAO_0000118>directly provides input for</obo:IAO_0000118>
+        <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
+        <obo:IAO_0000589>directly provides input for (process to process)</obo:IAO_0000589>
+        <rdfs:label xml:lang="en">provides input for</rdfs:label>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/RO_0002414 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002414">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0004047"/>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
+        <obo:IAO_0000115>transitive form of directly_provides_input_for</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
+        <obo:IAO_0000232>This is a grouping relation that should probably not be used in annotation. Consider instead the child relation &apos;provides input for&apos;.</obo:IAO_0000232>
+        <obo:IAO_0000589>transitively provides input for (process to process)</obo:IAO_0000589>
+        <rdfs:label xml:lang="en">transitively provides input for</rdfs:label>
+    </owl:ObjectProperty>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/RO_0002418 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002418">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002501"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002427"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+        <owl:propertyChainAxiom rdf:parseType="Collection">
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002418"/>
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
+        </owl:propertyChainAxiom>
         <obo:IAO_0000115>p is &apos;causally upstream or within&apos; q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.</obo:IAO_0000115>
         <obo:IAO_0000116>We would like to make this disjoint with &apos;preceded by&apos;, but this is prohibited in OWL2</obo:IAO_0000116>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
@@ -4856,7 +4741,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; positively regulates some p</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
         <rdfs:label>involved in positive regulation of</rdfs:label>
     </owl:ObjectProperty>
     
@@ -4876,7 +4760,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; negatively regulates some p</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
         <rdfs:label>involved in negative regulation of</rdfs:label>
     </owl:ObjectProperty>
     
@@ -4902,28 +4785,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002432">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
-        </owl:propertyChainAxiom>
         <obo:IAO_0000112>A protein that enables activity in a cytosol.</obo:IAO_0000112>
         <obo:IAO_0000115>c executes activity in d if and only if c enables p and p occurs_in d.  Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118>executes activity in</obo:IAO_0000118>
         <oboInOwl:hasExactSynonym>enables activity in</oboInOwl:hasExactSynonym>
-        <rdfs:comment></rdfs:comment>
         <rdfs:label>is active in</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Is_active_in</rdfs:seeAlso>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002432"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002581 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002581>
-    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002432"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
@@ -4948,8 +4816,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         <oboInOwl:hasExactSynonym>in pairwise interaction with</oboInOwl:hasExactSynonym>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label>interacts with</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/ro/docs/interaction-relations/</rdfs:seeAlso>
-        <skos:closeMatch rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/MI_0914</skos:closeMatch>
     </owl:ObjectProperty>
     
 
@@ -4964,8 +4830,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         <obo:IAO_0000118>binds</obo:IAO_0000118>
         <obo:IAO_0000118>molecularly binds with</obo:IAO_0000118>
         <rdfs:label>molecularly interacts with</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ECO_0000353"/>
-        <skos:closeMatch rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/MI_0915</skos:closeMatch>
     </owl:ObjectProperty>
     
 
@@ -5064,24 +4928,11 @@ For example, A and B may be gene products and binding of B by A positively regul
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002479">
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
-        </owl:propertyChainAxiom>
         <obo:IAO_0000115>p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label>has part that occurs in</rdfs:label>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002479"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002581 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002581>
-    </owl:Axiom>
     
 
 
@@ -5131,7 +4982,6 @@ For example, A and B may be gene products and binding of B by A positively regul
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002502">
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <rdfs:label>depends on</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/BFO_0000169"/>
     </owl:ObjectProperty>
     
 
@@ -5170,8 +5020,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002464"/>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <rdfs:label>interaction relation helper property</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29"/>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/ro/docs/interaction-relations/</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5221,7 +5069,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000589>directly regulates (processual)</obo:IAO_0000589>
-        <obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
@@ -5328,12 +5175,10 @@ For example, A and B may be gene products and binding of B by A positively regul
         <obo:IAO_0000115>p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.</obo:IAO_0000115>
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000589>directly positively regulates (process to process)</obo:IAO_0000589>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:label>directly positively regulates</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Directly_positively_regulates</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5346,12 +5191,10 @@ For example, A and B may be gene products and binding of B by A positively regul
         <obo:IAO_0000115>p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.</obo:IAO_0000115>
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000589>directly negatively regulates (process to process)</obo:IAO_0000589>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:label>directly negatively regulates</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Directly_negatively_regulates</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5434,12 +5277,10 @@ For example, A and B may be gene products and binding of B by A positively regul
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0004047"/>
         </owl:propertyChainAxiom>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002264"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-01-26T23:49:30Z</oboInOwl:creation_date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of or within, positive effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5452,12 +5293,10 @@ For example, A and B may be gene products and binding of B by A positively regul
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0004046"/>
         </owl:propertyChainAxiom>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002264"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-01-26T23:49:51Z</oboInOwl:creation_date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of or within, negative effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5472,12 +5311,10 @@ For example, A and B may be gene products and binding of B by A positively regul
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002304"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>c &apos;acts upstream of, positive effect&apos; p if c is enables f, and f is causally upstream of p, and the direction of f is positive</obo:IAO_0000115>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002263"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-01-26T23:53:14Z</oboInOwl:creation_date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of, positive effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of,_positive_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5492,12 +5329,10 @@ For example, A and B may be gene products and binding of B by A positively regul
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002305"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>c &apos;acts upstream of, negative effect&apos; p if c is enables f, and f is causally upstream of p, and the direction of f is negative</obo:IAO_0000115>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002263"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-01-26T23:53:22Z</oboInOwl:creation_date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of, negative effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of,_negative_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5506,11 +5341,9 @@ For example, A and B may be gene products and binding of B by A positively regul
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0004046">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-03-13T23:55:05Z</oboInOwl:creation_date>
         <rdfs:label>causally upstream of or within, negative effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5519,11 +5352,9 @@ For example, A and B may be gene products and binding of B by A positively regul
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0004047">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-03-13T23:55:19Z</oboInOwl:creation_date>
         <rdfs:label>causally upstream of or within, positive effect</rdfs:label>
-        <rdfs:seeAlso rdf:resource="https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect"/>
     </owl:ObjectProperty>
     
 
@@ -5567,7 +5398,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <terms:contributor rdf:resource="https://orcid.org/0000-0002-8461-9745"/>
         <oboInOwl:hasExactSynonym>triggered by process</oboInOwl:hasExactSynonym>
         <rdfs:label xml:lang="en">realized in response to</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit</rdfs:seeAlso>
     </owl:ObjectProperty>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0009501"/>
@@ -5729,6 +5559,17 @@ For example, A and B may be gene products and binding of B by A positively regul
     
 
 
+    <!-- http://purl.obolibrary.org/obo/RO_0020105 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0020105">
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001062"/>
+        <obo:IAO_0000115>This property only applies to anatomical entities.</obo:IAO_0000115>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0001-6677-8489"/>
+        <rdfs:label>is anatomical entity</rdfs:label>
+    </owl:ObjectProperty>
+    
+
+
     <!-- http://purl.org/obo/owl/OBO_REL#has_disposition -->
 
     <owl:ObjectProperty rdf:about="http://purl.org/obo/owl/OBO_REL#has_disposition">
@@ -6127,6 +5968,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -6269,7 +6111,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
         <obo:IAO_0000115 xml:lang="en">A control strategy start time information item that is based on a condition that triggers the control strategy.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A control strategy start time information item that is based on a condition that triggers the control strategy.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">control strategy reactive start time information</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete control strategy reactive start time information</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -6280,10 +6122,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000012">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000029"/>
         <obo:IAO_0000115 xml:lang="en">A numeral that is part of a simulation time step action specification.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A number of time step units in a time step of a simulation.  
-
-For example, if the time step is 6 hours, then this value is 6.
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>numberOfUnitsOfTimeInOneSimulatorStep</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation time step value</rdfs:label>
     </owl:Class>
@@ -6330,10 +6169,7 @@ For example, if the time step is 6 hours, then this value is 6.
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">The action specification that specifies the number of time steps a simulation is going to run.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The number of time steps in a simulator run.
-
-For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>runLength</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation run length</rdfs:label>
     </owl:Class>
@@ -6394,11 +6230,7 @@ Note that the susceptible and infectious organisms can be of different species.<
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
-        <obo:IAO_0000600 xml:lang="en">A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  
-
-Note that the susceptible and infected organisms can be of different species.
-
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>latentPeriodDuration</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs</rdfs:comment>
         <rdfs:comment xml:lang="en">The duration of the period between when an organism becomes infected and when it becomes infectious.</rdfs:comment>
@@ -6463,11 +6295,10 @@ Note that the susceptible and infected organisms can be of different species.
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">The count of (simulated organisms) in a simulated population.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
-        <obo:IAO_0000600 xml:lang="en">The number of simulated organisms in a simulated population.  The number does not have to be an integer.  </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of simulated organisms in a simulated population.  The number does not have to be an integer.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  
 
-Any ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’
-</rdfs:comment>
+Any ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’</rdfs:comment>
         <rdfs:label xml:lang="en">count of simulated population</rdfs:label>
     </owl:Class>
     
@@ -6478,7 +6309,7 @@ Any ideas?  I’ve considered and rejected allowing individual organisms to be f
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000023">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000084"/>
         <obo:IAO_0000115 xml:lang="en">An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">vaccination dose schedule</rdfs:label>
     </owl:Class>
     
@@ -6493,8 +6324,7 @@ Any ideas?  I’ve considered and rejected allowing individual organisms to be f
         <rdfs:comment xml:lang="en">MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class &quot;eligibility rule&quot; in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.</rdfs:comment>
         <rdfs:comment xml:lang="en">MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.
 
-It is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.
-</rdfs:comment>
+It is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.</rdfs:comment>
         <rdfs:label xml:lang="en">vaccination compliance</rdfs:label>
     </owl:Class>
     
@@ -6626,8 +6456,8 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:someValuesFrom>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">infectious disease control strategy execution</rdfs:label>
     </owl:Class>
     
@@ -6753,6 +6583,7 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -6908,10 +6739,9 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:someValuesFrom>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A simulated organism in a simulated population that is not susceptible. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A simulated organism in a simulated population that is not susceptible.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. 
-Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.
-</obo:IAO_0000600>
+Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">simulation of recovered organism</rdfs:label>
     </owl:Class>
     
@@ -6980,7 +6810,7 @@ Note that the name for this concept, were it to be named based on its intent, wo
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">The number of susceptible organisms that each infected organism infects.  ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ReproductionNumber</apollo_sv:APOLLO_SV_0000040>
@@ -7090,8 +6920,8 @@ Preventable outcomes include but are not limited to infection, infectiousness, s
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000049">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000243"/>
-        <obo:IAO_0000115 xml:lang="en">The value of the time interval between an organism&apos;s taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">The value of the time interval between an organism&apos;s taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">antiviral efficacy delay</rdfs:label>
     </owl:Class>
     
@@ -7102,7 +6932,7 @@ Preventable outcomes include but are not limited to infection, infectiousness, s
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000050">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0302867"/>
         <obo:IAO_0000115 xml:lang="en">The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The fraction of individuals in a simulated population that will accept antiviral treatment if offered. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The fraction of individuals in a simulated population that will accept antiviral treatment if offered.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>antiviral cm compliance</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class &quot;eligibility rule&quot; in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.</rdfs:comment>
         <rdfs:comment xml:lang="en">MW: Since the estimates that modelers use are from real populations, I have two questions:
@@ -7119,7 +6949,7 @@ MB: This issue will need to be taken care of in the axiomatization of simulated
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000051">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000795"/>
-        <obo:IAO_0000115 xml:lang="en">An action specification giving the number of doses of an antiviral to be made available during a specific time interval. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">An action specification giving the number of doses of an antiviral to be made available during a specific time interval.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">Counts of antiviral doses that become available in a specific location per time step unit.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">antiviral supply schedule</rdfs:label>
     </owl:Class>
@@ -7274,13 +7104,12 @@ MB: This issue will need to be taken care of in the axiomatization of simulated
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000060">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000070"/>
-        <obo:IAO_0000115>The simulation of an antiviral control measure. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The simulation of an antiviral control measure.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>antiviral control measure</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn&apos;t able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).
 AND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.
-Maybe we need to discuss this.
-</rdfs:comment>
+Maybe we need to discuss this.</rdfs:comment>
         <rdfs:label xml:lang="en">simulation of antiviral control measure</rdfs:label>
     </owl:Class>
     
@@ -7405,8 +7234,7 @@ Maybe we need to discuss this.
 
 One property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.
 
-While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.
-</rdfs:comment>
+While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.</rdfs:comment>
         <rdfs:label xml:lang="en">simulation time series</rdfs:label>
     </owl:Class>
     
@@ -7468,6 +7296,12 @@ While in many pieces of fiction the order in which the purely intentional entiti
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000067"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000038"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates a temporal interval of pre-specified length.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates a temporal interval of pre-specified length.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>simulation time step</apollo_sv:APOLLO_SV_0000040>
@@ -7565,12 +7399,8 @@ The time step value and unit are specified using a scalar value specification.</
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates an entity and its properties.
-
-</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates an entity and its properties.
-
-</obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates an entity and its properties.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates an entity and its properties.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>simulation</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation</rdfs:label>
     </owl:Class>
@@ -7701,7 +7531,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">the mean or expectation of a distribution</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>μ</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">μ</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete μ</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -7713,7 +7543,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">standard deviation</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>sigma</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">σ</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete σ</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -7735,7 +7565,7 @@ The time step value and unit are specified using a scalar value specification.</
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000079">
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated log normal distribution</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete log normal distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -7796,7 +7626,7 @@ The time step value and unit are specified using a scalar value specification.</
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">control strategy dose schedule</rdfs:label>
     </owl:Class>
     
@@ -7838,6 +7668,33 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                                <owl:someValuesFrom>
+                                    <owl:Class>
+                                        <owl:intersectionOf rdf:parseType="Collection">
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000038"/>
+                                            <owl:Restriction>
+                                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000156"/>
+                                                <owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
+                                                <owl:onClass rdf:resource="http://purl.obolibrary.org/obo/BFO_0000182"/>
+                                            </owl:Restriction>
+                                        </owl:intersectionOf>
+                                    </owl:Class>
+                                </owl:someValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000111 xml:lang="en">age structure data set</obo:IAO_0000111>
         <obo:IAO_0000115>A data set consisting of measurements of age organized in age brackets.</obo:IAO_0000115>
         <obo:IAO_0000600>A data set consisting of measurements of age organized in age brackets.</obo:IAO_0000600>
@@ -7937,13 +7794,44 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000025"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/PCO_0000000"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
+                                <owl:allValuesFrom>
+                                    <owl:Class>
+                                        <owl:intersectionOf rdf:parseType="Collection">
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
+                                            <owl:Restriction>
+                                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000142"/>
+                                            </owl:Restriction>
+                                        </owl:intersectionOf>
+                                    </owl:Class>
+                                </owl:allValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A vaccination efficacy that results from a vaccination efficacy study.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>VaccinationEfficacyMeasured</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’
 
-2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.
-</rdfs:comment>
+2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.</rdfs:comment>
         <rdfs:label xml:lang="en">measured vaccination efficacy</rdfs:label>
     </owl:Class>
     
@@ -7967,6 +7855,7 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000471"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -8041,6 +7930,12 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PCO_0000001"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">Two or more distinct populations that are part of the same biotic ecosystem.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">Two or more distinct populations that are part of the same biotic ecosystem.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>community</apollo_sv:APOLLO_SV_0000040>
@@ -8056,7 +7951,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">a probability distribution over a discrete random variable</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>discrete probability distribution</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label>deprecated discrete probability distribution</rdfs:label>
+        <rdfs:label>obsolete discrete probability distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -8076,8 +7971,8 @@ The time step value and unit are specified using a scalar value specification.</
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000097">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <obo:IAO_0000115 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region. </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region. </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>Ecosystem</apollo_sv:APOLLO_SV_0000040>
         <dc:creator xml:lang="en">William R. Hogan</dc:creator>
         <rdfs:label xml:lang="en">ecosystem</rdfs:label>
@@ -8537,19 +8432,16 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000114"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  
 
-Note that the susceptible and infectious organisms can be of different species.
-
-</obo:IAO_0000600>
+Note that the susceptible and infectious organisms can be of different species.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>InfectionAcquisition</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.
 The likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   
-An infection is acquired from an infectious organism or a contaminated thing. 
-</rdfs:comment>
-        <rdfs:comment xml:lang="en">Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing</rdfs:comment>
+An infection is acquired from an infectious organism or a contaminated thing.</rdfs:comment>
+        <rdfs:comment xml:lang="en">Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing.</rdfs:comment>
         <rdfs:label xml:lang="en">infection acquisition</rdfs:label>
     </owl:Class>
     
@@ -8720,7 +8612,7 @@ An infection is acquired from an infectious organism or a contaminated thing.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000125">
         <obo:IAO_0000600 xml:lang="en">The time steps that a school will be in session.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">school calendar</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete school calendar</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -8790,8 +8682,7 @@ An infection is acquired from an infectious organism or a contaminated thing.
         <obo:IAO_0000115 xml:lang="en">A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.
 
-The event could be infection acquisition, vaccination, antiviral treatment, etc.
-</obo:IAO_0000600>
+The event could be infection acquisition, vaccination, antiviral treatment, etc.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>reactiveControlMeasureThreshold</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">reactive control strategy threshold</rdfs:label>
     </owl:Class>
@@ -8896,7 +8787,7 @@ For example, once a vaccination control strategy starts, individual vaccinations
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000137">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000032"/>
-        <obo:IAO_0000600 xml:lang="en">the number of distinct antigenic strains in a vaccine product </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of distinct antigenic strains in a vaccine product.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>valence</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">vaccine valence</rdfs:label>
     </owl:Class>
@@ -9149,7 +9040,7 @@ For example, once a vaccination control strategy starts, individual vaccinations
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000143">
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <rdfs:comment xml:lang="en">replaced with VO &apos;vaccine function&apos;</rdfs:comment>
-        <rdfs:label xml:lang="en">vaccine disposition</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete vaccine disposition</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9213,7 +9104,7 @@ Somehow, it&apos;s not innate and it&apos;s temporary, ie, the body will eventua
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000146">
         <obo:IAO_0000600 xml:lang="en">Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">it is the same thing as transmission coefficient</rdfs:comment>
-        <rdfs:label xml:lang="en">beta</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete beta</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9234,7 +9125,7 @@ Somehow, it&apos;s not innate and it&apos;s temporary, ie, the body will eventua
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000148">
         <obo:IAO_0000600 xml:lang="en">random number seed</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">random number seed</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete random number seed</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9689,7 +9580,7 @@ I checked because an infection and immunity census would involve two different c
         <obo:IAO_0000115 xml:lang="en">An ecosystem in which a population of hosts is undergoing at least one infection.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An ecosystem in which a population of hosts is undergoing at least one infection.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">MIDAS scenario</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete MIDAS scenario</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9919,7 +9810,7 @@ I checked because an infection and immunity census would involve two different c
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An independent continuant that is the localization of a pathogen, but is not undergoing an infection.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ContaminatedThing</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:comment xml:lang="en">A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    </rdfs:comment>
+        <rdfs:comment xml:lang="en">A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.</rdfs:comment>
         <rdfs:label xml:lang="en">contaminated thing</rdfs:label>
     </owl:Class>
     
@@ -10345,6 +10236,12 @@ I checked because an infection and immunity census would involve two different c
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000015"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>SimulatorTimeSpecification</apollo_sv:APOLLO_SV_0000040>
@@ -10462,7 +10359,7 @@ The infectious disease scenario typically also includes a lot of additional data
         <obo:IAO_0000115 xml:lang="en">A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.</rdfs:comment>
-        <rdfs:comment xml:lang="en">This census should exclude infection, immunity, treatment, or contamination.  </rdfs:comment>
+        <rdfs:comment xml:lang="en">This census should exclude infection, immunity, treatment, or contamination.</rdfs:comment>
         <rdfs:label xml:lang="en">population and environment census</rdfs:label>
     </owl:Class>
     
@@ -10548,6 +10445,7 @@ Note that the infected and susceptible organisms may be of different species.</o
     <!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000194 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000194">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000086"/>
         <rdfs:subClassOf>
             <owl:Class>
                 <owl:intersectionOf rdf:parseType="Collection">
@@ -10574,6 +10472,27 @@ Note that the infected and susceptible organisms may be of different species.</o
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000007"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                                <owl:someValuesFrom>
+                                    <owl:Restriction>
+                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
+                                        <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000090"/>
+                                    </owl:Restriction>
+                                </owl:someValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000112 xml:lang="en">vaccination control strategy, antiviral control strategy</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">An infectious disease control strategy that immediately targets individuals.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
@@ -10609,7 +10528,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000197">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000188"/>
-        <rdfs:comment xml:lang="en">An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. </rdfs:comment>
+        <rdfs:comment xml:lang="en">An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved.</rdfs:comment>
         <rdfs:label xml:lang="en">agent level population and environment census</rdfs:label>
     </owl:Class>
     
@@ -10619,7 +10538,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000198">
         <rdfs:comment xml:lang="en">At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics.</rdfs:comment>
-        <rdfs:label xml:lang="en">agent model ecosystem census description</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete agent model ecosystem census description</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -10629,7 +10548,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000199">
         <rdfs:comment xml:lang="en">The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census).</rdfs:comment>
-        <rdfs:label xml:lang="en">compartment model population and environment census</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete compartment model population and environment census</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -10662,7 +10581,7 @@ Note that the infected and susceptible organisms may be of different species.</o
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000202">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
         <apollo_sv:APOLLO_SV_0000040>ApolloIndexableItem</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:comment xml:lang="en">A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. </rdfs:comment>
+        <rdfs:comment xml:lang="en">A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved.</rdfs:comment>
         <rdfs:label xml:lang="en">indexable Apollo item</rdfs:label>
     </owl:Class>
     
@@ -10910,9 +10829,9 @@ Note that the infected and sucseptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000215">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
-        <obo:IAO_0000115 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.</obo:IAO_0000115>
         <obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Probability_distribution</obo:IAO_0000119>
-        <obo:IAO_0000600 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ProbabilityDistribution</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">probability distribution</rdfs:label>
     </owl:Class>
@@ -11496,7 +11415,7 @@ can&apos;t recall whether we should use process or processual_entity for future
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0100001>http://purl.obolibrary.org/obo/STATO_0000321</obo:IAO_0100001>
         <apollo_sv:APOLLO_SV_0000040>NonparametricProbabilityDistribution</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">nonparametric probability distribution</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete nonparametric probability distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -11790,8 +11709,7 @@ For example, it may take time to communicate to workers to stop vaccinating and
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An infection acquisition from an individual who is infectious.
 
-The individual acquiring the infection can be of a different species than the one who is infectious.
-</obo:IAO_0000600>
+The individual acquiring the infection can be of a different species than the one who is infectious.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>InfectionAcquisitionFromInfectedHost</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">infection acquisition from infectious host</rdfs:label>
     </owl:Class>
@@ -11833,8 +11751,7 @@ The individual acquiring the infection can be of a different species than the on
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.
 
-In epidemic simulation, it can be &apos;simulator time&apos; where time zero is the starting point of an infectious disease scenario, or it can be &apos;control strategy time&apos; where time zero is the time at which the control strategy is initiated.
-</obo:IAO_0000600>
+In epidemic simulation, it can be &apos;simulator time&apos; where time zero is the starting point of an infectious disease scenario, or it can be &apos;control strategy time&apos; where time zero is the time at which the control strategy is initiated.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>timeScale</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">time scale name</rdfs:label>
     </owl:Class>
@@ -12151,8 +12068,7 @@ For example, the trigger could occur once the incidence or prevalence of the inf
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">The unit of measure for the supply schedule of an individual treatment.
 
-For example, &apos;daily dose&apos;.
-</obo:IAO_0000600>
+For example, &apos;daily dose&apos;.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>supplyScheduleUnits</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">individual treatment strategy supply schedule unit of measure</rdfs:label>
     </owl:Class>
@@ -12205,8 +12121,7 @@ For example, &apos;daily dose&apos;.</obo:IAO_0000600>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A specification of the criteria an organism must meet to be considered to be in some abnormal state.
 
-The abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.
-</obo:IAO_0000600>
+The abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>CaseDefinition</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">case definition</rdfs:label>
     </owl:Class>
@@ -12536,7 +12451,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000651"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0032504"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0048609"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
@@ -13233,7 +13148,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -13256,7 +13171,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -13908,7 +13823,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -13931,7 +13846,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -13981,7 +13896,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:someValuesFrom>
                                             <owl:Class>
                                                 <owl:intersectionOf rdf:parseType="Collection">
-                                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                                     <owl:Restriction>
                                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
                                                         <owl:someValuesFrom>
@@ -14020,7 +13935,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:someValuesFrom>
                                     <owl:Class>
                                         <owl:intersectionOf rdf:parseType="Collection">
-                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
                                                 <owl:someValuesFrom>
@@ -14071,7 +13986,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -14094,7 +14009,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -14256,7 +14171,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000371"/>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:intersectionOf>
                             </owl:Class>
@@ -14275,7 +14190,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000371"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -14767,7 +14682,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated homeostasis</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete homeostasis</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -15181,7 +15096,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A count of individuals in a population who meet an infection case definition during a particular time interval.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated infection case count</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete infection case count</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -15737,7 +15652,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A one-dimensional temporal region occupied by a place closure control strategy.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">closure period</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete closure period</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -16299,7 +16214,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A time measurement datum of the length of the temporal interval occupied by a gonotropic period.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">gonotrophic period duration</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete gonotrophic period duration</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -16572,7 +16487,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000600 xml:lang="en">An identifier curated by ORCID, Inc. to denote some academic author.</obo:IAO_0000600>
         <obo:IAO_0100001 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/IAO_0000708</obo:IAO_0100001>
         <apollo_sv:APOLLO_SV_0000040>orcId</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">ORCID</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete ORCID</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -18167,7 +18082,6 @@ has specified input some case definition.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">census of treatment facilities</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">treatment facilities census</obo:IAO_0000118>
-        <obo:IAO_0000118 xml:lang="en">treatment facility census</obo:IAO_0000118>
         <obo:IAO_0000600 xml:lang="en">A census that counts the number of treatment facilities of some kind in a particular geographical region.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">NOTE: this class counts the facilities themselves, not patients (people) in those facilities.  For example, how many hospitals in a state.  Not how many patients are in a hospital or hospitals in a state.</rdfs:comment>
         <rdfs:label xml:lang="en">treatment facility census</rdfs:label>
@@ -19291,6 +19205,7 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -19322,6 +19237,7 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -19995,7 +19911,6 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <obo:IAO_0000602>(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] </obo:IAO_0000602>
         <obo:IAO_0000602>(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] </obo:IAO_0000602>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
-        <rdfs:label xml:lang="en">realizable</rdfs:label>
         <rdfs:label xml:lang="en">realizable entity</rdfs:label>
     </owl:Class>
     <owl:Axiom>
@@ -20129,24 +20044,13 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <obo:IAO_0000112 xml:lang="en">the shape of this hole.</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">the smell of this portion of mozzarella</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.</obo:IAO_0000115>
-        <obo:IAO_0000115 xml:lang="en">b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &amp;gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1  i &amp;lt; j  n, ci  and cj share no common parts, are such that for each 1  i  n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant &amp; there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">Specifically dependent continuant doesn&apos;t have a closure axiom because the subclasses don&apos;t necessarily exhaust all possibilites. We&apos;re not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.</obo:IAO_0000116>
-        <obo:IAO_0000602>(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] </obo:IAO_0000602>
         <obo:IAO_0000602>(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] </obo:IAO_0000602>
         <rdfs:comment xml:lang="en">A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.</rdfs:comment>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
-        <rdfs:label xml:lang="en">characteristic</rdfs:label>
         <rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
-        <rdfs:seeAlso>https://github.com/OBOFoundry/COB/issues/65</rdfs:seeAlso>
-        <rdfs:seeAlso>https://github.com/oborel/obo-relations/pull/284</rdfs:seeAlso>
     </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget xml:lang="en">b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &amp;gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1  i &amp;lt; j  n, ci  and cj share no common parts, are such that for each 1  i  n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/131-004"/>
-    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
@@ -20160,12 +20064,6 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000005"/>
         <rdfs:comment>per discussion with Barry Smith</rdfs:comment>
     </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
-        <owl:annotatedTarget>(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/131-004"/>
-    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
@@ -20311,6 +20209,13 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <owl:annotatedTarget>An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects </owl:annotatedTarget>
         <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000011"/>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+        <owl:annotatedTarget>An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects </owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000011"/>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000301"/>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
@@ -20609,6 +20514,7 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60</obo:IAO_0000116>
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.</obo:IAO_0000116>
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.</obo:IAO_0000116>
         <obo:IAO_0000600 xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</obo:IAO_0000600>
         <obo:IAO_0000601 xml:lang="en">Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])</obo:IAO_0000601>
         <obo:IAO_0000601 xml:lang="en">every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])</obo:IAO_0000601>
@@ -20943,6 +20849,28 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
     
 
 
+    <!-- http://purl.obolibrary.org/obo/COB_0000022 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000115 xml:lang="en">A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">&apos;Maximal functionally integrated unit&apos; is intended to express unity, which Barry considers synonymous with BFO &apos;object&apos;.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">Includes virus - we will later have a class for cellular organisms.</obo:IAO_0000116>
+        <rdfs:label xml:lang="en">organism</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/COB_0000035 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000035">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
+        <rdfs:label xml:lang="en">completely executed planned process</rdfs:label>
+    </owl:Class>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/DOID_0060478 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_0060478">
@@ -21066,11 +20994,26 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
     <!-- http://purl.obolibrary.org/obo/DRON_00000005 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_00000005">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000030"/>
-        <obo:IAO_0000115 xml:lang="en">a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role</obo:IAO_0000115>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DRON_00000074"/>
+        <obo:IAO_0000115 xml:lang="en">A drug product that is bearer of a clinical drug role.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">William Hogan</obo:IAO_0000117>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/dron.owl</obo:IAO_0000412>
-        <dc:creator xml:lang="en">William Hogan</dc:creator>
+        <rdfs:comment xml:lang="en">We changed the label to &apos;clinical drug product&apos; because it was clear that the part of the definition re: bearer of a &quot;clinical drug role&quot; made it such. Other drugs don&apos;t have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf &quot;drug product&quot;, which also required changing the definition here.</rdfs:comment>
+        <rdfs:label xml:lang="en">clinical drug product</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/DRON_00000074 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_00000074">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+        <obo:IAO_0000115 xml:lang="en">A material entity that (1) contains at least one scattered molecular aggregate as part and (2) is intended, when administered to an organism, to produce some therapeutic and/or psychoactive effect.</obo:IAO_0000115>
+        <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0001-6378-1703"/>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0002-5039-2052"/>
+        <rdfs:comment xml:lang="en">The &quot;intention&quot; part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered.</rdfs:comment>
+        <rdfs:comment xml:lang="en">The psychoactive effect is added for illicit drugs such as crack cocaine.</rdfs:comment>
+        <rdfs:comment xml:lang="en">We are including prophylactic and diagnostic effects / usage under the more general heading of &apos;therapeutic&apos;.</rdfs:comment>
         <rdfs:label xml:lang="en">drug product</rdfs:label>
     </owl:Class>
     
@@ -22064,12 +22007,11 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003674">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">This is the same as GO molecular function</obo:IAO_0000116>
         <oboInOwl:hasExactSynonym>molecular function</oboInOwl:hasExactSynonym>
         <oboInOwl:id>GO:0003674</oboInOwl:id>
-        <rdfs:comment>Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code &apos;no data&apos; (ND), is used to indicate this. Despite its name, this is not a type of &apos;function&apos; in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.</rdfs:comment>
-        <rdfs:comment>This is the same as GO molecular function</rdfs:comment>
+        <rdfs:comment>Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code &apos;no data&apos; (ND), is used to indicate this. Despite its name, this is not a type of &apos;function&apos; in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.</rdfs:comment>
         <rdfs:label xml:lang="en">gene product or complex activity</rdfs:label>
         <rdfs:label>molecular_function</rdfs:label>
     </owl:Class>
@@ -22135,11 +22077,8 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0008150">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <obo:IAO_0000115>A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.</obo:IAO_0000115>
-        <obo:IAO_0000115>A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.</obo:IAO_0000115>
         <obo:IAO_0000115>Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/24968</obo:IAO_0000233>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
         <oboInOwl:created_by>jl</oboInOwl:created_by>
         <oboInOwl:creation_date>2012-09-19T15:05:24Z</oboInOwl:creation_date>
@@ -22160,9 +22099,7 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_plant"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_pombe"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_yeast"/>
-        <rdfs:comment>A biological process is an evolved process</rdfs:comment>
         <rdfs:comment>Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code &apos;no data&apos; (ND), is used to indicate this.</rdfs:comment>
-        <rdfs:comment>Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code &apos;no data&apos; (ND), is used to indicate this.</rdfs:comment>
         <rdfs:label xml:lang="en">biological process</rdfs:label>
         <rdfs:label>biological_process</rdfs:label>
     </owl:Class>
@@ -22181,6 +22118,7 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, &apos;complete&apos; its life cycle.</obo:IAO_0000115>
         <oboInOwl:hasAlternativeId>GO:0022415</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-162906</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>Wikipedia:Viral_life_cycle</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>virus process</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
@@ -22201,6 +22139,12 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:hasDbXref>GOC:jl</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:mah</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0016032"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-162906</owl:annotatedTarget>
+        <rdfs:label>HIV Infection</rdfs:label>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0016032"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
@@ -22257,6 +22201,9 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0016032"/>
         <obo:IAO_0000115>A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.</obo:IAO_0000115>
         <oboInOwl:hasAlternativeId>GO:0019067</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-162588</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-168255</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-9609646</oboInOwl:hasDbXref>
         <oboInOwl:hasNarrowSynonym>viral assembly, maturation, egress, and release</oboInOwl:hasNarrowSynonym>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:hasRelatedSynonym>lytic viral life cycle</oboInOwl:hasRelatedSynonym>
@@ -22272,6 +22219,24 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <owl:annotatedTarget>A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>ISBN:1555811272</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0019058"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-162588</owl:annotatedTarget>
+        <rdfs:label>Budding and maturation of HIV virion</rdfs:label>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0019058"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-168255</owl:annotatedTarget>
+        <rdfs:label>Influenza Infection</rdfs:label>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0019058"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-9609646</owl:annotatedTarget>
+        <rdfs:label>HCMV Infection</rdfs:label>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0019058"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
@@ -22310,7 +22275,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0007610"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0048609"/>
         <obo:IAO_0000115>The specific behavior of an organism that is associated with reproduction.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/23491</obo:IAO_0000233>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
         <oboInOwl:created_by>jl</oboInOwl:created_by>
         <oboInOwl:creation_date>2012-09-19T16:01:37Z</oboInOwl:creation_date>
@@ -22342,10 +22306,10 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000651"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0022414"/>
         <obo:IAO_0000115>A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/22929</obo:IAO_0000233>
         <oboInOwl:hasDbXref>Wikipedia:Sexual_reproduction</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:id>GO:0019953</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate"/>
         <rdfs:comment>Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.</rdfs:comment>
         <rdfs:label>sexual reproduction</rdfs:label>
     </owl:Class>
@@ -22364,7 +22328,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000651"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0022414"/>
         <obo:IAO_0000115>A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/22929</obo:IAO_0000233>
         <oboInOwl:hasDbXref>Wikipedia:Asexual_reproduction</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:hasRelatedSynonym>parthenogenesis</oboInOwl:hasRelatedSynonym>
@@ -22394,10 +22357,11 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0022414">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/27054</obo:IAO_0000233>
         <oboInOwl:created_by>jl</oboInOwl:created_by>
         <oboInOwl:creation_date>2012-09-19T15:56:06Z</oboInOwl:creation_date>
+        <oboInOwl:hasAlternativeId>GO:0019952</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044702</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasAlternativeId>GO:0050876</oboInOwl:hasAlternativeId>
         <oboInOwl:hasDbXref>Wikipedia:Reproduction</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:hasRelatedSynonym>single organism reproductive process</oboInOwl:hasRelatedSynonym>
@@ -22427,7 +22391,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0032501">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>Any biological process, occurring at the level of a multicellular organism, pertinent to its function.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/27189</obo:IAO_0000233>
         <oboInOwl:created_by>jl</oboInOwl:created_by>
         <oboInOwl:creation_date>2012-09-19T16:07:47Z</oboInOwl:creation_date>
         <oboInOwl:hasAlternativeId>GO:0044707</oboInOwl:hasAlternativeId>
@@ -22453,35 +22416,11 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     
 
 
-    <!-- http://purl.obolibrary.org/obo/GO_0032504 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0032504">
-        <obo:IAO_0000115>OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/27054</obo:IAO_0000233>
-        <obo:IAO_0100001>GO:0048609</obo:IAO_0100001>
-        <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
-        <oboInOwl:id>GO:0032504</oboInOwl:id>
-        <rdfs:comment>The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process.</rdfs:comment>
-        <rdfs:label>obsolete multicellular organism reproduction</rdfs:label>
-        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0032504"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref>GOC:isa_complete</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>GOC:jid</oboInOwl:hasDbXref>
-    </owl:Axiom>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/GO_0044403 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044403">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044419"/>
         <obo:IAO_0000115>A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/14807</obo:IAO_0000233>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/20191</obo:IAO_0000233>
         <oboInOwl:hasAlternativeId>GO:0043298</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044404</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0072519</oboInOwl:hasAlternativeId>
@@ -22518,7 +22457,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0051704"/>
         <obo:IAO_0000115>Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.</obo:IAO_0000115>
         <obo:IAO_0000115>Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/18563</obo:IAO_0000233>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
         <oboInOwl:hasAlternativeId>GO:0030260</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044411</oboInOwl:hasAlternativeId>
@@ -22528,6 +22466,7 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:hasAlternativeId>GO:0075052</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0085027</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0085028</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-173107</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>entry into host</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>host invasion</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>host penetration</oboInOwl:hasExactSynonym>
@@ -22561,6 +22500,12 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <owl:annotatedTarget>Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:vw</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0044409"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-173107</owl:annotatedTarget>
+        <rdfs:label>Binding and entry of HIV virion</rdfs:label>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0044409"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
@@ -22605,7 +22550,7 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044419">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>Any process evolved to enable an interaction with an organism of a different species.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/20191</obo:IAO_0000233>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-9824443</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>interaction with another species</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>interspecies interaction</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>interspecies interaction between organisms</oboInOwl:hasExactSynonym>
@@ -22623,6 +22568,12 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <owl:annotatedTarget>Any process evolved to enable an interaction with an organism of a different species.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:cc</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0044419"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-9824443</owl:annotatedTarget>
+        <rdfs:label>Parasitic Infection Pathways</rdfs:label>
+    </owl:Axiom>
     
 
 
@@ -22631,8 +22582,8 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0048609">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0022414"/>
         <obo:IAO_0000115>The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/27054</obo:IAO_0000233>
         <oboInOwl:hasBroadSynonym>organismal reproductive process</oboInOwl:hasBroadSynonym>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-1474165</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>reproductive process in a multicellular organism</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:id>GO:0048609</oboInOwl:id>
@@ -22648,6 +22599,12 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:hasDbXref>GOC:jid</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:tb</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0048609"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-1474165</owl:annotatedTarget>
+        <rdfs:label>Reproduction</rdfs:label>
+    </owl:Axiom>
     
 
 
@@ -22668,7 +22625,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0051701">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044403"/>
         <obo:IAO_0000115>An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/20191</obo:IAO_0000233>
         <oboInOwl:hasAlternativeId>GO:0044112</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044116</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044117</oboInOwl:hasAlternativeId>
@@ -22676,6 +22632,8 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:hasAlternativeId>GO:0044121</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044123</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044125</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-9635486</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-9658195</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>interaction with host</oboInOwl:hasExactSynonym>
         <oboInOwl:hasNarrowSynonym>growth of symbiont in host</oboInOwl:hasNarrowSynonym>
         <oboInOwl:hasNarrowSynonym>growth of symbiont in host cell</oboInOwl:hasNarrowSynonym>
@@ -22691,6 +22649,18 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <owl:annotatedTarget>An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:cc</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0051701"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-9635486</owl:annotatedTarget>
+        <rdfs:label>Infection with Mycobacterium tuberculosis</rdfs:label>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0051701"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-9658195</owl:annotatedTarget>
+        <rdfs:label>Leishmania infection</rdfs:label>
+    </owl:Axiom>
     
 
 
@@ -23114,6 +23084,12 @@ Previous. An information content entity is a non-realizable information entity t
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000032">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
+                <owl:someValuesFrom rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
@@ -24585,6 +24561,12 @@ GO   gene ontology</obo:IAO_0000112>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000018"/>
             </owl:Restriction>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000407"/>
+                <owl:someValuesFrom rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000407"/>
@@ -24886,6 +24868,7 @@ GO   gene ontology</obo:IAO_0000112>
     <!-- http://purl.obolibrary.org/obo/IAO_0000443 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000443">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -24940,6 +24923,7 @@ GO   gene ontology</obo:IAO_0000112>
     <!-- http://purl.obolibrary.org/obo/IAO_0000572 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000572">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -24985,6 +24969,7 @@ points together with a line.</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/IAO_0000574 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000574">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -25135,6 +25120,7 @@ points together with a line.</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/IAO_0000580 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000580">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -26195,6 +26181,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
     <!-- http://purl.obolibrary.org/obo/IAO_0000650 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000650">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -26385,20 +26372,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
-                    </owl:Restriction>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
-                        <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0020010"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -26413,10 +26386,8 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000111 xml:lang="en">identifier</obo:IAO_0000111>
-        <obo:IAO_0000115 xml:lang="en">An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
-        <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">proper name</obo:IAO_0000118>
         <obo:IAO_0000233 xml:lang="en">https://github.com/information-artifact-ontology/IAO/issues/237</obo:IAO_0000233>
@@ -26457,12 +26428,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <owl:equivalentClass>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0020000"/>
-            </owl:Restriction>
-        </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -26471,9 +26437,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.</obo:IAO_0000115>
-        <obo:IAO_0000115 xml:lang="en">An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
-        <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">dubbing process</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">naming</obo:IAO_0000118>
@@ -26487,22 +26451,9 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
     <!-- http://purl.obolibrary.org/obo/IAO_0020015 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0020015">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0020000"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
-                        <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0020000"/>
-        <obo:IAO_0000115 xml:lang="en">A personal name is a proper name identifying an individual person.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">An identifier referring to an individual entity that is ascribed personhood by the user of the identifier.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
-        <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000119>http://en.wikipedia.org/wiki/Personal_name</obo:IAO_0000119>
         <obo:IAO_0000233 xml:lang="en">https://github.com/information-artifact-ontology/IAO/issues/237</obo:IAO_0000233>
@@ -26555,11 +26506,9 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0020000"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
-        <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">code map</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">code system</obo:IAO_0000118>
@@ -26590,7 +26539,7 @@ When there is no such string, it is almost always because the entities take the
     <!-- http://purl.obolibrary.org/obo/IAO_0021003 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0021003">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <obo:IAO_0000112 xml:lang="en">Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
@@ -27023,6 +26972,12 @@ No imports</obo:IAO_0000115>
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/IDO_0000618"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000031"/>
         <obo:IAO_0000115 xml:lang="en">A disposition to initiate processes that result in a disorder.</obo:IAO_0000115>
@@ -27073,6 +27028,12 @@ No imports</obo:IAO_0000115>
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
@@ -27667,6 +27628,12 @@ No imports</obo:IAO_0000115>
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000031"/>
         <obo:IAO_0000115 xml:lang="en">A disposition that is the ability to mount a normal immune response.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
@@ -27776,7 +27743,7 @@ No imports</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/IDO_0000629 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000629">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
@@ -29935,6 +29902,16 @@ No imports</obo:IAO_0000115>
     
 
 
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_131567 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
+        <rdfs:label>cellular organisms</rdfs:label>
+    </owl:Class>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_1329799 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1329799">
@@ -31831,8 +31808,12 @@ No imports</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_2759 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2759">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:23020233</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:30257078</oboInOwl:hasDbXref>
         <rdfs:label>Eukaryota</rdfs:label>
         <rdfs:label xml:lang="en">Eukaryota</rdfs:label>
     </owl:Class>
@@ -33277,6 +33258,8 @@ No imports</obo:IAO_0000115>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_40674">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_32524"/>
         <obo:IAO_0000118 xml:lang="en">mammals</obo:IAO_0000118>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
+        <rdfs:label>Mammalia</rdfs:label>
         <rdfs:label xml:lang="en">Mammalia</rdfs:label>
     </owl:Class>
     
@@ -36895,6 +36878,8 @@ No imports</obo:IAO_0000115>
         <obo:IAO_0000118 xml:lang="en">Primata</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">primate</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">primates</obo:IAO_0000118>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
+        <rdfs:label>Primates</rdfs:label>
         <rdfs:label xml:lang="en">Primates</rdfs:label>
     </owl:Class>
     
@@ -37150,12 +37135,10 @@ No imports</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_9606 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2759"/>
-        <obo:IAO_0000111 xml:lang="en">Homo sapiens</obo:IAO_0000111>
-        <obo:IAO_0000118>human being</obo:IAO_0000118>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9443"/>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
         <rdfs:label>Homo sapiens</rdfs:label>
-        <rdfs:label xml:lang="en">Homo sapiens</rdfs:label>
     </owl:Class>
     
 
@@ -37791,7 +37774,6 @@ No imports</obo:IAO_0000115>
                 </owl:someValuesFrom>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000111>planned process</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">planned process</obo:IAO_0000111>
         <obo:IAO_0000112>Injecting mice with a vaccine in order to test its efficacy</obo:IAO_0000112>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
@@ -37800,12 +37782,8 @@ No imports</obo:IAO_0000115>
         <obo:IAO_0000116>&apos;Plan&apos; includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn&apos;t have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)</obo:IAO_0000116>
         <obo:IAO_0000116>We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some 
   objectives is a planned process.</obo:IAO_0000116>
-        <obo:IAO_0000116>We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some 
-objectives is a planned process.</obo:IAO_0000116>
         <obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
         <obo:IAO_0000119>branch derived</obo:IAO_0000119>
-        <obo:IAO_0000232>6/11/9: Edited at workshop. Used to include: is initiated by an agent</obo:IAO_0000232>
-        <obo:IAO_0000232 xml:lang="en">This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
         <rdfs:label xml:lang="en">planned process</rdfs:label>
     </owl:Class>
@@ -38061,28 +38039,13 @@ for now.</obo:IAO_0000116>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
         <obo:IAO_0000111>device</obo:IAO_0000111>
         <obo:IAO_0000112>A voltmeter is a measurement device which is intended to perform some measure function.</obo:IAO_0000112>
-        <obo:IAO_0000112>An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.</obo:IAO_0000112>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
         <obo:IAO_0000115>A device is a processed material which is designed to perform some function or functions</obo:IAO_0000115>
-        <obo:IAO_0000115>A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.</obo:IAO_0000115>
-        <obo:IAO_0000116>2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of &quot;device&quot;, and are enumerating the types of roles that a reagent can perform.
-
-2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions.  Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear.  For example:
-
-(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component.  This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.
-
-(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.
-
-(3) A gel running  box  is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it.  This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.
-
-In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation).  In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.</obo:IAO_0000116>
         <obo:IAO_0000116>food should not classify as a device - counter example for using manufacturer and not device. macroscopic only</obo:IAO_0000116>
         <obo:IAO_0000116>if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn&apos;t work before as we had manufacturing as part of  the definition. device was needed, but couldn&apos;t define in Philadelphia. If we decide  that in addition to function there are also capabilities for which a device is created we will include these in the definition.</obo:IAO_0000116>
         <obo:IAO_0000117>PERSON: Helen Parkinson</obo:IAO_0000117>
         <obo:IAO_0000118>instrument</obo:IAO_0000118>
         <obo:IAO_0000119>OBI Vancouver workshop 2010</obo:IAO_0000119>
-        <obo:IAO_0000119>OBI development call 2012-12-17.</obo:IAO_0000119>
         <rdfs:comment>would include reagents</rdfs:comment>
         <rdfs:label>device</rdfs:label>
     </owl:Class>
@@ -38431,19 +38394,8 @@ https://www.doi.org/</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000045"/>
         <obo:IAO_0000111 xml:lang="en">organism</obo:IAO_0000111>
-        <obo:IAO_0000112 xml:lang="en">animal</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">fungus</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">plant</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">virus</obo:IAO_0000112>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000121"/>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
         <obo:IAO_0000115 xml:lang="en">A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.</obo:IAO_0000115>
-        <obo:IAO_0000116>10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and &apos;other organisms&apos;)</obo:IAO_0000116>
-        <obo:IAO_0000116>13-02-2009:
-OBI doesn&apos;t take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus.
-This issue is outside the scope of OBI.</obo:IAO_0000116>
-        <obo:IAO_0000117>GROUP: OBI Biomaterial Branch</obo:IAO_0000117>
-        <obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/Organism</obo:IAO_0000119>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
         <apollo_sv:APOLLO_SV_0000040>Individual</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">organism</rdfs:label>
@@ -38454,6 +38406,7 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
     <!-- http://purl.obolibrary.org/obo/OBI_0200000 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200000">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -38465,6 +38418,7 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000112>The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.</obo:IAO_0000112>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+        <obo:IAO_0000115 xml:lang="en">A completely executed planned process that produces output data from input data.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">A data transformation is a process which produces output data from input data</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">A planned process that produces output data from input data.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
@@ -38661,12 +38615,11 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
     <!-- http://purl.obolibrary.org/obo/OGMS_0000014 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000014">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
         <obo:IAO_0000115 xml:lang="en">A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2010-07-19T10:18:02Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>clinical finding</rdfs:label>
     </owl:Class>
     
@@ -38680,8 +38633,6 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T10:21:58Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <apollo_sv:APOLLO_SV_0000040>result</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label>laboratory finding</rdfs:label>
     </owl:Class>
     
@@ -38695,7 +38646,6 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2010-07-19T11:13:49Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>phenotype</rdfs:label>
     </owl:Class>
     
@@ -38709,7 +38659,6 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:18:05Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>clinical phenotype</rdfs:label>
     </owl:Class>
     
@@ -38724,7 +38673,6 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:21:20Z</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
-        <apollo_sv:APOLLO_SV_0000040>disease</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label>disease</rdfs:label>
     </owl:Class>
     
@@ -38734,16 +38682,8 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000032">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
-        <obo:IAO_0000115 xml:lang="en">A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
-        <obo:IAO_0000117 xml:lang="en">Barry Smith</obo:IAO_0000117>
-        <obo:IAO_0000117 xml:lang="en">Richard H. Scheuermann</obo:IAO_0000117>
-        <obo:IAO_0000117 xml:lang="en">Werner Ceusters</obo:IAO_0000117>
-        <obo:IAO_0000119 xml:lang="en">Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. 
-
-Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:22:01Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>homeostasis</rdfs:label>
     </owl:Class>
     
@@ -38758,7 +38698,6 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:39:44Z</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>disorder</rdfs:label>
     </owl:Class>
     
@@ -38786,14 +38725,11 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000063">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <obo:IAO_0000111>disease course</obo:IAO_0000111>
         <obo:IAO_0000115 xml:lang="en">The totality of all processes through which a given disease instance is realized.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:55:44Z</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ido.owl</obo:IAO_0000412>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>disease course</rdfs:label>
     </owl:Class>
     
@@ -38808,7 +38744,6 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
         <obo:IAO_0000119>http://code.google.com/p/ogms/issues/detail?id=3</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2010-01-25T04:51:11Z</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:comment>From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087</rdfs:comment>
         <rdfs:label>extended organism</rdfs:label>
     </owl:Class>
@@ -38818,16 +38753,11 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
     <!-- http://purl.obolibrary.org/obo/OGMS_0000090 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000090">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
-        <obo:IAO_0000115 xml:lang="en">A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder</obo:IAO_0000115>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000096"/>
+        <obo:IAO_0000115 xml:lang="en">A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://code.google.com/p/ogms/issues/detail?id=35</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2010-03-31T04:51:11Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <apollo_sv:APOLLO_SV_0000040>Treatment</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:comment xml:lang="en">Apollo-SV currently defines two subclasses of treatment.
-See vaccination and antiviral treatment.  
-</rdfs:comment>
         <rdfs:label>treatment</rdfs:label>
     </owl:Class>
     
@@ -38836,14 +38766,15 @@ See vaccination and antiviral treatment.
     <!-- http://purl.obolibrary.org/obo/OGMS_0000092 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000092">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000182"/>
-        <obo:IAO_0000115 xml:lang="en">A processual entity which has as parts all the processes in which a given organism is participant.</obo:IAO_0000115>
-        <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <obo:IAO_0000115 xml:lang="en">A process which has as parts all the processes in which a given organism is participant.</obo:IAO_0000115>
+        <obo:IAO_0000117>Albert Goldfain
+Richard Scheuermann
+Sagar Jain</obo:IAO_0000117>
         <obo:IAO_0000119>http://code.google.com/p/ogms/issues/detail?id=38</obo:IAO_0000119>
-        <obo:IAO_0000232>creation date: 2010-03-31T04:51:11Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <obo:IAO_0000600 xml:lang="en">A processual entity which has as parts all the processes in which a given organism is participant.</obo:IAO_0000600>
-        <apollo_sv:APOLLO_SV_0000040>LifeCycle</apollo_sv:APOLLO_SV_0000040>
+        <obo:IAO_0000232>creation date: 2010-03-31T04:51:11Z
+
+EDIT: 10 NOV 2015</obo:IAO_0000232>
         <rdfs:label>life course</rdfs:label>
     </owl:Class>
     
@@ -38852,12 +38783,14 @@ See vaccination and antiviral treatment.
     <!-- http://purl.obolibrary.org/obo/OGMS_0000096 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000096">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <obo:IAO_0000115 xml:lang="en">A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process</obo:IAO_0000115>
-        <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <obo:IAO_0000115 xml:lang="en">A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient</obo:IAO_0000115>
+        <obo:IAO_0000117>Albert Goldfain
+Sagar Jain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
-        <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
+        <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z
+editor date: 2017-04-18</obo:IAO_0000232>
         <rdfs:label>health care process</rdfs:label>
     </owl:Class>
     
@@ -38866,13 +38799,12 @@ See vaccination and antiviral treatment.
     <!-- http://purl.obolibrary.org/obo/OGMS_0000097 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000097">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000096"/>
         <obo:IAO_0000115 xml:lang="en">A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role.  The health care provider role and patient are realized during the health care encounter</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
+        <oboInOwl:hasExactSynonym xml:lang="en">healthcare encounter</oboInOwl:hasExactSynonym>
         <rdfs:label>health care encounter</rdfs:label>
     </owl:Class>
     
@@ -38881,12 +38813,14 @@ See vaccination and antiviral treatment.
     <!-- http://purl.obolibrary.org/obo/OGMS_0000098 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000098">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000097"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000096"/>
+        <obo:IAO_0000115 xml:lang="en">TODO</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <apollo_sv:APOLLO_SV_0000040>hospitalization</apollo_sv:APOLLO_SV_0000040>
+        <rdfs:comment>09/16/2020
+Is this same as admission? 
+Is this the same as inpatient encounter?</rdfs:comment>
         <rdfs:label>hospitalization</rdfs:label>
     </owl:Class>
     
@@ -38896,10 +38830,10 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000099">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000097"/>
+        <obo:IAO_0000115 xml:lang="en">TODO</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>outpatient encounter</rdfs:label>
     </owl:Class>
     
@@ -38913,7 +38847,6 @@ See vaccination and antiviral treatment.
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>inpatient encounter</rdfs:label>
     </owl:Class>
     
@@ -38923,11 +38856,11 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000101">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000097"/>
+        <obo:IAO_0000115 xml:lang="en">A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <rdfs:label>ED encounter</rdfs:label>
+        <rdfs:label>emergency department encounter</rdfs:label>
     </owl:Class>
     
 
@@ -38936,10 +38869,14 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000105">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <obo:IAO_0000115 xml:lang="en">A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course.</obo:IAO_0000115>
-        <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+        <obo:IAO_0000115>A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course.</obo:IAO_0000116>
+        <obo:IAO_0000117>Albert Goldfain
+Richard Scheuermann
+Sagar Jain</obo:IAO_0000117>
+        <obo:IAO_0000118>recurrent</obo:IAO_0000118>
         <obo:IAO_0000119>http://code.google.com/p/ogms/issues/detail?id=73</obo:IAO_0000119>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
+        <dc:date>10 NOV 2015</dc:date>
         <rdfs:label xml:lang="en">relapse</rdfs:label>
     </owl:Class>
     
@@ -38964,7 +38901,12 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000001">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000026"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000050"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A social role inhering in a human being.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
@@ -38986,8 +38928,8 @@ See vaccination and antiviral treatment.
         <obo:IAO_0000115 xml:lang="en">A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
-        <obo:IAO_0000118 xml:lang="en">health care role</obo:IAO_0000118>
-        <rdfs:label xml:lang="en">human health care role</rdfs:label>
+        <oboInOwl:hasExactSynonym xml:lang="en">healthcare role</oboInOwl:hasExactSynonym>
+        <rdfs:label xml:lang="en">health care role</rdfs:label>
     </owl:Class>
     
 
@@ -38996,8 +38938,13 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000011">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000010"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
-        <obo:IAO_0000115 xml:lang="en">A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.</obo:IAO_0000115>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <obo:IAO_0000115 xml:lang="en">A health care role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Amanda Hicks</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">patient</obo:IAO_0000118>
@@ -39021,6 +38968,7 @@ See vaccination and antiviral treatment.
         <obo:IAO_0000115 xml:lang="en">A role that inheres in an organization and that is realized by the providing of services in a health care encounter.</obo:IAO_0000115>
         <dc:contributor>Mathias Brochhausen</dc:contributor>
         <dc:creator>Amanda Hicks</dc:creator>
+        <oboInOwl:hasExactSynonym xml:lang="en">healthcare provider organization role</oboInOwl:hasExactSynonym>
         <rdfs:label xml:lang="en">health care provider organization role</rdfs:label>
     </owl:Class>
     
@@ -39037,7 +38985,7 @@ See vaccination and antiviral treatment.
                     <owl:Class>
                         <owl:intersectionOf rdf:parseType="Collection">
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000030"/>
-                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000022"/>
                         </owl:intersectionOf>
                     </owl:Class>
                 </owl:allValuesFrom>
@@ -39084,8 +39032,13 @@ Ditto for its current descendants.</rdfs:comment>
     <!-- http://purl.obolibrary.org/obo/OMRSE_00000026 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000026">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00002072"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A role in human social processes that inheres in an organism.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan
 Mathias Brochhausen</obo:IAO_0000117>
@@ -39104,6 +39057,7 @@ Ditto for its current descendants.</rdfs:comment>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000027">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000025"/>
         <obo:IAO_0000115 xml:lang="en">An organization social role that, if realized, is realized by either a health care process or an ancillary health care process</obo:IAO_0000115>
+        <oboInOwl:hasExactSynonym xml:lang="en">organization healthcare role</oboInOwl:hasExactSynonym>
         <rdfs:comment xml:lang="en">Previous definition: An organization social role played by an organization in health care processes.</rdfs:comment>
         <rdfs:label xml:lang="en">organization health care role</rdfs:label>
     </owl:Class>
@@ -39125,7 +39079,12 @@ Ditto for its current descendants.</rdfs:comment>
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000011"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000050"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A patient role that inheres in a human being.</obo:IAO_0000115>
         <rdfs:label xml:lang="en">human patient role</rdfs:label>
     </owl:Class>
@@ -39169,102 +39128,6 @@ Amanda Hicks</obo:IAO_0000117>
     
 
 
-    <!-- http://purl.obolibrary.org/obo/OMRSE_00000048 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000048">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000023"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:label xml:lang="en">material entity role</rdfs:label>
-    </owl:Class>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/OMRSE_00000049 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000049">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000048"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:label xml:lang="en">organism role</rdfs:label>
-    </owl:Class>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/OMRSE_00000050 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000050">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:label xml:lang="en">Homo sapiens role</rdfs:label>
-    </owl:Class>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/OMRSE_00000051 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000051">
@@ -39279,7 +39142,7 @@ Amanda Hicks</obo:IAO_0000117>
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000048"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
@@ -39466,7 +39329,12 @@ Amanda Hicks</obo:IAO_0000117>
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000061"/>
-        <rdfs:subClassOf rdf:nodeID="genid2640"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000068"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000245"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
@@ -39477,16 +39345,6 @@ Amanda Hicks</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <rdfs:label xml:lang="en">facility</rdfs:label>
     </owl:Class>
-    <owl:Restriction rdf:nodeID="genid2640">
-        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000068"/>
-        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000245"/>
-    </owl:Restriction>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000062"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
-        <owl:annotatedTarget rdf:nodeID="genid2640"/>
-        <owl:versionInfo>09/09/2017</owl:versionInfo>
-    </owl:Axiom>
     
 
 
@@ -39630,6 +39488,7 @@ Amanda Hicks</obo:IAO_0000117>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000097"/>
             </owl:Restriction>
         </rdfs:subClassOf>
+        <oboInOwl:hasExactSynonym xml:lang="en">healthcare function</oboInOwl:hasExactSynonym>
         <rdfs:label xml:lang="en">health care function</rdfs:label>
     </owl:Class>
     
@@ -39638,7 +39497,13 @@ Amanda Hicks</obo:IAO_0000117>
     <!-- http://purl.obolibrary.org/obo/OMRSE_00002072 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00002072">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000048"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
@@ -40180,38 +40045,34 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000061">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
-        <obo:IAO_0000115>Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism&apos;s own genome.</obo:IAO_0000115>
         <obo:IAO_0000115>Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism&apos;s own genome.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_4751"/>
         <oboInOwl:hasDbXref>AAO:0010825</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CARO:0000003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EHDAA2:0003003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EMAPA:0</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00007001</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FAO:0000001</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:305751</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:67135</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GAID:781</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>HAO:0000003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MA:0003000</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>MESH:A13</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MESH:D000825</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>SCTID:362889002</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0000037</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001823</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001759</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WBbt:0000100</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0003000</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0000037</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>http://dbpedia.org/ontology/AnatomicalStructure</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>biological structure</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>connected biological structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0000061</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>anatomical structure</rdfs:label>
     </owl:Class>
@@ -40230,29 +40091,85 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000071 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
+        <obo:IAO_0000115>End of the life of an organism.</obo:IAO_0000115>
+        <oboInOwl:hasDbXref>XAO:0000437</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>XtroDO:0000085</oboInOwl:hasDbXref>
+        <oboInOwl:hasRelatedSynonym>death</oboInOwl:hasRelatedSynonym>
+        <oboInOwl:id>UBERON:0000071</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <rdfs:label>death stage</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>End of the life of an organism.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>XAO:0000437</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000105 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000105">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <obo:IAO_0000115>A spatiotemporal region encompassing some part of the life cycle of an organism.</obo:IAO_0000115>
+        <obo:IAO_0000116>this class represents a proper part of the life cycle of an organism. The class &apos;life cycle&apos; should not be placed here</obo:IAO_0000116>
+        <oboInOwl:hasDbXref>BILS:0000105</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>EFO:0000399</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FBdv:00007012</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FMA:24120</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>MESH:D008018</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PdumDv:0000090</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>WBls:0000002</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>XAO:1000000</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>ZFS:0000000</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>ZFS:0100000</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>ncithesaurus:Developmental_Stage</oboInOwl:hasDbXref>
+        <oboInOwl:hasNarrowSynonym>developmental stage</oboInOwl:hasNarrowSynonym>
+        <oboInOwl:hasNarrowSynonym>stage</oboInOwl:hasNarrowSynonym>
+        <oboInOwl:id>UBERON:0000105</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#efo_slim"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
+        <rdfs:label>life cycle stage</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A spatiotemporal region encompassing some part of the life cycle of an organism.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>https://orcid.org/0000-0002-6601-2165</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0000465 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000465">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001062"/>
         <obo:IAO_0000115>Anatomical entity that has mass.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_4751"/>
         <oboInOwl:hasDbXref>AAO:0010264</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000006</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000006</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CARO:0000006</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EHDAA2:0003006</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00007016</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:67165</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>HAO:0000006</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0001836</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001826</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001721</oboInOwl:hasDbXref>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0000465</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>material anatomical entity</rdfs:label>
     </owl:Class>
@@ -40268,16 +40185,13 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <!-- http://purl.obolibrary.org/obo/UBERON_0000467 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000467">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000480"/>
-        <obo:IAO_0000115>Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia].</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:UBPROP_0000001>Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]</obo:UBPROP_0000001>
-        <obo:UBPROP_0000001>Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]</obo:UBPROP_0000001>
-        <obo:UBPROP_0000001>Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]</obo:UBPROP_0000001>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000061"/>
+        <obo:IAO_0000115>Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.</obo:IAO_0000115>
         <oboInOwl:hasBroadSynonym>system</oboInOwl:hasBroadSynonym>
         <oboInOwl:hasDbXref>AAO:0000007</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000011</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000011</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>BIRNLEX:14</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BSA:0000049</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CALOHA:TS-2088</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CARO:0000011</oboInOwl:hasDbXref>
@@ -40285,16 +40199,13 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>EHDAA:392</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EMAPA:16103</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EV:0100000</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00004856</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:7149</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>HAO:0000011</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MA:0000003</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>NIF_GrossAnatomy:birnlex_14</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>NCIT:C12919</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>SCTID:278195005</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0001439</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001831</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>UMLS:C0460002</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001725</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0005746</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0005763</oboInOwl:hasDbXref>
@@ -40302,16 +40213,51 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>XAO:0003002</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0001439</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>galen:AnatomicalSystem</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>ncithesaurus:Organ_System</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>body system</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>connected anatomical system</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>organ system</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:hasRelatedSynonym>anatomical systems</oboInOwl:hasRelatedSynonym>
         <oboInOwl:id>UBERON:0000467</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#pheno_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#uberon_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>anatomical system</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/EHDAA2_0001330"/>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000011</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
+        <owl:annotatedTarget>system</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>GO:0048731</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget>body system</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>BIRNLEX:14</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget>connected anatomical system</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000011</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
+        <owl:annotatedTarget>anatomical systems</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>ZFA:0001439</oboInOwl:hasDbXref>
+        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/OMO_0003004"/>
+    </owl:Axiom>
     
 
 
@@ -40320,38 +40266,57 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000479">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0010000"/>
         <obo:IAO_0000115>Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
+        <obo:IAO_0000116>changed label and definition to reflect CARO2</obo:IAO_0000116>
         <oboInOwl:hasDbXref>AAO:0000607</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AAO:0010054</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000043</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000043</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>BIRNLEX:19</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CALOHA:TS-2090</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CARO:0000043</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EHDAA2:0003043</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00007003</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>EMAPA:35868</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:9637</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>HAO:0000043</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MA:0003002</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>MESH:A10</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>NIF_GrossAnatomy:birnlex_19</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>MESH:D014024</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>NCIT:C12801</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0001477</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001844</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>UMLS:C0040300</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001757</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0005729</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0003040</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0001477</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>galen:Tissue</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>ncithesaurus:Tissue</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>portion of tissue</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>tissue portion</oboInOwl:hasExactSynonym>
         <oboInOwl:hasNarrowSynonym>simple tissue</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0000479</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#pheno_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
-        <rdfs:comment>Editor note: changed label and definition to reflect CARO2</rdfs:comment>
         <rdfs:label>tissue</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000479"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000043</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000479"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget>portion of tissue</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000043</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000479"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
+        <owl:annotatedTarget>simple tissue</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>AEO:0000043</oboInOwl:hasDbXref>
+    </owl:Axiom>
     
 
 
@@ -40360,7 +40325,7 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000480">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000061"/>
         <obo:IAO_0000115>Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
+        <obo:IAO_0000116>Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]</obo:IAO_0000116>
         <oboInOwl:hasDbXref>AAO:0010008</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000054</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000054</oboInOwl:hasDbXref>
@@ -40372,21 +40337,34 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>VHOG:0001724</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0003001</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0001512</oboInOwl:hasDbXref>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0000480</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>anatomical group</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000480"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000054</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>http://orcid.org/0000-0001-9114-8737</oboInOwl:hasDbXref>
+    </owl:Axiom>
     
 
 
     <!-- http://purl.obolibrary.org/obo/UBERON_0001062 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001062">
+        <owl:equivalentClass>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0020105"/>
+                <owl:hasSelf rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:hasSelf>
+            </owl:Restriction>
+        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
         <obo:IAO_0000115>Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.</obo:IAO_0000115>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_4751"/>
         <oboInOwl:hasDbXref>AAO:0010841</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000000</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BFO:0000004</oboInOwl:hasDbXref>
@@ -40400,12 +40378,13 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>NCIT:C12219</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0100000</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001822</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>UMLS:C1515976</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0000100</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0000000</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0100000</oboInOwl:hasDbXref>
         <oboInOwl:id>UBERON:0001062</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>anatomical entity</rdfs:label>
     </owl:Class>
@@ -40416,44 +40395,43 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>FMA:62955</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>http://orcid.org/0000-0001-9114-8737</oboInOwl:hasDbXref>
     </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001062"/>
-        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
-        <owl:annotatedTarget>UMLS:C1515976</owl:annotatedTarget>
-        <oboInOwl:source>ncithesaurus:Anatomic_Structure_System_or_Substance</oboInOwl:source>
-    </owl:Axiom>
     
 
 
     <!-- http://purl.obolibrary.org/obo/UBERON_0002405 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002405">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
         <obo:IAO_0000115>Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:UBPROP_0000003>The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]</obo:UBPROP_0000003>
         <oboInOwl:hasDbXref>AAO:0011003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000104</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>BTO:0005810</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:9825</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GAID:328</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MA:0002711</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>MESH:A15.382</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>MESH:D007107</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>NCIT:C12735</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>SCTID:362590003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0001159</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>UMLS:C0020962</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001247</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>Wikipedia:Immune_system</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0003152</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0001159</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>ncithesaurus:Immune_System</oboInOwl:hasDbXref>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0002405</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#pheno_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#uberon_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#vertebrate_core"/>
-        <rdfs:comment>This class was created automatically from a combination of ontologies</rdfs:comment>
         <rdfs:label>immune system</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002405"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>Wikipedia:Immune_system</oboInOwl:hasDbXref>
+    </owl:Axiom>
     
 
 
@@ -40462,15 +40440,12 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0010000">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000061"/>
         <obo:IAO_0000115>An anatomical structure that has more than one cell as a part.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_4751"/>
         <oboInOwl:hasDbXref>CARO:0010000</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00100313</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>multicellular structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0010000</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>multicellular anatomical structure</rdfs:label>
     </owl:Class>
@@ -40492,33 +40467,21 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <!-- http://purl.obolibrary.org/obo/UBERON_0035943 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0035943">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000035"/>
         <obo:IAO_0000115>A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0035943</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>life cycle temporal boundary</rdfs:label>
     </owl:Class>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/UBERON_0035944 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035943"/>
-        <obo:IAO_0000115>A life cycle temporal boundary that marks the end of the life cycle of the organism.</obo:IAO_0000115>
-        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <oboInOwl:hasExactSynonym>end of life cycle</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>moment of death</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>time of death</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
-        <oboInOwl:hasRelatedSynonym>death</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasRelatedSynonym>end of life</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:id>UBERON:0035944</oboInOwl:id>
-        <rdfs:label>life-death temporal boundary</rdfs:label>
-    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035943"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>https://orcid.org/0000-0002-6601-2165</oboInOwl:hasDbXref>
+    </owl:Axiom>
     
 
 
@@ -40950,9 +40913,13 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">failed exploratory term</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">Terms created as placeholders with the expectation of being permanent should instead be deprecated using the &quot;placeholder removed&quot; (obo:IAO_0000226) justification.</obo:IAO_0000116>
         <obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">failed exploratory term</rdfs:label>
     </owl:Thing>
     
@@ -40975,6 +40942,7 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
         <obo:IAO_0000111 xml:lang="en">organizational term</obo:IAO_0000111>
         <obo:IAO_0000115 xml:lang="en">Term created to ease viewing/sort terms for development purpose, and will not be included in a release</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">term created to ease viewing/sort terms for development purpose, and will not be included in a release</obo:IAO_0000115>
         <rdfs:label xml:lang="en">organizational term</rdfs:label>
     </owl:NamedIndividual>
@@ -41047,6 +41015,10 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">placeholder removed</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined.</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider.</obo:IAO_0000116>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">placeholder removed</rdfs:label>
     </owl:Thing>
     
@@ -41057,7 +41029,11 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000227">
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">terms merged</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term has been combined with one or more other terms to create a more encompassing (merged) term.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">An editor note should explain what were the merged terms and the reason for the merge.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge.</obo:IAO_0000116>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">terms merged</rdfs:label>
     </owl:NamedIndividual>
     
@@ -41068,7 +41044,11 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000228">
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">term imported</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term has been replaced by a term imported from another ontology.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001.</obo:IAO_0000116>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">term imported</rdfs:label>
     </owl:NamedIndividual>
     
@@ -41079,7 +41059,11 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000229">
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">term split</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term has been split into two or more new terms.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001.</obo:IAO_0000116>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">term split</rdfs:label>
     </owl:NamedIndividual>
     
@@ -41180,9 +41164,12 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000115 xml:lang="en">The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype.</obo:IAO_0000116>
         <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
         <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/77</obo:IAO_0000233>
         <obo:IAO_0000234>https://orcid.org/0000-0001-5208-3432</obo:IAO_0000234>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label>out of scope</rdfs:label>
     </owl:NamedIndividual>
     
@@ -41423,13 +41410,10 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
     <rdf:Description rdf:about="urn:swrl#e">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
-    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ro.owl#z">
-        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
-    </rdf:Description>
-    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ro.owl#y">
+    <rdf:Description rdf:about="urn:swrl:var#e">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
-    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ro.owl#x">
+    <rdf:Description rdf:about="urn:swrl:var#d">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
     <rdf:Description rdf:about="urn:swrl:var#y">
@@ -41490,10 +41474,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                 <rdf:first>
                     <rdf:Description>
-                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002180"/>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
                         <swrl:argument1 rdf:resource="urn:swrl:var#w"/>
-                        <swrl:argument2 rdf:resource="urn:swrl:var#p"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41501,9 +41484,10 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                         <rdf:first>
                             <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002180"/>
                                 <swrl:argument1 rdf:resource="urn:swrl:var#w"/>
+                                <swrl:argument2 rdf:resource="urn:swrl:var#p"/>
                             </rdf:Description>
                         </rdf:first>
                         <rdf:rest>
@@ -41581,6 +41565,49 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
             </rdf:Description>
         </swrl:head>
     </rdf:Description>
+    <rdf:Description>
+        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
+        <swrl:body>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                        <rdf:first>
+                            <rdf:Description>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#d"/>
+                            </rdf:Description>
+                        </rdf:first>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+                    </rdf:Description>
+                </rdf:rest>
+            </rdf:Description>
+        </swrl:body>
+        <swrl:head>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000091"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+            </rdf:Description>
+        </swrl:head>
+    </rdf:Description>
     <rdf:Description>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>
@@ -41631,9 +41658,10 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                 <rdf:first>
                     <rdf:Description>
-                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
-                        <swrl:argument1 rdf:resource="urn:swrl#d"/>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41641,10 +41669,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                         <rdf:first>
                             <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
-                                <swrl:argument1 rdf:resource="urn:swrl#e"/>
-                                <swrl:argument2 rdf:resource="urn:swrl#d"/>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#d"/>
                             </rdf:Description>
                         </rdf:first>
                         <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41658,9 +41685,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
-                        <swrl:argument1 rdf:resource="urn:swrl#e"/>
-                        <swrl:argument2 rdf:resource="urn:swrl#d"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41675,7 +41702,7 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
+                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
                         <swrl:argument1 rdf:resource="urn:swrl#d"/>
                     </rdf:Description>
                 </rdf:first>
@@ -41701,7 +41728,7 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
                         <swrl:argument1 rdf:resource="urn:swrl#e"/>
                         <swrl:argument2 rdf:resource="urn:swrl#d"/>
                     </rdf:Description>
@@ -41711,9 +41738,6 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
         </swrl:head>
     </rdf:Description>
     <rdf:Description>
-        <swrla:isRuleEnabled rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</swrla:isRuleEnabled>
-        <rdfs:comment>MF(X)-directly_regulates-&gt;MF(Y)-enabled_by-&gt;GP(Z) =&gt; MF(Y)-has_input-&gt;GP(Y) e.g. if &apos;protein kinase activity&apos;(X) directly_regulates &apos;protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z</rdfs:comment>
-        <rdfs:label>infer input from direct reg</rdfs:label>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>
             <rdf:Description>
@@ -41721,9 +41745,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
-                        <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#z"/>
-                        <swrl:argument2 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#y"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41731,37 +41755,12 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                         <rdf:first>
                             <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
-                                <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#x"/>
-                                <swrl:argument2 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#y"/>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#d"/>
                             </rdf:Description>
                         </rdf:first>
-                        <rdf:rest>
-                            <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
-                                <rdf:first>
-                                    <rdf:Description>
-                                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
-                                        <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#x"/>
-                                    </rdf:Description>
-                                </rdf:first>
-                                <rdf:rest>
-                                    <rdf:Description>
-                                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
-                                        <rdf:first>
-                                            <rdf:Description>
-                                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
-                                                <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#y"/>
-                                            </rdf:Description>
-                                        </rdf:first>
-                                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
-                                    </rdf:Description>
-                                </rdf:rest>
-                            </rdf:Description>
-                        </rdf:rest>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
                     </rdf:Description>
                 </rdf:rest>
             </rdf:Description>
@@ -41772,9 +41771,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002233"/>
-                        <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#x"/>
-                        <swrl:argument2 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#z"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41782,9 +41781,6 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
         </swrl:head>
     </rdf:Description>
     <rdf:Description>
-        <rdfs:comment>GP(X)-enables-&gt;MF(Y)-has_part-&gt;MF(Z) =&gt; GP(X) enables MF(Z),
-e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase coupled transporter activity&apos; has_part &apos;ATPase activity&apos; then GP(X) enables &apos;ATPase activity&apos;</rdfs:comment>
-        <rdfs:label>enabling an MF enables its parts</rdfs:label>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>
             <rdf:Description>
@@ -41792,8 +41788,8 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
-                        <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
+                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
+                        <swrl:argument1 rdf:resource="urn:swrl#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41802,25 +41798,55 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                         <rdf:first>
                             <rdf:Description>
                                 <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
-                                <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
-                                <swrl:argument2 rdf:resource="urn:swrl:var#y"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                                <swrl:argument1 rdf:resource="urn:swrl#e"/>
+                                <swrl:argument2 rdf:resource="urn:swrl#d"/>
                             </rdf:Description>
                         </rdf:first>
-                        <rdf:rest>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+                    </rdf:Description>
+                </rdf:rest>
+            </rdf:Description>
+        </swrl:body>
+        <swrl:head>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
+                        <swrl:argument1 rdf:resource="urn:swrl#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl#d"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+            </rdf:Description>
+        </swrl:head>
+    </rdf:Description>
+    <rdf:Description>
+        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
+        <swrl:body>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                        <rdf:first>
                             <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
-                                <rdf:first>
-                                    <rdf:Description>
-                                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
-                                        <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
-                                    </rdf:Description>
-                                </rdf:first>
-                                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#d"/>
                             </rdf:Description>
-                        </rdf:rest>
+                        </rdf:first>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
                     </rdf:Description>
                 </rdf:rest>
             </rdf:Description>
@@ -41831,9 +41857,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
-                        <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
-                        <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41841,9 +41867,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
         </swrl:head>
     </rdf:Description>
     <rdf:Description>
-        <swrla:isRuleEnabled rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</swrla:isRuleEnabled>
-        <rdfs:comment>GP(X)-enables-&gt;MF(Y)-part_of-&gt;BP(Z) =&gt; GP(X) involved_in BP(Z) e.g. if X enables &apos;protein kinase activity&apos; and Y &apos;part of&apos; &apos;signal tranduction&apos; then X involved in &apos;signal transduction&apos;</rdfs:comment>
-        <rdfs:label>involved in BP</rdfs:label>
+        <rdfs:comment>GP(X)-enables-&gt;MF(Y)-has_part-&gt;MF(Z) =&gt; GP(X) enables MF(Z),
+e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase coupled transporter activity&apos; has_part &apos;ATPase activity&apos; then GP(X) enables &apos;ATPase activity&apos;</rdfs:comment>
+        <rdfs:label>enabling an MF enables its parts</rdfs:label>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>
             <rdf:Description>
@@ -41851,8 +41877,8 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
-                        <swrl:argument1 rdf:resource="urn:swrl:var#z"/>
+                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41861,9 +41887,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                         <rdf:first>
                             <rdf:Description>
                                 <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
-                                <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
-                                <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
+                                <swrl:argument2 rdf:resource="urn:swrl:var#y"/>
                             </rdf:Description>
                         </rdf:first>
                         <rdf:rest>
@@ -41872,9 +41898,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                                 <rdf:first>
                                     <rdf:Description>
                                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
-                                        <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
-                                        <swrl:argument2 rdf:resource="urn:swrl:var#y"/>
+                                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                                        <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
+                                        <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
                                     </rdf:Description>
                                 </rdf:first>
                                 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41890,7 +41916,7 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002331"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
                         <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
                         <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
                     </rdf:Description>
diff --git a/apollo_sv.json b/apollo_sv.json
index 97c710d..0998f69 100644
--- a/apollo_sv.json
+++ b/apollo_sv.json
@@ -49,9 +49,9 @@
         "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl.  When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)."
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2024-12-24"
+        "val" : "2026-03-13"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv.json"
+      "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv.json"
     },
     "nodes" : [ {
       "id" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160",
@@ -248,7 +248,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000011",
-      "lbl" : "control strategy reactive start time information",
+      "lbl" : "obsolete control strategy reactive start time information",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -273,7 +273,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A number of time step units in a time step of a simulation.  \n\nFor example, if the time step is 6 hours, then this value is 6.\n"
+          "val" : "A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "numberOfUnitsOfTimeInOneSimulatorStep"
@@ -318,7 +318,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The number of time steps in a simulator run.\n\nFor example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.\n"
+          "val" : "The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "runLength"
@@ -358,7 +358,7 @@
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  \n\nNote that the susceptible and infected organisms can be of different species.\n\n"
+          "val" : "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "latentPeriodDuration"
@@ -412,13 +412,13 @@
         "definition" : {
           "val" : "The count of (simulated organisms) in a simulated population."
         },
-        "comments" : [ "MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n" ],
+        "comments" : [ "MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The number of simulated organisms in a simulated population.  The number does not have to be an integer.  "
+          "val" : "The number of simulated organisms in a simulated population.  The number does not have to be an integer."
         } ]
       }
     }, {
@@ -431,7 +431,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. "
+          "val" : "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism."
         } ]
       }
     }, {
@@ -442,7 +442,7 @@
         "definition" : {
           "val" : "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination."
         },
-        "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.\n" ],
+        "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint."
@@ -495,11 +495,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  "
+          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  "
+          "val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease."
         } ]
       }
     }, {
@@ -641,11 +641,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A simulated organism in a simulated population that is not susceptible. "
+          "val" : "A simulated organism in a simulated population that is not susceptible."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.\n"
+          "val" : "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage."
         } ]
       }
     }, {
@@ -673,7 +673,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. "
+          "val" : "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
@@ -763,11 +763,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. "
+          "val" : "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. "
+          "val" : "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection."
         } ]
       }
     }, {
@@ -781,7 +781,7 @@
         "comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2.  If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. "
+          "val" : "The fraction of individuals in a simulated population that will accept antiviral treatment if offered."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "antiviral cm compliance"
@@ -793,7 +793,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "An action specification giving the number of doses of an antiviral to be made available during a specific time interval. "
+          "val" : "An action specification giving the number of doses of an antiviral to be made available during a specific time interval."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
@@ -907,9 +907,9 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The simulation of an antiviral control measure. "
+          "val" : "The simulation of an antiviral control measure."
         },
-        "comments" : [ "MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.\n" ],
+        "comments" : [ "MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism."
@@ -962,7 +962,7 @@
         "definition" : {
           "val" : "A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation."
         },
-        "comments" : [ "MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.\n" ],
+        "comments" : [ "MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation."
@@ -1037,11 +1037,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A purely intentional entity that simulates an entity and its properties.\n\n"
+          "val" : "A purely intentional entity that simulates an entity and its properties."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A purely intentional entity that simulates an entity and its properties.\n\n"
+          "val" : "A purely intentional entity that simulates an entity and its properties."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "simulation"
@@ -1119,7 +1119,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000076",
-      "lbl" : "μ",
+      "lbl" : "obsolete μ",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1133,7 +1133,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000077",
-      "lbl" : "σ",
+      "lbl" : "obsolete σ",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1160,7 +1160,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000079",
-      "lbl" : "deprecated log normal distribution",
+      "lbl" : "obsolete log normal distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1231,7 +1231,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. "
+          "val" : "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism."
         } ]
       }
     }, {
@@ -1301,7 +1301,7 @@
         "definition" : {
           "val" : "A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study."
         },
-        "comments" : [ "1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.\n" ],
+        "comments" : [ "1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A vaccination efficacy that results from a vaccination efficacy study."
@@ -1387,7 +1387,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000095",
-      "lbl" : "deprecated discrete probability distribution",
+      "lbl" : "obsolete discrete probability distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1416,11 +1416,11 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The sum of all biotic and abiotic entities in a geographical region. "
+          "val" : "The sum of all biotic and abiotic entities in a geographical region."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The sum of all biotic and abiotic entities in a geographical region. "
+          "val" : "The sum of all biotic and abiotic entities in a geographical region."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "Ecosystem"
@@ -1672,15 +1672,15 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources"
+          "val" : "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources."
         },
-        "comments" : [ "Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing. \n", "Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing" ],
+        "comments" : [ "Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing.", "Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species.\n\n"
+          "val" : "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "InfectionAcquisition"
@@ -1795,7 +1795,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000125",
-      "lbl" : "school calendar",
+      "lbl" : "obsolete school calendar",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -1881,7 +1881,7 @@
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc.\n"
+          "val" : "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "reactiveControlMeasureThreshold"
@@ -1955,7 +1955,7 @@
       "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "the number of distinct antigenic strains in a vaccine product "
+          "val" : "The number of distinct antigenic strains in a vaccine product."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "valence"
@@ -2035,7 +2035,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000143",
-      "lbl" : "vaccine disposition",
+      "lbl" : "obsolete vaccine disposition",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "replaced with VO 'vaccine function'" ],
@@ -2079,7 +2079,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000146",
-      "lbl" : "beta",
+      "lbl" : "obsolete beta",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "it is the same thing as transmission coefficient" ],
@@ -2104,7 +2104,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000148",
-      "lbl" : "random number seed",
+      "lbl" : "obsolete random number seed",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -2282,7 +2282,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000161",
-      "lbl" : "MIDAS scenario",
+      "lbl" : "obsolete MIDAS scenario",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -2382,7 +2382,7 @@
         "definition" : {
           "val" : "An independent continuant that is the localization of a pathogen, but is not undergoing an infection."
         },
-        "comments" : [ "A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    " ],
+        "comments" : [ "A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
@@ -2701,7 +2701,7 @@
         "definition" : {
           "val" : "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero."
         },
-        "comments" : [ "Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.", "This census should exclude infection, immunity, treatment, or contamination.  " ],
+        "comments" : [ "Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.", "This census should exclude infection, immunity, treatment, or contamination." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero."
@@ -2829,11 +2829,11 @@
       "lbl" : "agent level population and environment census",
       "type" : "CLASS",
       "meta" : {
-        "comments" : [ "An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. " ]
+        "comments" : [ "An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved." ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000198",
-      "lbl" : "agent model ecosystem census description",
+      "lbl" : "obsolete agent model ecosystem census description",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics." ],
@@ -2841,7 +2841,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000199",
-      "lbl" : "compartment model population and environment census",
+      "lbl" : "obsolete compartment model population and environment census",
       "type" : "CLASS",
       "meta" : {
         "comments" : [ "The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census)." ],
@@ -2878,7 +2878,7 @@
       "lbl" : "indexable Apollo item",
       "type" : "CLASS",
       "meta" : {
-        "comments" : [ "A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. " ],
+        "comments" : [ "A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "ApolloIndexableItem"
@@ -3110,14 +3110,14 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. "
+          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://en.wikipedia.org/wiki/Probability_distribution"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. "
+          "val" : "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "ProbabilityDistribution"
@@ -3696,7 +3696,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000249",
-      "lbl" : "nonparametric probability distribution",
+      "lbl" : "obsolete nonparametric probability distribution",
       "type" : "CLASS",
       "meta" : {
         "basicPropertyValues" : [ {
@@ -3988,7 +3988,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious.\n"
+          "val" : "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "InfectionAcquisitionFromInfectedHost"
@@ -4046,7 +4046,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated.\n"
+          "val" : "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "timeScale"
@@ -4439,7 +4439,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'.\n"
+          "val" : "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "supplyScheduleUnits"
@@ -4506,7 +4506,7 @@
           "val" : "William R. Hogan"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.\n"
+          "val" : "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
           "val" : "CaseDefinition"
@@ -5877,7 +5877,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000370",
-      "lbl" : "deprecated homeostasis",
+      "lbl" : "obsolete homeostasis",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -6436,7 +6436,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000399",
-      "lbl" : "deprecated infection case count",
+      "lbl" : "obsolete infection case count",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -7211,7 +7211,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000435",
-      "lbl" : "closure period",
+      "lbl" : "obsolete closure period",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -8080,7 +8080,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000475",
-      "lbl" : "gonotrophic period duration",
+      "lbl" : "obsolete gonotrophic period duration",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -8492,7 +8492,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000496",
-      "lbl" : "ORCID",
+      "lbl" : "obsolete ORCID",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
@@ -10390,9 +10390,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "treatment facilities census"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "treatment facility census"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A census that counts the number of treatment facilities of some kind in a particular geographical region."
@@ -12159,21 +12156,12 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000602",
-          "val" : "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] "
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000602",
           "val" : "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] "
         }, {
           "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
           "val" : "http://purl.obolibrary.org/obo/bfo.owl"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://github.com/OBOFoundry/COB/issues/65"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://github.com/oborel/obo-relations/pull/284"
         } ]
       }
     }, {
@@ -12356,6 +12344,9 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects "
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects "
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."
@@ -12722,6 +12713,9 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"
@@ -13025,6 +13019,26 @@
       "meta" : {
         "comments" : [ "The usage or intended usage of a drug product to act against a viral infection of a host." ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/COB_0000022",
+      "lbl" : "organism",
+      "type" : "CLASS",
+      "meta" : {
+        "definition" : {
+          "val" : "A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome"
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "Includes virus - we will later have a class for cellular organisms."
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/COB_0000035",
+      "lbl" : "completely executed planned process",
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/DOID_0060478",
       "lbl" : "Zika fever",
@@ -13238,21 +13252,36 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/DRON_00000005",
-      "lbl" : "drug product",
+      "lbl" : "clinical drug product",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role"
+          "val" : "A drug product that is bearer of a clinical drug role."
         },
+        "comments" : [ "We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a \"clinical drug role\" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf \"drug product\", which also required changing the definition here." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "William Hogan"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/DRON_00000074",
+      "lbl" : "drug product",
+      "type" : "CLASS",
+      "meta" : {
+        "definition" : {
+          "val" : "A material entity that (1) contains at least one scattered molecular aggregate as part and (2) is intended, when administered to an organism, to produce some therapeutic and/or psychoactive effect."
+        },
+        "comments" : [ "The \"intention\" part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered.", "The psychoactive effect is added for illicit drugs such as crack cocaine.", "We are including prophylactic and diagnostic effects / usage under the more general heading of 'therapeutic'." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
+          "val" : "William R. Hogan"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/dron.owl"
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0001-6378-1703"
         }, {
-          "pred" : "http://purl.org/dc/elements/1.1/creator",
-          "val" : "William Hogan"
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0002-5039-2052"
         } ]
       }
     }, {
@@ -14121,10 +14150,14 @@
           "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.",
           "xrefs" : [ "GOC:pdt" ]
         },
-        "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ],
+        "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "molecular function"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This is the same as GO molecular function"
         } ]
       }
     }, {
@@ -14198,7 +14231,7 @@
         "definition" : {
           "val" : "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end."
         },
-        "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ],
+        "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -14217,9 +14250,6 @@
           "val" : "Wikipedia:Biological_process"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/24968"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/go.owl"
         }, {
@@ -14265,6 +14295,8 @@
           "val" : "virulence"
         } ],
         "xrefs" : [ {
+          "val" : "Reactome:R-HSA-162906"
+        }, {
           "val" : "Wikipedia:Viral_life_cycle"
         } ],
         "basicPropertyValues" : [ {
@@ -14321,6 +14353,13 @@
           "val" : "viral replication",
           "xrefs" : [ "GOC:bf", "GOC:jl" ]
         } ],
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-162588"
+        }, {
+          "val" : "Reactome:R-HSA-168255"
+        }, {
+          "val" : "Reactome:R-HSA-9609646"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "GO:0019067"
@@ -14355,9 +14394,6 @@
           "val" : "single-organism reproductive behavior"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/23491"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/go.owl"
         }, {
@@ -14390,13 +14426,11 @@
           "xrefs" : [ "Wikipedia:Sexual_reproduction" ]
         },
         "comments" : [ "Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ],
         "xrefs" : [ {
           "val" : "Wikipedia:Sexual_reproduction"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/22929"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
         } ]
@@ -14419,9 +14453,6 @@
           "val" : "Wikipedia:Asexual_reproduction"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/22929"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
         } ]
@@ -14444,17 +14475,20 @@
           "val" : "Wikipedia:Reproduction"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/27054"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "jl"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-09-19T15:56:06Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "GO:0019952"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "GO:0044702"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "GO:0050876"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
@@ -14479,9 +14513,6 @@
           "val" : "single-multicellular organism process"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/27189"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "jl"
         }, {
@@ -14498,28 +14529,6 @@
           "val" : "biological_process"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/GO_0032504",
-      "lbl" : "obsolete multicellular organism reproduction",
-      "type" : "CLASS",
-      "meta" : {
-        "definition" : {
-          "val" : "OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.",
-          "xrefs" : [ "GOC:isa_complete", "GOC:jid" ]
-        },
-        "comments" : [ "The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process." ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/27054"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "GO:0048609"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "biological_process"
-        } ],
-        "deprecated" : true
-      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/GO_0044403",
       "lbl" : "biological process involved in symbiotic interaction",
@@ -14562,12 +14571,6 @@
           "val" : "symbiotic process"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/14807"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/20191"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "GO:0043298"
         }, {
@@ -14663,10 +14666,10 @@
           "pred" : "hasRelatedSynonym",
           "val" : "other organism invasion"
         } ],
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-173107"
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/18563"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/go.owl"
         }, {
@@ -14721,10 +14724,10 @@
           "pred" : "hasExactSynonym",
           "val" : "interspecies interaction with other organisms"
         } ],
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-9824443"
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/20191"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
         } ]
@@ -14746,10 +14749,10 @@
           "pred" : "hasExactSynonym",
           "val" : "reproductive process in a multicellular organism"
         } ],
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-1474165"
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/27054"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "biological_process"
         } ]
@@ -14795,10 +14798,12 @@
           "pred" : "hasNarrowSynonym",
           "val" : "growth of symbiont in host vacuole"
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
-          "val" : "https://github.com/geneontology/go-ontology/issues/20191"
+        "xrefs" : [ {
+          "val" : "Reactome:R-HSA-9635486"
         }, {
+          "val" : "Reactome:R-HSA-9658195"
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "GO:0044112"
         }, {
@@ -19946,9 +19951,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "proper name"
@@ -19992,7 +19994,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."
+          "val" : "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
@@ -20000,9 +20002,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "dubbing process"
@@ -20032,9 +20031,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://en.wikipedia.org/wiki/Personal_name"
@@ -20114,9 +20110,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "code map"
@@ -23331,6 +23324,15 @@
           "val" : "Micrococcus pneumoniae"
         } ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/NCBITaxon_131567",
+      "lbl" : "cellular organisms",
+      "type" : "CLASS",
+      "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        } ]
+      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1329799",
       "lbl" : "Archelosauria",
@@ -25324,6 +25326,13 @@
       "lbl" : "Eukaryota",
       "type" : "CLASS",
       "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        }, {
+          "val" : "PMID:23020233"
+        }, {
+          "val" : "PMID:30257078"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl"
@@ -26723,6 +26732,9 @@
       "lbl" : "Mammalia",
       "type" : "CLASS",
       "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "mammals"
@@ -30550,6 +30562,9 @@
       "lbl" : "Primates",
       "type" : "CLASS",
       "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "Primata"
@@ -30782,13 +30797,10 @@
       "lbl" : "Homo sapiens",
       "type" : "CLASS",
       "meta" : {
+        "xrefs" : [ {
+          "val" : "GC_ID:1"
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "Homo sapiens"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "human being"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl"
         } ]
@@ -31353,9 +31365,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "planned process"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "planned process"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "Injecting mice with a vaccine in order to test its efficacy"
@@ -31368,21 +31377,12 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \n  objectives is a planned process."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Bjoern Peters"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "branch derived"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "6/11/9: Edited at workshop. Used to include: is initiated by an agent"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/obi.owl"
@@ -31751,7 +31751,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent."
+          "val" : "A device is a processed material which is designed to perform some function or functions"
         },
         "comments" : [ "would include reagents" ],
         "basicPropertyValues" : [ {
@@ -31760,18 +31760,9 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "A voltmeter is a measurement device which is intended to perform some measure function."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
-          "val" : "http://purl.obolibrary.org/obo/IAO_0000122"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
           "val" : "http://purl.obolibrary.org/obo/IAO_0000123"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions.  Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear.  For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component.  This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running  box  is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it.  This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation).  In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only"
@@ -31787,9 +31778,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "OBI Vancouver workshop 2010"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
-          "val" : "OBI development call 2012-12-17."
         } ]
       }
     }, {
@@ -32270,36 +32258,9 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "organism"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "animal"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "fungus"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "plant"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "virus"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
           "val" : "http://purl.obolibrary.org/obo/IAO_0000121"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
-          "val" : "http://purl.obolibrary.org/obo/IAO_0000122"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
-          "val" : "13-02-2009:\nOBI doesn't take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "GROUP: OBI Biomaterial Branch"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
-          "val" : "WEB: http://en.wikipedia.org/wiki/Organism"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/obi.owl"
@@ -32658,9 +32619,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2010-07-19T10:18:02Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32680,12 +32638,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2009-06-23T10:21:58Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "result"
         } ]
       }
     }, {
@@ -32705,9 +32657,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2010-07-19T11:13:49Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32727,9 +32676,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2009-06-23T11:18:05Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32752,9 +32698,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "disease"
         } ]
       }
     }, {
@@ -32762,30 +32705,12 @@
       "lbl" : "homeostasis",
       "type" : "CLASS",
       "meta" : {
-        "definition" : {
-          "val" : "A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning."
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Barry Smith"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Richard H. Scheuermann"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Werner Ceusters"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
-          "val" : "Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. \n\nLink: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2009-06-23T11:22:01Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32808,9 +32733,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32836,9 +32758,6 @@
           "val" : "The totality of all processes through which a given disease instance is realized."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "disease course"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
         }, {
@@ -32850,12 +32769,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ido.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32879,9 +32792,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32890,9 +32800,8 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder"
+          "val" : "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process"
         },
-        "comments" : [ "Apollo-SV currently defines two subclasses of treatment.\nSee vaccination and antiviral treatment.  \n" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -32902,12 +32811,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2010-03-31T04:51:11Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "Treatment"
         } ]
       }
     }, {
@@ -32916,26 +32819,17 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A processual entity which has as parts all the processes in which a given organism is participant."
+          "val" : "A process which has as parts all the processes in which a given organism is participant."
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Albert Goldfain"
+          "val" : "Albert Goldfain\nRichard Scheuermann\nSagar Jain"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://code.google.com/p/ogms/issues/detail?id=38"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "creation date: 2010-03-31T04:51:11Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
-          "val" : "A processual entity which has as parts all the processes in which a given organism is participant."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "LifeCycle"
+          "val" : "creation date: 2010-03-31T04:51:11Z\n\nEDIT: 10 NOV 2015"
         } ]
       }
     }, {
@@ -32944,20 +32838,17 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process"
+          "val" : "A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient"
         },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Albert Goldfain"
+          "val" : "Albert Goldfain\nSagar Jain"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
-          "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
+          "val" : "creation date: 2011-02-21T09:57:44Z\neditor date: 2017-04-18"
         } ]
       }
     }, {
@@ -32968,6 +32859,10 @@
         "definition" : {
           "val" : "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role.  The health care provider role and patient are realized during the health care encounter"
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "healthcare encounter"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -32977,9 +32872,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -32987,6 +32879,10 @@
       "lbl" : "hospitalization",
       "type" : "CLASS",
       "meta" : {
+        "definition" : {
+          "val" : "TODO"
+        },
+        "comments" : [ "09/16/2020\nIs this same as admission? \nIs this the same as inpatient encounter?" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -32996,12 +32892,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
-          "val" : "hospitalization"
         } ]
       }
     }, {
@@ -33009,6 +32899,9 @@
       "lbl" : "outpatient encounter",
       "type" : "CLASS",
       "meta" : {
+        "definition" : {
+          "val" : "TODO"
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -33018,9 +32911,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -33040,16 +32930,16 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OGMS_0000101",
-      "lbl" : "ED encounter",
+      "lbl" : "emergency department encounter",
       "type" : "CLASS",
       "meta" : {
+        "definition" : {
+          "val" : "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Albert Goldfain"
@@ -33059,9 +32949,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "creation date: 2011-02-21T09:57:44Z"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
         } ]
       }
     }, {
@@ -33070,17 +32957,23 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course."
+          "val" : "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease."
         },
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course."
+        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Albert Goldfain"
+          "val" : "Albert Goldfain\nRichard Scheuermann\nSagar Jain"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
+          "val" : "recurrent"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "http://code.google.com/p/ogms/issues/detail?id=73"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/ogms.owl"
+          "pred" : "http://purl.org/dc/elements/1.1/date",
+          "val" : "10 NOV 2015"
         } ]
       }
     }, {
@@ -33126,21 +33019,22 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00000010",
-      "lbl" : "human health care role",
+      "lbl" : "health care role",
       "type" : "CLASS",
       "meta" : {
         "definition" : {
           "val" : "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis."
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "healthcare role"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Mathias Brochhausen"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "William R. Hogan"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "health care role"
         } ]
       }
     }, {
@@ -33149,7 +33043,7 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter."
+          "val" : "A health care role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter."
         },
         "comments" : [ "In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications." ],
         "basicPropertyValues" : [ {
@@ -33174,6 +33068,10 @@
         "definition" : {
           "val" : "A role that inheres in an organization and that is realized by the providing of services in a health care encounter."
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "healthcare provider organization role"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.org/dc/elements/1.1/contributor",
           "val" : "Mathias Brochhausen"
@@ -33237,7 +33135,11 @@
         "definition" : {
           "val" : "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process"
         },
-        "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ]
+        "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "organization healthcare role"
+        } ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00000030",
@@ -33262,18 +33164,6 @@
           "val" : "William R. Hogan\nAmanda Hicks"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/OMRSE_00000048",
-      "lbl" : "material entity role",
-      "type" : "CLASS"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/OMRSE_00000049",
-      "lbl" : "organism role",
-      "type" : "CLASS"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/OMRSE_00000050",
-      "lbl" : "Homo sapiens role",
-      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00000051",
       "lbl" : "organization role",
@@ -33467,7 +33357,13 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00000172",
       "lbl" : "health care function",
-      "type" : "CLASS"
+      "type" : "CLASS",
+      "meta" : {
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "healthcare function"
+        } ]
+      }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMRSE_00002072",
       "lbl" : "role in human social processes",
@@ -34272,7 +34168,7 @@
           "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.",
           "xrefs" : [ "CARO:0000003" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "biological structure"
@@ -34294,7 +34190,7 @@
         }, {
           "val" : "EMAPA:0"
         }, {
-          "val" : "FBbt:00007001"
+          "val" : "FAO:0000001"
         }, {
           "val" : "FMA:305751"
         }, {
@@ -34305,8 +34201,6 @@
           "val" : "HAO:0000003"
         }, {
           "val" : "MA:0003000"
-        }, {
-          "val" : "MESH:A13"
         }, {
           "val" : "MESH:D000825"
         }, {
@@ -34317,27 +34211,77 @@
           "val" : "TGMA:0001823"
         }, {
           "val" : "VHOG:0001759"
-        }, {
-          "val" : "WBbt:0000100"
         }, {
           "val" : "XAO:0003000"
         }, {
           "val" : "ZFA:0000037"
         }, {
           "val" : "http://dbpedia.org/ontology/AnatomicalStructure"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0000071",
+      "lbl" : "death stage",
+      "type" : "CLASS",
+      "meta" : {
+        "definition" : {
+          "val" : "End of the life of an organism.",
+          "xrefs" : [ "XAO:0000437" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset" ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "death"
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
+        "xrefs" : [ {
+          "val" : "XAO:0000437"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
+          "val" : "XtroDO:0000085"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0000105",
+      "lbl" : "life cycle stage",
+      "type" : "CLASS",
+      "meta" : {
+        "definition" : {
+          "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism.",
+          "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "synonyms" : [ {
+          "pred" : "hasNarrowSynonym",
+          "val" : "developmental stage"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751"
+          "pred" : "hasNarrowSynonym",
+          "val" : "stage"
+        } ],
+        "xrefs" : [ {
+          "val" : "BILS:0000105"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
+          "val" : "EFO:0000399"
+        }, {
+          "val" : "FBdv:00007012"
+        }, {
+          "val" : "FMA:24120"
+        }, {
+          "val" : "MESH:D008018"
+        }, {
+          "val" : "PdumDv:0000090"
+        }, {
+          "val" : "WBls:0000002"
+        }, {
+          "val" : "XAO:1000000"
+        }, {
+          "val" : "ZFS:0000000"
+        }, {
+          "val" : "ZFS:0100000"
+        }, {
+          "val" : "ncithesaurus:Developmental_Stage"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here"
         } ]
       }
     }, {
@@ -34349,7 +34293,7 @@
           "val" : "Anatomical entity that has mass.",
           "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "xrefs" : [ {
           "val" : "AAO:0010264"
         }, {
@@ -34360,8 +34304,6 @@
           "val" : "CARO:0000006"
         }, {
           "val" : "EHDAA2:0003006"
-        }, {
-          "val" : "FBbt:00007016"
         }, {
           "val" : "FMA:67165"
         }, {
@@ -34372,19 +34314,6 @@
           "val" : "TGMA:0001826"
         }, {
           "val" : "VHOG:0001721"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
         } ]
       }
     }, {
@@ -34393,18 +34322,30 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]."
+          "val" : "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.",
+          "xrefs" : [ "CARO:0000011" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "synonyms" : [ {
           "pred" : "hasBroadSynonym",
-          "val" : "system"
+          "val" : "system",
+          "xrefs" : [ "GO:0048731" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "body system",
+          "xrefs" : [ "BIRNLEX:14" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "body system"
+          "val" : "connected anatomical system",
+          "xrefs" : [ "CARO:0000011" ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "organ system"
+        }, {
+          "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004",
+          "pred" : "hasRelatedSynonym",
+          "val" : "anatomical systems",
+          "xrefs" : [ "ZFA:0001439" ]
         } ],
         "xrefs" : [ {
           "val" : "AAO:0000007"
@@ -34412,6 +34353,8 @@
           "val" : "AEO:0000011"
         }, {
           "val" : "BILA:0000011"
+        }, {
+          "val" : "BIRNLEX:14"
         }, {
           "val" : "BSA:0000049"
         }, {
@@ -34426,8 +34369,6 @@
           "val" : "EMAPA:16103"
         }, {
           "val" : "EV:0100000"
-        }, {
-          "val" : "FBbt:00004856"
         }, {
           "val" : "FMA:7149"
         }, {
@@ -34435,17 +34376,13 @@
         }, {
           "val" : "MA:0000003"
         }, {
-          "val" : "NIF_GrossAnatomy:birnlex_14"
-        }, {
-          "val" : "OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ"
+          "val" : "NCIT:C12919"
         }, {
           "val" : "SCTID:278195005"
         }, {
           "val" : "TAO:0001439"
         }, {
           "val" : "TGMA:0001831"
-        }, {
-          "val" : "UMLS:C0460002"
         }, {
           "val" : "VHOG:0001725"
         }, {
@@ -34460,27 +34397,6 @@
           "val" : "ZFA:0001439"
         }, {
           "val" : "galen:AnatomicalSystem"
-        }, {
-          "val" : "ncithesaurus:Organ_System"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
-          "val" : "Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
-          "val" : "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
-          "val" : "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/EHDAA2_0001330"
         } ]
       }
     }, {
@@ -34489,19 +34405,21 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation."
+          "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.",
+          "xrefs" : [ "CARO:0000043" ]
         },
-        "comments" : [ "Editor note: changed label and definition to reflect CARO2" ],
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "portion of tissue"
+          "val" : "portion of tissue",
+          "xrefs" : [ "CARO:0000043" ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "tissue portion"
         }, {
           "pred" : "hasNarrowSynonym",
-          "val" : "simple tissue"
+          "val" : "simple tissue",
+          "xrefs" : [ "AEO:0000043" ]
         } ],
         "xrefs" : [ {
           "val" : "AAO:0000607"
@@ -34511,6 +34429,8 @@
           "val" : "AEO:0000043"
         }, {
           "val" : "BILA:0000043"
+        }, {
+          "val" : "BIRNLEX:19"
         }, {
           "val" : "CALOHA:TS-2090"
         }, {
@@ -34518,7 +34438,7 @@
         }, {
           "val" : "EHDAA2:0003043"
         }, {
-          "val" : "FBbt:00007003"
+          "val" : "EMAPA:35868"
         }, {
           "val" : "FMA:9637"
         }, {
@@ -34526,15 +34446,13 @@
         }, {
           "val" : "MA:0003002"
         }, {
-          "val" : "MESH:A10"
+          "val" : "MESH:D014024"
         }, {
-          "val" : "NIF_GrossAnatomy:birnlex_19"
+          "val" : "NCIT:C12801"
         }, {
           "val" : "TAO:0001477"
         }, {
           "val" : "TGMA:0001844"
-        }, {
-          "val" : "UMLS:C0040300"
         }, {
           "val" : "VHOG:0001757"
         }, {
@@ -34545,15 +34463,10 @@
           "val" : "ZFA:0001477"
         }, {
           "val" : "galen:Tissue"
-        }, {
-          "val" : "ncithesaurus:Tissue"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "changed label and definition to reflect CARO2"
         } ]
       }
     }, {
@@ -34562,9 +34475,10 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue."
+          "val" : "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.",
+          "xrefs" : [ "CARO:0000054", "http://orcid.org/0000-0001-9114-8737" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "xrefs" : [ {
           "val" : "AAO:0010008"
         }, {
@@ -34589,11 +34503,8 @@
           "val" : "ZFA:0001512"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]"
         } ]
       }
     }, {
@@ -34605,7 +34516,7 @@
           "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.",
           "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "xrefs" : [ {
           "val" : "AAO:0010841"
         }, {
@@ -34632,21 +34543,12 @@
           "val" : "TAO:0100000"
         }, {
           "val" : "TGMA:0001822"
-        }, {
-          "val" : "UMLS:C1515976"
         }, {
           "val" : "WBbt:0000100"
         }, {
           "val" : "XAO:0000000"
         }, {
           "val" : "ZFA:0100000"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751"
         } ]
       }
     }, {
@@ -34655,14 +34557,16 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies."
+          "val" : "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.",
+          "xrefs" : [ "Wikipedia:Immune_system" ]
         },
-        "comments" : [ "This class was created automatically from a combination of ontologies" ],
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ],
         "xrefs" : [ {
           "val" : "AAO:0011003"
         }, {
           "val" : "BILA:0000104"
+        }, {
+          "val" : "BTO:0005810"
         }, {
           "val" : "FMA:9825"
         }, {
@@ -34670,15 +34574,13 @@
         }, {
           "val" : "MA:0002711"
         }, {
-          "val" : "MESH:A15.382"
+          "val" : "MESH:D007107"
         }, {
-          "val" : "OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA"
+          "val" : "NCIT:C12735"
         }, {
           "val" : "SCTID:362590003"
         }, {
           "val" : "TAO:0001159"
-        }, {
-          "val" : "UMLS:C0020962"
         }, {
           "val" : "VHOG:0001247"
         }, {
@@ -34687,18 +34589,6 @@
           "val" : "XAO:0003152"
         }, {
           "val" : "ZFA:0001159"
-        }, {
-          "val" : "ncithesaurus:Immune_System"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003",
-          "val" : "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
         } ]
       }
     }, {
@@ -34710,7 +34600,7 @@
           "val" : "An anatomical structure that has more than one cell as a part.",
           "xrefs" : [ "CARO:0010000" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "multicellular structure",
@@ -34718,21 +34608,6 @@
         } ],
         "xrefs" : [ {
           "val" : "CARO:0010000"
-        }, {
-          "val" : "FBbt:00100313"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002175",
-          "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
         } ]
       }
     }, {
@@ -34741,51 +34616,10 @@
       "type" : "CLASS",
       "meta" : {
         "definition" : {
-          "val" : "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity."
+          "val" : "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.",
+          "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
-        } ]
-      }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/UBERON_0035944",
-      "lbl" : "life-death temporal boundary",
-      "type" : "CLASS",
-      "meta" : {
-        "definition" : {
-          "val" : "A life cycle temporal boundary that marks the end of the life cycle of the organism."
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "end of life cycle"
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "moment of death"
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "time of death"
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "death"
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "end of life"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/uberon.owl"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "uberon"
-        } ]
+        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/UO_0000000",
@@ -35168,7 +35002,7 @@
           "val" : "http://www.geneontology.org/formats/oboInOwl"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition",
-          "val" : "_:genid2147487128"
+          "val" : "_:genid2147487145"
         } ]
       }
     }, {
@@ -35176,7 +35010,7 @@
       "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000004",
-      "lbl" : "basis of",
+      "lbl" : "obsolete basis of",
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
@@ -35188,7 +35022,7 @@
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
-        "comments" : [ "p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. " ],
+        "comments" : [ "p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption." ],
         "deprecated" : true
       }
     }, {
@@ -35215,7 +35049,7 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "definition" : {
-          "val" : "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. "
+          "val" : "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times."
         },
         "comments" : [ "Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222." ]
       }
@@ -35231,7 +35065,7 @@
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000116",
-      "lbl" : "causally_precedes",
+      "lbl" : "obsolete causally_precedes",
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
@@ -35310,45 +35144,15 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000002"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000003"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000004"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000017"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000019"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000020"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000031"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "external"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
           "val" : "part_of"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf"
         }, {
           "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Part_of"
         } ]
       }
     }, {
@@ -35413,15 +35217,6 @@
         },
         "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000054"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000054s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000054ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "obsolete_is_realized_by"
         }, {
@@ -35489,17 +35284,11 @@
       "type" : "PROPERTY",
       "propertyType" : "OBJECT",
       "meta" : {
+        "definition" : {
+          "val" : "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process"
+        },
         "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000055"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000055s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000055ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "realizes"
         }, {
@@ -35547,9 +35336,6 @@
         }, {
           "pred" : "http://purl.org/dc/elements/1.1/source",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by"
-        }, {
-          "pred" : "http://purl.org/dc/terms/source",
-          "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by"
         } ]
       }
     }, {
@@ -35614,9 +35400,6 @@
         }, {
           "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
           "val" : "http://purl.obolibrary.org/obo/bfo.owl"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Occurs_in"
         } ]
       }
     }, {
@@ -35728,15 +35511,6 @@
           "val" : "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000110"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000110s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000110ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "c-has-part_at"
         }, {
@@ -35769,15 +35543,6 @@
           "val" : "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000111"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000111s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000111ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "c-has-ppart_at"
         }, {
@@ -35839,15 +35604,6 @@
           "val" : "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000117"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000117s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000117ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "o-has-part"
         }, {
@@ -35892,15 +35648,6 @@
           "val" : "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000118"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000118s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000118ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "o-has-ppart"
         }, {
@@ -35979,15 +35726,6 @@
           "val" : "[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])"
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000132"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000132s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000132ed"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/BFO_0000179",
           "val" : "o-part-of"
         }, {
@@ -36223,19 +35961,7 @@
       "id" : "http://purl.obolibrary.org/obo/BFO_0000167",
       "lbl" : "has participant at all times",
       "type" : "PROPERTY",
-      "propertyType" : "OBJECT",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-          "val" : "BFO_0000167"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-          "val" : "BFO_0000167s"
-        }, {
-          "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-          "val" : "BFO_0000167ed"
-        } ]
-      }
+      "propertyType" : "OBJECT"
     }, {
       "id" : "http://purl.obolibrary.org/obo/BFO_0000169",
       "lbl" : "specifically depends on at some time",
@@ -36915,6 +36641,9 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
           "val" : "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/source",
+          "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204."
         } ]
       }
     }, {
@@ -37011,6 +36740,9 @@
           "val" : "The inverse property of is_specified_output_of"
         },
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
+          "val" : "has specified output"
+        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "has_specified_output"
         }, {
@@ -37056,6 +36788,9 @@
           "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."
         },
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
+          "val" : "is specified output of"
+        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "is_specified_output_of"
         }, {
@@ -37154,8 +36889,7 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "http://purl.obolibrary.org/obo/OBIB_0000732"
-        } ],
-        "deprecated" : true
+        } ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000048",
@@ -37349,17 +37083,11 @@
           "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "is concretized as"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/obi.owl"
         } ]
       }
     }, {
@@ -37369,12 +37097,9 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "definition" : {
-          "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."
+          "val" : "A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "concretizes"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "is_concretization_of"
         }, {
@@ -37383,9 +37108,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
-          "val" : "http://purl.obolibrary.org/obo/obi.owl"
         } ]
       }
     }, {
@@ -37666,9 +37388,6 @@
         }, {
           "pred" : "http://purl.org/dc/terms/source",
           "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Located_in"
         } ]
       }
     }, {
@@ -37900,7 +37619,7 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "David Osumi-Sutherland"
+          "val" : "https://orcid.org/0000-0002-7073-9172"
         } ]
       }
     }, {
@@ -37913,7 +37632,7 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "David Osumi-Sutherland"
+          "val" : "https://orcid.org/0000-0002-7073-9172"
         } ]
       }
     }, {
@@ -37946,7 +37665,7 @@
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "David Osumi-Sutherland"
+          "val" : "https://orcid.org/0000-0002-7073-9172"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "starts_at_end_of"
@@ -37975,18 +37694,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-7073-9172"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "David Osumi-Sutherland"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "ends_at_start_of"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "meets"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002575",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000063"
         } ]
       }
     }, {
@@ -38001,6 +37714,9 @@
           "val" : "RO:0002093"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
+          "val" : "https://orcid.org/0000-0002-7073-9172"
+        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "David Osumi-Sutherland"
         }, {
@@ -38075,9 +37791,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"
         }, {
           "pred" : "http://xmlns.com/foaf/0.1/page",
           "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"
@@ -38105,9 +37818,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency"
         } ]
       }
     }, {
@@ -38201,9 +37911,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "negatively regulates (process to process)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002211"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "external"
@@ -38234,9 +37941,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "positively regulates (process to process)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002211"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "external"
@@ -38293,9 +37997,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "has function in"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/"
         } ]
       }
     }, {
@@ -38332,8 +38033,7 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "http://purl.obolibrary.org/obo/RO_0002500"
-        } ],
-        "deprecated" : true
+        } ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002220",
@@ -38409,9 +38109,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
           "val" : "http://purl.obolibrary.org/obo/obi.owl"
-        }, {
-          "pred" : "http://purl.org/dc/terms/source",
-          "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"
         } ]
       }
     }, {
@@ -38430,9 +38127,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "Allen"
@@ -38457,9 +38151,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "started by"
@@ -38484,9 +38175,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.org/dc/elements/1.1/source",
           "val" : "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl"
@@ -38508,9 +38196,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "finished by"
@@ -38583,9 +38268,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "consumes"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Has_input"
         } ]
       }
     }, {
@@ -38610,9 +38292,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "produces"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Has_output"
         } ]
       }
     }, {
@@ -38628,9 +38307,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision."
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of"
         } ]
       }
     }, {
@@ -38650,9 +38326,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway."
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within"
         } ]
       }
     }, {
@@ -38691,17 +38364,7 @@
           "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q."
         },
         "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ],
-        "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002411"
-        }, {
-          "pred" : "http://purl.org/dc/terms/creator",
-          "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect"
-        } ]
+        "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002305",
@@ -38712,17 +38375,7 @@
         "definition" : {
           "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q."
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002411"
-        }, {
-          "pred" : "http://purl.org/dc/terms/creator",
-          "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect"
-        } ]
+        "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ]
       }
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002314",
@@ -38748,9 +38401,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
           "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/"
         } ]
       }
     }, {
@@ -38840,9 +38490,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized."
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Enables"
         } ]
       }
     }, {
@@ -38897,9 +38544,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "enables part of"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Involved_in"
         } ]
       }
     }, {
@@ -38915,9 +38559,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Enabled_by"
         } ]
       }
     }, {
@@ -39113,12 +38754,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "indirectly activates"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002579",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002213"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates"
         } ]
       }
     }, {
@@ -39136,12 +38771,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "indirectly inhibits"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002579",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002212"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates"
         } ]
       }
     }, {
@@ -39201,9 +38830,52 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/RO_0002413",
+      "lbl" : "provides input for",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT",
+      "meta" : {
+        "definition" : {
+          "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c."
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
+          "val" : "https://orcid.org/0000-0002-6601-2165"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
+          "val" : "directly provides input for"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
+          "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
+          "val" : "directly provides input for (process to process)"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/RO_0002414",
+      "lbl" : "transitively provides input for",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT",
+      "meta" : {
+        "definition" : {
+          "val" : "transitive form of directly_provides_input_for"
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000428"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
+          "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002575",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002411"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
+          "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
+          "val" : "transitively provides input for (process to process)"
         } ]
       }
     }, {
@@ -39274,9 +38946,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002428"
         } ]
       }
     }, {
@@ -39291,9 +38960,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002428"
         } ]
       }
     }, {
@@ -39326,7 +38992,6 @@
           "val" : "c executes activity in d if and only if c enables p and p occurs_in d.  Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.",
           "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ]
         },
-        "comments" : [ "" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "enables activity in"
@@ -39340,9 +39005,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "executes activity in"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Is_active_in"
         } ]
       }
     }, {
@@ -39371,12 +39033,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
           "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules."
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"
-        }, {
-          "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch",
-          "val" : "http://purl.obolibrary.org/obo/MI_0914"
         } ]
       }
     }, {
@@ -39397,12 +39053,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
           "val" : "molecularly binds with"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ECO_0000353"
-        }, {
-          "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch",
-          "val" : "http://purl.obolibrary.org/obo/MI_0915"
         } ]
       }
     }, {
@@ -39580,9 +39230,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000169"
         } ]
       }
     }, {
@@ -39631,12 +39278,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "https://orcid.org/0000-0002-6601-2165"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"
         } ]
       }
     }, {
@@ -39692,9 +39333,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "directly regulates (processual)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0002575",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002211"
         } ]
       }
     }, {
@@ -39812,12 +39450,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "directly positively regulates (process to process)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002578"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Directly_positively_regulates"
         } ]
       }
     }, {
@@ -39836,12 +39468,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000589",
           "val" : "directly negatively regulates (process to process)"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002578"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Directly_negatively_regulates"
         } ]
       }
     }, {
@@ -39923,17 +39549,11 @@
       "meta" : {
         "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002264"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-26T23:49:30Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"
         } ]
       }
     }, {
@@ -39944,17 +39564,11 @@
       "meta" : {
         "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002264"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-26T23:49:51Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"
         } ]
       }
     }, {
@@ -39968,17 +39582,11 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002263"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-26T23:53:14Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"
         } ]
       }
     }, {
@@ -39992,17 +39600,11 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002263"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-26T23:53:22Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"
         } ]
       }
     }, {
@@ -40012,17 +39614,11 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004050",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002418"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-03-13T23:55:05Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"
         } ]
       }
     }, {
@@ -40032,17 +39628,11 @@
       "propertyType" : "OBJECT",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0004049",
-          "val" : "http://purl.obolibrary.org/obo/RO_0002418"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "https://orcid.org/0000-0002-6601-2165"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-03-13T23:55:19Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect"
         } ]
       }
     }, {
@@ -40097,9 +39687,6 @@
         }, {
           "pred" : "http://purl.org/dc/terms/contributor",
           "val" : "https://orcid.org/0000-0002-8461-9745"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"
         } ]
       }
     }, {
@@ -40281,6 +39868,20 @@
           "val" : "https://orcid.org/0000-0002-8688-6599"
         } ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/RO_0020105",
+      "lbl" : "is anatomical entity",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT",
+      "meta" : {
+        "definition" : {
+          "val" : "This property only applies to anatomical entities."
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0001-6677-8489"
+        } ]
+      }
     }, {
       "id" : "http://purl.org/obo/owl/OBO_REL#has_disposition",
       "lbl" : "obsolete has_disposition",
@@ -40506,12 +40107,21 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "failed exploratory term"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "Terms created as placeholders with the expectation of being permanent should instead be deprecated using the \"placeholder removed\" (obo:IAO_0000226) justification."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Person:Alan Ruttenberg"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Person:Alan Ruttenberg"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40623,9 +40233,21 @@
       "lbl" : "placeholder removed",
       "type" : "INDIVIDUAL",
       "meta" : {
+        "definition" : {
+          "val" : "The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "placeholder removed"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40633,12 +40255,24 @@
       "lbl" : "terms merged",
       "type" : "INDIVIDUAL",
       "meta" : {
+        "definition" : {
+          "val" : "The term has been combined with one or more other terms to create a more encompassing (merged) term."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "terms merged"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "An editor note should explain what were the merged terms and the reason for the merge."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40646,12 +40280,24 @@
       "lbl" : "term imported",
       "type" : "INDIVIDUAL",
       "meta" : {
+        "definition" : {
+          "val" : "The term has been replaced by a term imported from another ontology."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "term imported"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40659,12 +40305,24 @@
       "lbl" : "term split",
       "type" : "INDIVIDUAL",
       "meta" : {
+        "definition" : {
+          "val" : "The term has been split into two or more new terms."
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
           "val" : "term split"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001."
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40811,6 +40469,9 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
+          "val" : "This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "http://orcid.org/0000-0001-5208-3432"
@@ -40820,6 +40481,12 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000234",
           "val" : "https://orcid.org/0000-0001-5208-3432"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0001-6875-5360"
+        }, {
+          "pred" : "http://purl.org/dc/elements/1.1/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
         } ]
       }
     }, {
@@ -40836,18 +40503,6 @@
       "meta" : {
         "comments" : [ "\"An area unit which is equal to an area enclosed by a square with sides each 1 meter long.\" [NIST:NIST]" ]
       }
-    }, {
-      "id" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://protege.stanford.edu/plugins/owl/protege#defaultLanguage",
       "type" : "PROPERTY",
@@ -40861,7 +40516,7 @@
         "comments" : [ "This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed." ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "National Library of Medicine Identifier\n"
+          "val" : "National Library of Medicine Identifier"
         } ]
       }
     }, {
@@ -41320,9 +40975,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
           "val" : "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
-          "val" : "http://purl.obolibrary.org/obo/iao.owl"
         } ]
       }
     }, {
@@ -41966,6 +41618,10 @@
           "val" : "https://orcid.org/0000-0002-8688-6599"
         } ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/OMO_0003004",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0001900",
       "lbl" : "temporal interpretation",
@@ -41976,61 +41632,14 @@
           "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"
-        }, {
           "pred" : "http://xmlns.com/foaf/0.1/page",
           "val" : "https://github.com/oborel/obo-relations/wiki/ROAndTime"
         } ]
       }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002175",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002259",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002575",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002579",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002581",
-      "lbl" : "is a defining property chain axiom",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION",
-      "meta" : {
-        "definition" : {
-          "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL"
-        }
-      }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002582",
-      "lbl" : "is a defining property chain axiom where second argument is reflexive",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION",
-      "meta" : {
-        "definition" : {
-          "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R."
-        }
-      }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0004049",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0004050",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0040042",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/STATO_0000032",
       "lbl" : "STATO alternative term",
@@ -42202,17 +41811,31 @@
       "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco",
       "lbl" : "eco subset",
       "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
-          "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/"
-        } ]
-      }
+      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#human_subset",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#mouse_subset",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim",
       "type" : "PROPERTY",
@@ -42322,10 +41945,6 @@
       "id" : "http://purl.org/dc/terms/contributor",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://purl.org/dc/terms/creator",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.org/dc/terms/description",
       "type" : "PROPERTY",
@@ -42342,10 +41961,6 @@
       "id" : "http://purl.org/dc/terms/title",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://usefulinc.com/ns/doap#bug-database",
       "type" : "PROPERTY",
@@ -42355,15 +41970,17 @@
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+      "lbl" : "created by",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#default-namespace",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+      "lbl" : "creation date",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
@@ -42393,9 +42010,21 @@
       }
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
-      "lbl" : "database_cross_reference",
+      "lbl" : "has cross-reference",
       "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
+      "propertyType" : "ANNOTATION",
+      "meta" : {
+        "definition" : {
+          "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI."
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
+          "val" : "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string"
+        }, {
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
+        } ]
+      }
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition",
       "lbl" : "has_definition",
@@ -42441,10 +42070,6 @@
           "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19"
         } ]
       }
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
       "lbl" : "has_obo_namespace",
@@ -42490,10 +42115,6 @@
       "lbl" : "shorthand",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#source",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://www.referent-tracking.com/RTS_00000001",
       "lbl" : "ontology IUI",
@@ -42533,10 +42154,6 @@
       "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
-    }, {
-      "id" : "http://www.w3.org/2004/02/skos/core#closeMatch",
-      "type" : "PROPERTY",
-      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://xmlns.com/foaf/0.1/homepage",
       "type" : "PROPERTY",
@@ -42588,6 +42205,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000007",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000594"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008",
       "pred" : "is_a",
@@ -42712,6 +42333,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032",
       "pred" : "http://purl.obolibrary.org/obo/OBI_0000312",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033",
       "pred" : "is_a",
@@ -42848,6 +42473,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000066",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000070"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000066",
+      "pred" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000067",
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000038"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000068",
       "pred" : "is_a",
@@ -42956,6 +42585,14 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000109"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089",
+      "pred" : "http://purl.obolibrary.org/obo/IAO_0000136",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000025"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090",
       "pred" : "is_a",
@@ -42984,6 +42621,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000094",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000027"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000094",
+      "pred" : "http://purl.obolibrary.org/obo/RO_0002351",
+      "obj" : "http://purl.obolibrary.org/obo/PCO_0000001"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000095",
       "pred" : "is_a",
@@ -43404,6 +43045,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000183",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000183",
+      "pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000015"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184",
       "pred" : "is_a",
@@ -43448,6 +43093,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000193",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000027"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000086"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000195",
       "pred" : "is_a",
@@ -43955,7 +43604,7 @@
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000312",
       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/GO_0032504"
+      "obj" : "http://purl.obolibrary.org/obo/GO_0048609"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000312",
       "pred" : "http://purl.obolibrary.org/obo/RO_0002218",
@@ -45380,6 +45029,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000795",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000794"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796",
       "pred" : "is_a",
@@ -45388,6 +45041,10 @@
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796",
       "pred" : "http://purl.obolibrary.org/obo/OBI_0000299",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000100"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000797",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000797",
       "pred" : "is_a",
@@ -45556,6 +45213,14 @@
       "sub" : "http://purl.obolibrary.org/obo/CHEBI_36044",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000023"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/COB_0000022",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/COB_0000035",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000015"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/DOID_0060478",
       "pred" : "is_a",
@@ -45579,7 +45244,11 @@
     }, {
       "sub" : "http://purl.obolibrary.org/obo/DRON_00000005",
       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/BFO_0000030"
+      "obj" : "http://purl.obolibrary.org/obo/DRON_00000074"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/DRON_00000074",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000040"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/ENVO_00010483",
       "pred" : "is_a",
@@ -46044,6 +45713,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000032",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000109"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IAO_0000032",
+      "pred" : "http://purl.obolibrary.org/obo/IAO_0000039",
+      "obj" : "http://www.w3.org/2002/07/owl#Thing"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000033",
       "pred" : "is_a",
@@ -46404,6 +46077,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000400",
       "pred" : "http://purl.obolibrary.org/obo/IAO_0000219",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000018"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IAO_0000400",
+      "pred" : "http://purl.obolibrary.org/obo/IAO_0000407",
+      "obj" : "http://www.w3.org/2002/07/owl#Thing"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000401",
       "pred" : "is_a",
@@ -46456,6 +46133,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000442",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000023"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IAO_0000443",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000443",
       "pred" : "is_a",
@@ -46476,6 +46157,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000445",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000310"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IAO_0000572",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000572",
       "pred" : "is_a",
@@ -46492,6 +46177,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000573",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000038"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IAO_0000574",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000574",
       "pred" : "is_a",
@@ -46540,6 +46229,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000579",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0020020"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IAO_0000580",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000580",
       "pred" : "is_a",
@@ -46860,6 +46553,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000648",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000646"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IAO_0000650",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0000650",
       "pred" : "is_a",
@@ -46920,6 +46617,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IAO_0020001",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IAO_0000030"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IAO_0020010",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0020010",
       "pred" : "is_a",
@@ -46951,7 +46652,7 @@
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0021003",
       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/OBI_0000011"
+      "obj" : "http://purl.obolibrary.org/obo/COB_0000035"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IAO_0021009",
       "pred" : "is_a",
@@ -47052,10 +46753,18 @@
       "sub" : "http://purl.obolibrary.org/obo/IDO_0000450",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000016"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IDO_0000450",
+      "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000040"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IDO_0000452",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/IDO_0000450"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IDO_0000452",
+      "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
+      "obj" : "http://purl.obolibrary.org/obo/OBI_0100026"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IDO_0000453",
       "pred" : "is_a",
@@ -47260,6 +46969,10 @@
       "sub" : "http://purl.obolibrary.org/obo/IDO_0000618",
       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000016"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/IDO_0000618",
+      "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
+      "obj" : "http://purl.obolibrary.org/obo/OBI_0100026"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IDO_0000623",
       "pred" : "is_a",
@@ -47283,7 +46996,7 @@
     }, {
       "sub" : "http://purl.obolibrary.org/obo/IDO_0000629",
       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049"
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       "pred" : "is_a",
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@@ -48248,6 +47965,10 @@
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       "pred" : "is_a",
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       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/BFO_0000040"
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+      "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
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       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048"
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000023"
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       "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
@@ -49927,13 +49628,7 @@
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       "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000068",
-      "obj" : "http://purl.obolibrary.org/obo/OBI_0000245",
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-          "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-          "val" : "09/09/2017"
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+      "obj" : "http://purl.obolibrary.org/obo/OBI_0000245"
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       "pred" : "http://purl.obolibrary.org/obo/RO_0000053",
@@ -49969,7 +49664,11 @@
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       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048"
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000023"
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+      "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002072",
+      "pred" : "http://purl.obolibrary.org/obo/RO_0000052",
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000040"
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       "sub" : "http://purl.obolibrary.org/obo/PATO_0000001",
       "pred" : "is_a",
@@ -50102,6 +49801,14 @@
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       "pred" : "is_a",
       "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/UBERON_0000071",
+      "pred" : "is_a",
+      "obj" : "http://purl.obolibrary.org/obo/UBERON_0000105"
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@@ -50113,7 +49820,7 @@
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       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/UBERON_0000480"
+      "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061"
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@@ -50129,7 +49836,7 @@
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       "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467"
+      "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465"
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@@ -50137,11 +49844,7 @@
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-      "pred" : "is_a",
-      "obj" : "http://purl.obolibrary.org/obo/UBERON_0035943"
+      "obj" : "http://purl.obolibrary.org/obo/BFO_0000035"
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@@ -50534,10 +50237,6 @@
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       "pred" : "subPropertyOf",
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       "pred" : "subPropertyOf",
@@ -50586,14 +50285,6 @@
       "sub" : "http://purl.obolibrary.org/obo/RO_0000057",
       "pred" : "subPropertyOf",
       "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty"
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-      "pred" : "subPropertyOf",
-      "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty"
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       "sub" : "http://purl.obolibrary.org/obo/RO_0000079",
       "pred" : "subPropertyOf",
@@ -50966,6 +50657,18 @@
       "sub" : "http://purl.obolibrary.org/obo/RO_0002412",
       "pred" : "subPropertyOf",
       "obj" : "http://purl.obolibrary.org/obo/RO_0002411"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/RO_0002413",
+      "pred" : "subPropertyOf",
+      "obj" : "http://purl.obolibrary.org/obo/RO_0002412"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/RO_0002413",
+      "pred" : "subPropertyOf",
+      "obj" : "http://purl.obolibrary.org/obo/RO_0002414"
+    }, {
+      "sub" : "http://purl.obolibrary.org/obo/RO_0002414",
+      "pred" : "subPropertyOf",
+      "obj" : "http://purl.obolibrary.org/obo/RO_0004047"
     }, {
       "sub" : "http://purl.obolibrary.org/obo/RO_0002418",
       "pred" : "subPropertyOf",
@@ -52006,27 +51709,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052",
         "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606"
       } ]
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-      "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ],
-      "restrictions" : [ {
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-        "fillerId" : "http://purl.obolibrary.org/obo/BFO_0000040"
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@@ -52110,7 +51792,7 @@
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-      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ],
+      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035", "http://purl.obolibrary.org/obo/OBI_0000011" ],
       "allValuesFromEdges" : [ {
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         "pred" : "http://purl.obolibrary.org/obo/OBI_0000312",
@@ -52126,18 +51808,6 @@
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         "obj" : "http://purl.obolibrary.org/obo/OBI_0000245"
@@ -52244,7 +51914,7 @@
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-      "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ]
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035", "http://purl.obolibrary.org/obo/OBI_0000011" ]
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       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ],
@@ -52323,6 +51993,10 @@
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       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ],
       "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414",
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ],
+      "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ]
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       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002434",
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ],
@@ -52391,6 +52065,9 @@
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       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ],
       "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/RO_0020105",
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000039",
       "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000003" ]
@@ -52419,18 +52096,9 @@
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       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ]
@@ -52446,9 +52114,6 @@
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       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ]
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-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ]
@@ -52482,9 +52147,6 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002596",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002211" ]
@@ -52524,6 +52186,9 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002234",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002230", "http://purl.obolibrary.org/obo/RO_0002234" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002413",
+      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002234", "http://purl.obolibrary.org/obo/RO_0002233" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002314", "http://purl.obolibrary.org/obo/BFO_0000050" ]
@@ -52536,9 +52201,6 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ]
-    }, {
-      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432",
-      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ]
@@ -52605,6 +52267,9 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ]
+    }, {
+      "predicateId" : "http://purl.obolibrary.org/obo/RO_0002418",
+      "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002418", "http://purl.obolibrary.org/obo/BFO_0000050" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211",
       "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ]
diff --git a/apollo_sv.obo b/apollo_sv.obo
index 4de3220..dde0851 100644
--- a/apollo_sv.obo
+++ b/apollo_sv.obo
@@ -1,7 +1,8 @@
 format-version: 1.2
-data-version: releases/2024-12-24
+data-version: releases/2026-03-13
 subsetdef: attribute_slim ""
 subsetdef: common_anatomy ""
+subsetdef: efo_slim ""
 subsetdef: gocheck_do_not_annotate ""
 subsetdef: goslim_agr ""
 subsetdef: goslim_candida ""
@@ -20,12 +21,19 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
+subsetdef: human_reference_atlas ""
+subsetdef: human_subset ""
+subsetdef: mouse_subset ""
 subsetdef: mpath_slim ""
+subsetdef: pheno_slim ""
 subsetdef: ro-eco ""
 subsetdef: RO:0002259 ""
 subsetdef: scalar_slim ""
+subsetdef: uberon_slim ""
 subsetdef: unit_group_slim ""
 subsetdef: upper_level ""
+subsetdef: vertebrate_core ""
+synonymtypedef: OMO:0003004 ""
 idspace: ace_lexicon http://attempto.ifi.uzh.ch/ace_lexicon# 
 idspace: dc http://purl.org/dc/elements/1.1/ 
 idspace: doap http://usefulinc.com/ns/doap# 
@@ -48,7 +56,7 @@ property_value: dc:contributor "Mike Wagner" xsd:string
 property_value: dc:contributor "Shawn T. Brown" xsd:string
 property_value: dc:contributor "William R. Hogan" xsd:string
 property_value: dc:creator "Mathias Brochhausen" xsd:string
-property_value: owl:versionInfo "2024-12-24" xsd:string
+property_value: owl:versionInfo "2026-03-13" xsd:string
 property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI
 property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string
 property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string
@@ -125,6 +133,7 @@ property_value: IAO:0000600 "A software application that provides a model of a r
 id: APOLLO_SV:00000008
 name: software development
 def: "A planned process that has specified output a software product and that involves the creation of source code." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -151,7 +160,7 @@ property_value: IAO:0000600 "An identifier that refers to all versions of a spec
 
 [Term]
 id: APOLLO_SV:00000011
-name: control strategy reactive start time information
+name: obsolete control strategy reactive start time information
 def: "A control strategy start time information item that is based on a condition that triggers the control strategy." []
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A control strategy start time information item that is based on a condition that triggers the control strategy." xsd:string
@@ -163,7 +172,7 @@ name: simulation time step value
 def: "A numeral that is part of a simulation time step action specification." []
 is_a: IAO:0000029 ! numeral
 property_value: APOLLO_SV:0000040 "numberOfUnitsOfTimeInOneSimulatorStep" xsd:string
-property_value: IAO:0000600 "A number of time step units in a time step of a simulation.  \n\nFor example, if the time step is 6 hours, then this value is 6.\n" xsd:string
+property_value: IAO:0000600 "A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6." xsd:string
 
 [Term]
 id: APOLLO_SV:00000013
@@ -188,7 +197,7 @@ def: "The action specification that specifies the number of time steps a simulat
 is_a: APOLLO_SV:00000793 ! epidemic simulator action specification
 relationship: has_part APOLLO_SV:00000068 ! simulation time step action specification
 property_value: APOLLO_SV:0000040 "runLength" xsd:string
-property_value: IAO:0000600 "The number of time steps in a simulator run.\n\nFor example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.\n" xsd:string
+property_value: IAO:0000600 "The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero." xsd:string
 
 [Term]
 id: APOLLO_SV:00000016
@@ -205,11 +214,10 @@ id: APOLLO_SV:00000017
 name: latent period duration
 def: "A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts." []
 comment: MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs
-comment: The duration of the period between when an organism becomes infected and when it becomes infectious.
 is_a: APOLLO_SV:00000243 ! duration
 property_value: APOLLO_SV:0000040 "latentPeriodDuration" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  \n\nNote that the susceptible and infected organisms can be of different species.\n\n" xsd:string
+property_value: IAO:0000600 "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species." xsd:string
 
 [Term]
 id: APOLLO_SV:00000018
@@ -239,31 +247,29 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 id: APOLLO_SV:00000022
 name: count of simulated population
 def: "The count of (simulated organisms) in a simulated population." []
-comment: MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n
+comment: MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  \n\nAny ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "The number of simulated organisms in a simulated population.  The number does not have to be an integer.  " xsd:string
+property_value: IAO:0000600 "The number of simulated organisms in a simulated population.  The number does not have to be an integer." xsd:string
 
 [Term]
 id: APOLLO_SV:00000023
 name: vaccination dose schedule
 def: "An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent." []
 is_a: APOLLO_SV:00000084 ! control strategy dose schedule
-property_value: IAO:0000600 "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. " xsd:string
+property_value: IAO:0000600 "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism." xsd:string
 
 [Term]
 id: APOLLO_SV:00000024
 name: vaccination compliance
 def: "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination." []
 comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
-comment: MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.\n
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: IAO:0000600 "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint." xsd:string
 
 [Term]
 id: APOLLO_SV:00000025
 name: vaccination efficacy
 def: "The infectious disease treatment efficacy of a vaccine." []
-comment: need to generate class restriction.  Something like:\n\n'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance'))\n\nwe'd also like to say that the protective resistance disposition began to exist during the process.  \n\ncan't recall whether we should use process or processual_entity for future BFO compatibility.
 comment: Notes: \n1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer
 is_a: APOLLO_SV:00000227 ! infectious disease treatment efficacy
 property_value: APOLLO_SV:0000040 "vaccinationEfficacies" xsd:string
@@ -283,18 +289,18 @@ comment: Motivating use case is Synthia synthetic population data.
 is_a: APOLLO_SV:00000173 ! census
 intersection_of: APOLLO_SV:00000173 ! census
 intersection_of: IAO:0000136 OMRSE:00000064 ! is about school facility
-intersection_of: OBI:0000312 APOLLO_SV:00000026 ! is_specified_output_of facility survey
-intersection_of: OBI:0000312 APOLLO_SV:00000026 {all_only="true"} ! is_specified_output_of facility survey
+intersection_of: OBI:0000312 APOLLO_SV:00000026 ! is specified output of facility survey
+intersection_of: OBI:0000312 APOLLO_SV:00000026 {all_only="true"} ! is specified output of facility survey
 relationship: IAO:0000136 OMRSE:00000064 ! is about school facility
-relationship: OBI:0000312 APOLLO_SV:00000026 ! is_specified_output_of facility survey
+relationship: OBI:0000312 APOLLO_SV:00000026 ! is specified output of facility survey
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
 id: APOLLO_SV:00000029
 name: infectious disease control strategy execution
-def: "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  " []
+def: "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease." []
 is_a: OBI:0000011 ! planned process
-property_value: IAO:0000600 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  " xsd:string
+property_value: IAO:0000600 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease." xsd:string
 
 [Term]
 id: APOLLO_SV:00000030
@@ -322,8 +328,8 @@ name: count
 def: "A measurement datum that is the output of counting." []
 is_a: IAO:0000109 ! measurement datum
 intersection_of: IAO:0000027 ! data item
-intersection_of: OBI:0000312 APOLLO_SV:00000033 ! is_specified_output_of counting
-relationship: OBI:0000312 APOLLO_SV:00000033 ! is_specified_output_of counting
+intersection_of: OBI:0000312 APOLLO_SV:00000033 ! is specified output of counting
+relationship: OBI:0000312 APOLLO_SV:00000033 ! is specified output of counting
 property_value: APOLLO_SV:0000040 "count" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A measurement datum that is the output of counting." xsd:string
@@ -332,10 +338,11 @@ property_value: IAO:0000600 "A measurement datum that is the output of counting.
 id: APOLLO_SV:00000033
 name: counting
 def: "The planned process of finding the number of elements in a finite set of objects." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 intersection_of: OBI:0000011 ! planned process
-intersection_of: OBI:0000299 APOLLO_SV:00000032 ! has_specified_output count
-relationship: OBI:0000299 APOLLO_SV:00000032 ! has_specified_output count
+intersection_of: OBI:0000299 APOLLO_SV:00000032 ! has specified output count
+relationship: OBI:0000299 APOLLO_SV:00000032 ! has specified output count
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Counting" xsd:string
 property_value: IAO:0000600 "The planned process of finding the number of elements in a finite set of objects." xsd:string
@@ -383,9 +390,9 @@ property_value: IAO:0000600 "A simulated organism in a simulated population that
 [Term]
 id: APOLLO_SV:00000041
 name: simulation of recovered organism
-def: "A simulated organism in a simulated population that is not susceptible. " []
+def: "A simulated organism in a simulated population that is not susceptible." []
 is_a: APOLLO_SV:00000034 ! simulation of organism
-property_value: IAO:0000600 "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.\n" xsd:string
+property_value: IAO:0000600 "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage." xsd:string
 
 [Term]
 id: APOLLO_SV:00000042
@@ -399,7 +406,7 @@ property_value: IAO:0000600 "The disease being simulated." xsd:string
 [Term]
 id: APOLLO_SV:00000043
 name: reproduction number
-def: "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. " []
+def: "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection." []
 property_value: APOLLO_SV:0000040 "ReproductionNumber" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "The number of susceptible organisms that each infected organism infects.  ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation." xsd:string
@@ -446,24 +453,23 @@ property_value: IAO:0000600 "The degree to which a particular antiviral drug red
 [Term]
 id: APOLLO_SV:00000049
 name: antiviral efficacy delay
-def: "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. " []
+def: "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role." []
 is_a: APOLLO_SV:00000243 ! duration
-property_value: IAO:0000600 "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. " xsd:string
+property_value: IAO:0000600 "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection." xsd:string
 
 [Term]
 id: APOLLO_SV:00000050
 name: antiviral compliance
 def: "The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible." []
 comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
-comment: MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2.  If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: APOLLO_SV:0000040 "antiviral cm compliance" xsd:string
-property_value: IAO:0000600 "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. " xsd:string
+property_value: IAO:0000600 "The fraction of individuals in a simulated population that will accept antiviral treatment if offered." xsd:string
 
 [Term]
 id: APOLLO_SV:00000051
 name: antiviral supply schedule
-def: "An action specification giving the number of doses of an antiviral to be made available during a specific time interval. " []
+def: "An action specification giving the number of doses of an antiviral to be made available during a specific time interval." []
 is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
 property_value: IAO:0000600 "Counts of antiviral doses that become available in a specific location per time step unit." xsd:string
 
@@ -479,7 +485,6 @@ id: APOLLO_SV:00000053
 name: simulation of organism awaiting control measure
 def: "A simulated organism that is assumed “eligible, willing and able” to participate with a particular control measure." []
 comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
-comment: This class will need more ontological reasoning, since the "willing" part of the definition is not representable in BFO to date.
 is_a: APOLLO_SV:00000034 ! simulation of organism
 disjoint_from: APOLLO_SV:00000058 ! simulation of organism not awaiting control measure
 property_value: IAO:0000600 "A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure." xsd:string
@@ -519,7 +524,6 @@ id: APOLLO_SV:00000058
 name: simulation of organism not awaiting control measure
 def: "A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular control measure." []
 comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
-comment: This class will need more ontological reasoning, since the "unwilling" part of the definition is not representable in BFO to date.
 property_value: IAO:0000600 "A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure." xsd:string
 
 [Term]
@@ -532,8 +536,8 @@ property_value: IAO:0000600 "This concept represents a simulated organism that h
 [Term]
 id: APOLLO_SV:00000060
 name: simulation of antiviral control measure
-def: "The simulation of an antiviral control measure. " []
-comment: MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.\n
+def: "The simulation of an antiviral control measure." []
+comment: MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.
 is_a: APOLLO_SV:00000070 ! simulation
 property_value: APOLLO_SV:0000040 "antiviral control measure" xsd:string
 property_value: IAO:0000600 "A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism." xsd:string
@@ -563,7 +567,7 @@ property_value: IAO:0000600 "A simulated organism in a simulated population has
 id: APOLLO_SV:00000064
 name: simulation time series
 def: "A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation." []
-comment: MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.\n
+comment: MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.
 is_a: IAO:0000584 ! time sampled measurement data set
 property_value: IAO:0000600 "A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation." xsd:string
 
@@ -575,7 +579,7 @@ comment: Class was originally created to correspond with an element from Apollo
 is_a: IAO:0000029 ! numeral
 intersection_of: IAO:0000029 ! numeral
 intersection_of: IAO:0000219 APOLLO_SV:00000005 ! denotes simulating of process of type X
-intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output_of identifier creating process
+intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is specified output of identifier creating process
 relationship: IAO:0000219 APOLLO_SV:00000005 ! denotes simulating of process of type X
 property_value: IAO:0000600 "The run id indexes a run of a specific simulator version on a specific simulated population, disease(s), and optionally control measures.  The simulator is responsible for generating a run id and ensuring its uniqueness." xsd:string
 
@@ -584,6 +588,7 @@ id: APOLLO_SV:00000066
 name: simulation of time step
 def: "A purely intentional entity that simulates a temporal interval of pre-specified length." []
 is_a: APOLLO_SV:00000070 ! simulation
+relationship: APOLLO_SV:00000067 BFO:0000038 ! simulates one-dimensional temporal region
 property_value: APOLLO_SV:0000040 "simulation time step" xsd:string
 property_value: IAO:0000600 "A purely intentional entity that simulates a temporal interval of pre-specified length." xsd:string
 
@@ -606,7 +611,7 @@ def: "A numeral that indexes a specific time step of a simulation." []
 is_a: IAO:0000029 ! numeral
 intersection_of: IAO:0000029 ! numeral
 intersection_of: IAO:0000219 APOLLO_SV:00000066 ! denotes simulation of time step
-intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output_of identifier creating process
+intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is specified output of identifier creating process
 relationship: IAO:0000219 APOLLO_SV:00000066 ! denotes simulation of time step
 property_value: APOLLO_SV:0000040 "simulatorTime" xsd:string
 property_value: IAO:0000600 "The time step number of a simulation." xsd:string
@@ -614,13 +619,13 @@ property_value: IAO:0000600 "The time step number of a simulation." xsd:string
 [Term]
 id: APOLLO_SV:00000070
 name: simulation
-def: "A purely intentional entity that simulates an entity and its properties.\n\n" []
+def: "A purely intentional entity that simulates an entity and its properties." []
 is_a: APOLLO_SV:00000000 ! purely intentional entity
 intersection_of: APOLLO_SV:00000000 ! purely intentional entity
 intersection_of: APOLLO_SV:00000067 BFO:0000001 ! simulates entity
 relationship: APOLLO_SV:00000067 BFO:0000001 ! simulates entity
 property_value: APOLLO_SV:0000040 "simulation" xsd:string
-property_value: IAO:0000600 "A purely intentional entity that simulates an entity and its properties.\n\n" xsd:string
+property_value: IAO:0000600 "A purely intentional entity that simulates an entity and its properties." xsd:string
 
 [Term]
 id: APOLLO_SV:00000071
@@ -665,7 +670,7 @@ property_value: IAO:0000600 "an objective of achieving satisfactory control of e
 
 [Term]
 id: APOLLO_SV:00000076
-name: μ
+name: obsolete μ
 is_a: oboInOwl:ObsoleteClass ! Obsolete Class
 property_value: APOLLO_SV:0000040 "μ" xsd:string
 property_value: IAO:0000600 "the mean or expectation of a distribution" xsd:string
@@ -673,7 +678,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000077
-name: σ
+name: obsolete σ
 is_a: oboInOwl:ObsoleteClass ! Obsolete Class
 property_value: APOLLO_SV:0000040 "sigma" xsd:string
 property_value: IAO:0000600 "standard deviation" xsd:string
@@ -688,7 +693,7 @@ property_value: IAO:0000600 "A continuous probability distribution whose charact
 
 [Term]
 id: APOLLO_SV:00000079
-name: deprecated log normal distribution
+name: obsolete log normal distribution
 is_a: oboInOwl:ObsoleteClass ! Obsolete Class
 property_value: IAO:0000600 "a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm" xsd:string
 is_obsolete: true
@@ -727,7 +732,7 @@ name: control strategy dose schedule
 def: "An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism." []
 is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
 relationship: part_of APOLLO_SV:00000086 ! infectious disease control strategy
-property_value: IAO:0000600 "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. " xsd:string
+property_value: IAO:0000600 "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism." xsd:string
 
 [Term]
 id: APOLLO_SV:00000085
@@ -767,8 +772,9 @@ property_value: IAO:0000600 "The count of individuals in an exposed population (
 id: APOLLO_SV:00000089
 name: measured vaccination efficacy
 def: "A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study." []
-comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.\n
+comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.
 is_a: IAO:0000109 ! measurement datum
+relationship: IAO:0000136 APOLLO_SV:00000025 ! is about vaccination efficacy
 property_value: APOLLO_SV:0000040 "VaccinationEfficacyMeasured" xsd:string
 property_value: IAO:0000600 "A vaccination efficacy that results from a vaccination efficacy study." xsd:string
 
@@ -776,12 +782,13 @@ property_value: IAO:0000600 "A vaccination efficacy that results from a vaccinat
 id: APOLLO_SV:00000090
 name: vaccination efficacy study design execution
 def: "a study design execution that has as its specified output one or more measured vaccination efficacy data items" []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000471 ! study design execution
 intersection_of: OBI:0000471 ! study design execution
 intersection_of: has_part APOLLO_SV:00000142 ! vaccination
-intersection_of: OBI:0000299 APOLLO_SV:00000089 ! has_specified_output measured vaccination efficacy
+intersection_of: OBI:0000299 APOLLO_SV:00000089 ! has specified output measured vaccination efficacy
 relationship: has_part APOLLO_SV:00000142 ! vaccination
-relationship: OBI:0000299 APOLLO_SV:00000089 ! has_specified_output measured vaccination efficacy
+relationship: OBI:0000299 APOLLO_SV:00000089 ! has specified output measured vaccination efficacy
 property_value: APOLLO_SV:0000040 "VaccinationEfficacyStudy" xsd:string
 property_value: IAO:0000600 "an experiment that measures vaccination efficacy from a sample of vaccinated and possibly unvaccinated individuals" xsd:string
 
@@ -811,14 +818,15 @@ property_value: IAO:0000600 "a type of interval estimate of a population paramet
 id: APOLLO_SV:00000094
 name: community
 def: "Two or more distinct populations that are part of the same biotic ecosystem." []
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
+relationship: RO:0002351 PCO:0000001 ! has member population
 property_value: APOLLO_SV:0000040 "community" xsd:string
 property_value: dc:creator "William R. Hogan" xsd:string
 property_value: IAO:0000600 "Two or more distinct populations that are part of the same biotic ecosystem." xsd:string
 
 [Term]
 id: APOLLO_SV:00000095
-name: deprecated discrete probability distribution
+name: obsolete discrete probability distribution
 is_a: oboInOwl:ObsoleteClass ! Obsolete Class
 property_value: APOLLO_SV:0000040 "discrete probability distribution" xsd:string
 property_value: IAO:0000600 "a probability distribution over a discrete random variable" xsd:string
@@ -833,11 +841,11 @@ is_obsolete: true
 [Term]
 id: APOLLO_SV:00000097
 name: ecosystem
-def: "The sum of all biotic and abiotic entities in a geographical region. " []
+def: "The sum of all biotic and abiotic entities in a geographical region." []
 is_a: BFO:0000040 ! material entity
 property_value: APOLLO_SV:0000040 "Ecosystem" xsd:string
 property_value: dc:creator "William R. Hogan" xsd:string
-property_value: IAO:0000600 "The sum of all biotic and abiotic entities in a geographical region. " xsd:string
+property_value: IAO:0000600 "The sum of all biotic and abiotic entities in a geographical region." xsd:string
 
 [Term]
 id: APOLLO_SV:00000098
@@ -912,8 +920,7 @@ id: APOLLO_SV:00000107
 name: atmosphere
 def: "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force" []
 comment: atmosphere of Earth, Earth's moon, Saturn, Titan, etc.
-comment: outer, gaseous layers of exoplanets are called extraterrestrial atmosphere.
-is_a: BFO:0000024 ! fiat object part
+is_a: BFO:0000024 ! fiat object
 property_value: dc:creator "William R. Hogan" xsd:string
 property_value: IAO:0000600 "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force" xsd:string
 
@@ -975,14 +982,13 @@ property_value: IAO:0000600 "A process of reproduction of a particular pathogen
 [Term]
 id: APOLLO_SV:00000115
 name: infection acquisition
-def: "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources" []
-comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing. \n
-comment: Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing
+def: "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources." []
+comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   \nAn infection is acquired from an infectious organism or a contaminated thing.
 is_a: GO:0044409 ! entry into host
 relationship: RO:0002411 APOLLO_SV:00000114 ! causally upstream of infection
 property_value: APOLLO_SV:0000040 "InfectionAcquisition" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000600 "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species.\n\n" xsd:string
+property_value: IAO:0000600 "A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  \n\nNote that the susceptible and infectious organisms can be of different species." xsd:string
 
 [Term]
 id: APOLLO_SV:00000117
@@ -1047,7 +1053,7 @@ property_value: IAO:0000600 "The number of time steps that a school closure cont
 
 [Term]
 id: APOLLO_SV:00000125
-name: school calendar
+name: obsolete school calendar
 property_value: IAO:0000600 "The time steps that a school will be in session." xsd:string
 is_obsolete: true
 
@@ -1094,7 +1100,7 @@ name: reactive control strategy threshold
 def: "A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy." []
 is_a: IAO:0000027 ! data item
 property_value: APOLLO_SV:0000040 "reactiveControlMeasureThreshold" xsd:string
-property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc.\n" xsd:string
+property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc." xsd:string
 
 [Term]
 id: APOLLO_SV:00000132
@@ -1137,7 +1143,7 @@ id: APOLLO_SV:00000137
 name: vaccine valence
 is_a: APOLLO_SV:00000032 ! count
 property_value: APOLLO_SV:0000040 "valence" xsd:string
-property_value: IAO:0000600 "the number of distinct antigenic strains in a vaccine product " xsd:string
+property_value: IAO:0000600 "The number of distinct antigenic strains in a vaccine product." xsd:string
 
 [Term]
 id: APOLLO_SV:00000138
@@ -1151,7 +1157,6 @@ id: APOLLO_SV:00000139
 name: control strategy compliance
 def: "A measurement datum about the fraction of individuals in a population that elect to participate in a control strategy when offered." []
 comment: the class restriction can be made more precise AH
-comment: the fraction of some population that is targeted for a control strategy that accepts it.  It can obviously also be interpreted as a probability that the average individual in the targeted population accepts/complies with the control strategy.  It is not simulated
 property_value: APOLLO_SV:0000040 "compliance" xsd:string
 property_value: IAO:0000600 "A fraction of eligible individuals in a population who receive an intervention or participate in a control strategy." xsd:string
 
@@ -1181,7 +1186,7 @@ property_value: IAO:0000600 "A treatment of an individual with antigenic materia
 
 [Term]
 id: APOLLO_SV:00000143
-name: vaccine disposition
+name: obsolete vaccine disposition
 comment: replaced with VO 'vaccine function'
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_obsolete: true
@@ -1192,7 +1197,7 @@ name: disposition to become contaminated with a pathogen
 is_a: BFO:0000016 ! disposition
 intersection_of: BFO:0000016 ! disposition
 intersection_of: BFO:0000054 APOLLO_SV:00000167 {all_some="true", all_only="true"} ! is realized by contamination acquisition
-relationship: RO:0000052 BFO:0000040 ! inheres in material entity
+relationship: RO:0000052 BFO:0000040 ! characteristic of material entity
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -1207,7 +1212,7 @@ property_value: IAO:0000600 "The dispostion of an organism of a particular biolo
 
 [Term]
 id: APOLLO_SV:00000146
-name: beta
+name: obsolete beta
 comment: it is the same thing as transmission coefficient
 property_value: IAO:0000600 "Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons." xsd:string
 is_obsolete: true
@@ -1221,7 +1226,7 @@ property_value: IAO:0000600 "Transmission parameter" xsd:string
 
 [Term]
 id: APOLLO_SV:00000148
-name: random number seed
+name: obsolete random number seed
 property_value: IAO:0000600 "random number seed" xsd:string
 is_obsolete: true
 
@@ -1261,10 +1266,10 @@ def: "A census that is the outcome of a population survey." []
 is_a: APOLLO_SV:00000173 ! census
 intersection_of: APOLLO_SV:00000173 ! census
 intersection_of: IAO:0000136 PCO:0000001 ! is about population
-intersection_of: OBI:0000312 APOLLO_SV:00000152 ! is_specified_output_of population survey
-intersection_of: OBI:0000312 APOLLO_SV:00000152 {all_only="true"} ! is_specified_output_of population survey
+intersection_of: OBI:0000312 APOLLO_SV:00000152 ! is specified output of population survey
+intersection_of: OBI:0000312 APOLLO_SV:00000152 {all_only="true"} ! is specified output of population survey
 relationship: IAO:0000136 PCO:0000001 ! is about population
-relationship: OBI:0000312 APOLLO_SV:00000152 ! is_specified_output_of population survey
+relationship: OBI:0000312 APOLLO_SV:00000152 ! is specified output of population survey
 property_value: IAO:0000600 "A census that is the outcome of a population survey." xsd:string
 
 [Term]
@@ -1280,7 +1285,6 @@ id: APOLLO_SV:00000155
 name: population infection survey
 def: "A population survey that counts the number of individuals in the population who are infected with a particular pathogen." []
 comment: Comment from Mike (to do!):\nI checked because an infection and immunity census would involve two different census methods.   One would be some kind of disease surveillance that counts infections.  The other is some kind of immunity census process based on seroprevalence studies or vaccination registries.
-comment: Equivalent class was:\n'population survey' and (has_part some \n(counting and (has_specified_output some \n(count and ('is about' some 'exposed population'))) and (has_specified_output some \n(count and ('is about' some 'infectious population'))) and (has_specified_output some \n(count and ('is about' some 'susceptible population'))) and (has_specified_output some \n(count and ('is about' some 'immune population')))))
 is_a: APOLLO_SV:00000152 ! population survey
 property_value: APOLLO_SV:0000040 "PopulationInfectionSurvey" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1299,10 +1303,10 @@ name: population infection and immunity census
 def: "A census that is the result of a population infection survey and a population immunity survey." []
 is_a: APOLLO_SV:00000173 ! census
 intersection_of: APOLLO_SV:00000173 ! census
-intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true"} ! is_specified_output_of population infection survey
-intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true", all_only="true"} ! is_specified_output_of population infection survey
-relationship: OBI:0000312 APOLLO_SV:00000003 ! is_specified_output_of population immunity survey
-relationship: OBI:0000312 APOLLO_SV:00000155 ! is_specified_output_of population infection survey
+intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true"} ! is specified output of population infection survey
+intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true", all_only="true"} ! is specified output of population infection survey
+relationship: OBI:0000312 APOLLO_SV:00000003 ! is specified output of population immunity survey
+relationship: OBI:0000312 APOLLO_SV:00000155 ! is specified output of population infection survey
 property_value: APOLLO_SV:0000040 "PopulationInfectionAndImmunityCensus" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "PII Census" xsd:string
@@ -1319,9 +1323,9 @@ name: population demographic census
 def: "A census that is the specific outcome of a population demographic survey." []
 is_a: APOLLO_SV:00000173 ! census
 intersection_of: APOLLO_SV:00000173 ! census
-intersection_of: OBI:0000312 APOLLO_SV:00000158 ! is_specified_output_of population demographic survey
-intersection_of: OBI:0000312 APOLLO_SV:00000158 {all_only="true"} ! is_specified_output_of population demographic survey
-relationship: OBI:0000312 APOLLO_SV:00000158 ! is_specified_output_of population demographic survey
+intersection_of: OBI:0000312 APOLLO_SV:00000158 ! is specified output of population demographic survey
+intersection_of: OBI:0000312 APOLLO_SV:00000158 {all_only="true"} ! is specified output of population demographic survey
+relationship: OBI:0000312 APOLLO_SV:00000158 ! is specified output of population demographic survey
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A census that is the specific outcome of a population demographic survey." xsd:string
 
@@ -1334,7 +1338,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000161
-name: MIDAS scenario
+name: obsolete MIDAS scenario
 def: "An ecosystem in which a population of hosts is undergoing at least one infection." []
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "An ecosystem in which a population of hosts is undergoing at least one infection." xsd:string
@@ -1381,7 +1385,7 @@ property_value: IAO:0000600 "A census that is the specified output of a agent-le
 id: APOLLO_SV:00000166
 name: contaminated thing
 def: "An independent continuant that is the localization of a pathogen, but is not undergoing an infection." []
-comment: A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    
+comment: A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.
 is_a: BFO:0000004 ! independent continuant
 property_value: APOLLO_SV:0000040 "ContaminatedThing" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1526,6 +1530,7 @@ name: simulator time specification
 def: "An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps)." []
 is_a: APOLLO_SV:00000793 ! epidemic simulator action specification
 relationship: has_part APOLLO_SV:00000015 ! simulation run length
+relationship: has_part APOLLO_SV:00000015 ! simulation run length
 relationship: has_part APOLLO_SV:00000068 ! simulation time step action specification
 property_value: APOLLO_SV:0000040 "SimulatorTimeSpecification" xsd:string
 property_value: IAO:0000600 "An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps)." xsd:string
@@ -1554,7 +1559,7 @@ id: APOLLO_SV:00000186
 name: contamination
 def: "The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism." []
 comment: the preferred term is biological contamination to distinguish from things like radiological contamination, contamination of the Gulf of Mexico with oil, the contamination of air with pollution, etc.
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: APOLLO_SV:0000040 "Contamination" xsd:string
 property_value: IAO:0000111 "biological contamination" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -1573,7 +1578,6 @@ id: APOLLO_SV:00000188
 name: population and environment census
 def: "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero." []
 comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.
-comment: This census should exclude infection, immunity, treatment, or contamination.  
 is_a: APOLLO_SV:00000173 ! census
 property_value: IAO:0000600 "A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero." xsd:string
 
@@ -1590,8 +1594,8 @@ name: contagious organism
 def: "A host who is able to transmit some infection to another organism." []
 is_a: APOLLO_SV:00000238 ! host organism
 intersection_of: APOLLO_SV:00000238 ! host organism
-intersection_of: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness
-relationship: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness
+intersection_of: RO:0000053 APOLLO_SV:00000182 ! bearer of contagiousness
+relationship: RO:0000053 APOLLO_SV:00000182 ! bearer of contagiousness
 property_value: APOLLO_SV:0000040 "infectious" xsd:string
 property_value: IAO:0000600 "An infected organism of a particular species who is able to transmit the infection to a susceptible organism of a particular species.\n\nNote that the infected and susceptible organisms may be of different species." xsd:string
 
@@ -1622,6 +1626,7 @@ property_value: IAO:0000600 "A data item inferring a vaccination efficacy based
 id: APOLLO_SV:00000194
 name: individual treatment control strategy
 def: "An infectious disease control strategy that immediately targets individuals." []
+is_a: APOLLO_SV:00000086 ! infectious disease control strategy
 property_value: APOLLO_SV:0000040 "IndividualTreatmentControlMeasure" xsd:string
 property_value: IAO:0000112 "vaccination control strategy, antiviral control strategy" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -1643,18 +1648,18 @@ is_a: APOLLO_SV:00000136 ! vaccination control strategy
 [Term]
 id: APOLLO_SV:00000197
 name: agent level population and environment census
-comment: An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. 
+comment: An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved.
 is_a: APOLLO_SV:00000188 ! population and environment census
 
 [Term]
 id: APOLLO_SV:00000198
-name: agent model ecosystem census description
+name: obsolete agent model ecosystem census description
 comment: At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics.
 is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000199
-name: compartment model population and environment census
+name: obsolete compartment model population and environment census
 comment: The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census).
 is_obsolete: true
 
@@ -1675,7 +1680,7 @@ property_value: IAO:0000600 "A census about contaminated things of a given type
 [Term]
 id: APOLLO_SV:00000202
 name: indexable Apollo item
-comment: A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. 
+comment: A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved.
 is_a: IAO:0000030 ! information content entity
 property_value: APOLLO_SV:0000040 "ApolloIndexableItem" xsd:string
 
@@ -1703,8 +1708,8 @@ name: susceptible organism
 def: "An organism that is the bearer of a susceptibility disposition." []
 is_a: OBI:0100026 ! organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000172 ! is bearer of susceptibility
-relationship: RO:0000053 APOLLO_SV:00000172 ! is bearer of susceptibility
+intersection_of: RO:0000053 APOLLO_SV:00000172 ! bearer of susceptibility
+relationship: RO:0000053 APOLLO_SV:00000172 ! bearer of susceptibility
 property_value: APOLLO_SV:0000040 "susceptible" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism of a particular species that can undergo infection with a particular pathogen." xsd:string
@@ -1715,8 +1720,8 @@ name: immune organism
 def: "An organism that is the bearer of an immune resistance disposition." []
 is_a: APOLLO_SV:00000207 ! resistant organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000151 ! is bearer of immune resistance to infection
-relationship: RO:0000053 APOLLO_SV:00000151 ! is bearer of immune resistance to infection
+intersection_of: RO:0000053 APOLLO_SV:00000151 ! bearer of immune resistance to infection
+relationship: RO:0000053 APOLLO_SV:00000151 ! bearer of immune resistance to infection
 property_value: APOLLO_SV:0000040 "immune" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species." xsd:string
@@ -1727,8 +1732,8 @@ name: resistant organism
 def: "an organism that is the bearer of resistance to infection" []
 is_a: OBI:0100026 ! organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000145 ! is bearer of resistance to infection
-relationship: RO:0000053 APOLLO_SV:00000145 ! is bearer of resistance to infection
+intersection_of: RO:0000053 APOLLO_SV:00000145 ! bearer of resistance to infection
+relationship: RO:0000053 APOLLO_SV:00000145 ! bearer of resistance to infection
 property_value: APOLLO_SV:0000040 "resistant" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism of a particular species that is unable to undergo infection with a particular pathogen." xsd:string
@@ -1797,11 +1802,11 @@ property_value: IAO:0000600 "An information content entity that specifies the va
 [Term]
 id: APOLLO_SV:00000215
 name: probability distribution
-def: "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. " []
+def: "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference." []
 is_a: IAO:0000030 ! information content entity
 property_value: APOLLO_SV:0000040 "ProbabilityDistribution" xsd:string
 property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Probability_distribution" xsd:string
-property_value: IAO:0000600 "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. " xsd:string
+property_value: IAO:0000600 "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference." xsd:string
 
 [Term]
 id: APOLLO_SV:00000216
@@ -1988,8 +1993,8 @@ name: pathogen
 def: "An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon." []
 is_a: OBI:0100026 ! organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000404 ! is bearer of infectiousness
-relationship: RO:0000053 APOLLO_SV:00000404 ! is bearer of infectiousness
+intersection_of: RO:0000053 APOLLO_SV:00000404 ! bearer of infectiousness
+relationship: RO:0000053 APOLLO_SV:00000404 ! bearer of infectiousness
 property_value: APOLLO_SV:0000040 "pathogen" xsd:string
 property_value: IAO:0000600 "An organism, virus, or prion that can infect another organism." xsd:string
 
@@ -2055,7 +2060,6 @@ id: APOLLO_SV:00000244
 name: disease unique identifier
 def: "a unique identifier that refers to a disease." []
 comment: This class is different from its superclass, in that the identifier is non-redundant with other identifiers in its context (such as a coding system or terminology or ontology).  The superclass admits of natural langugage names of diseases, whereas this one typically does not.
-comment: We still need to decide which coding schema to adopt.-MB
 is_a: APOLLO_SV:00000598 ! disease identifier
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "A unique identifier that refers to a particular type of disease." xsd:string
@@ -2097,7 +2101,7 @@ is_obsolete: true
 
 [Term]
 id: APOLLO_SV:00000249
-name: nonparametric probability distribution
+name: obsolete nonparametric probability distribution
 property_value: APOLLO_SV:0000040 "NonparametricProbabilityDistribution" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_obsolete: true
@@ -2227,7 +2231,7 @@ id: APOLLO_SV:00000264
 name: infection acquisition from contaminated thing
 def: "An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing." []
 is_a: APOLLO_SV:00000115 ! infection acquisition
-relationship: RO:0000057 APOLLO_SV:00000166 ! has_participant contaminated thing
+relationship: RO:0000057 APOLLO_SV:00000166 ! has participant contaminated thing
 property_value: APOLLO_SV:0000040 "InfectionAcquisitionFromContaminatedAbioticThing" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An infection acquisition from a contaminated thing." xsd:string
@@ -2239,7 +2243,7 @@ def: "An infection acquisition whereby a susceptible host acquires an infection
 is_a: APOLLO_SV:00000115 ! infection acquisition
 property_value: APOLLO_SV:0000040 "InfectionAcquisitionFromInfectedHost" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious.\n" xsd:string
+property_value: IAO:0000600 "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious." xsd:string
 
 [Term]
 id: APOLLO_SV:00000266
@@ -2267,7 +2271,7 @@ def: "An identifier that designates a scale according to which time is measured
 is_a: IAO:0020000 ! identifier
 property_value: APOLLO_SV:0000040 "timeScale" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated.\n" xsd:string
+property_value: IAO:0000600 "A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.\n\nIn epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated." xsd:string
 
 [Term]
 id: APOLLO_SV:00000269
@@ -2463,7 +2467,7 @@ def: "The unit of measure for the supply schedule of an individual treatment." [
 is_a: UO:0000000 ! unit
 property_value: APOLLO_SV:0000040 "supplyScheduleUnits" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'.\n" xsd:string
+property_value: IAO:0000600 "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'." xsd:string
 
 [Term]
 id: APOLLO_SV:00000293
@@ -2496,7 +2500,7 @@ def: "An information content entity that specifies the criteria that an organism
 is_a: IAO:0000030 ! information content entity
 property_value: APOLLO_SV:0000040 "CaseDefinition" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000600 "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.\n" xsd:string
+property_value: IAO:0000600 "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on." xsd:string
 
 [Term]
 id: APOLLO_SV:00000297
@@ -2548,8 +2552,8 @@ name: recovered organism
 def: "An organism that is the bearer of a naturally-acquired, active immune resistance to infection." []
 is_a: APOLLO_SV:00000206 ! immune organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000301 ! is bearer of naturally-acquired active immune resistance
-relationship: RO:0000053 APOLLO_SV:00000301 ! is bearer of naturally-acquired active immune resistance
+intersection_of: RO:0000053 APOLLO_SV:00000301 ! bearer of naturally-acquired active immune resistance
+relationship: RO:0000053 APOLLO_SV:00000301 ! bearer of naturally-acquired active immune resistance
 property_value: APOLLO_SV:0000040 "recovered" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism that has recovered from infection with a particular pathogen, is no longer infectious to other organisms of any species, and is not able to be infected again with that pathogen." xsd:string
@@ -2638,10 +2642,10 @@ id: APOLLO_SV:00000312
 name: individual mosquito reproduction
 def: "A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157)" []
 is_a: APOLLO_SV:00000651 ! reproduction
-is_a: GO:0032504 ! obsolete multicellular organism reproduction
+is_a: GO:0048609 ! multicellular organismal reproductive process
 intersection_of: APOLLO_SV:00000651 ! reproduction
-intersection_of: RO:0002218 NCBITaxon:7157 ! has active participant Culicidae
-relationship: RO:0002218 NCBITaxon:7157 ! has active participant Culicidae
+intersection_of: RO:0002218 NCBITaxon:7157 ! obsolete has active participant Culicidae
+relationship: RO:0002218 NCBITaxon:7157 ! obsolete has active participant Culicidae
 property_value: APOLLO_SV:0000040 "MosquitoReproduction" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "Reproduction of a single mosquito" xsd:string
@@ -2660,7 +2664,7 @@ property_value: IAO:0000600 "The duration of the gonotrophic cycle in a female m
 id: APOLLO_SV:00000314
 name: gonotrophic cycle
 def: "The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition)." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition)." xsd:string
 
@@ -2696,8 +2700,8 @@ name: drug treatment
 def: "A treatment with a drug product." []
 is_a: OGMS:0000090 ! treatment
 intersection_of: OGMS:0000090 ! treatment
-intersection_of: OBI:0000293 DRON:00000005 ! has_specified_input drug product
-relationship: OBI:0000293 DRON:00000005 ! has_specified_input drug product
+intersection_of: OBI:0000293 DRON:00000005 ! has_specified_input clinical drug product
+relationship: OBI:0000293 DRON:00000005 ! has_specified_input clinical drug product
 property_value: APOLLO_SV:0000040 "DrugTreatment" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "Treatment with a drug." xsd:string
@@ -2803,7 +2807,6 @@ id: APOLLO_SV:00000335
 name: chemical resistance to infection
 def: "A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism." []
 comment: As with all dispositions, chemical resistance need not be realized to exist.  The presence of cholorquine confers this disposition even if the person is never bitten by a mosquito, let alone a malaria-laden mosquito.
-comment: Examples: chemoprophylaxis of malaria with chloroquine, treatment of infections with antibiotics, antiviral treatment
 property_value: IAO:0000111 "chemical resistance to infection" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "chemoprotection" xsd:string
@@ -3177,7 +3180,7 @@ property_value: IAO:0000600 "An endosymbiotic mutualism that realizes a biologic
 
 [Term]
 id: APOLLO_SV:00000370
-name: deprecated homeostasis
+name: obsolete homeostasis
 def: "A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3442,7 +3445,7 @@ property_value: IAO:0000600 "A data set whose data items are about a host and it
 
 [Term]
 id: APOLLO_SV:00000399
-name: deprecated infection case count
+name: obsolete infection case count
 def: "A count of individuals in a population who meet an infection case definition during a particular time interval." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3484,7 +3487,6 @@ id: APOLLO_SV:00000403
 name: transmission tree
 def: "A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host." []
 comment: Because a set A is a subset of itself, we capture the possibility that all infected organisms in the epidemic are represented in the tree.
-comment: This definition allows for multiple trees in an epidemic because we did not require that the first case infected temporally be the index case, although the ideal situation is that there is one tree for the epidemic that includes the index case.
 is_a: OBI:0000658 ! data representational model
 property_value: APOLLO_SV:0000040 "TransmissionTree" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
@@ -3499,8 +3501,8 @@ comment: The disposition of Influenza A virus H3N2 subtype to infect human being
 is_a: BFO:0000016 ! disposition
 intersection_of: BFO:0000016 ! disposition
 intersection_of: BFO:0000054 APOLLO_SV:00000114 {all_only="true"} ! is realized by infection
-intersection_of: RO:0000052 OBI:0100026 ! inheres in organism
-relationship: RO:0000052 OBI:0100026 ! inheres in organism
+intersection_of: RO:0000052 OBI:0100026 ! characteristic of organism
+relationship: RO:0000052 OBI:0100026 ! characteristic of organism
 property_value: IAO:0000111 "infectious disposition" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "A disposition inhering in an organism of a particular biological taxon that is realized only by the organism participating in an infection as the reproducing organism inside another organism of a different particular biological taxon." xsd:string
@@ -3509,7 +3511,7 @@ property_value: IAO:0000600 "A disposition inhering in an organism of a particul
 id: APOLLO_SV:00000405
 name: potentially infectious contacting
 def: "A biological process that brings the organism into sufficiently close physical proximity to a pathogen population, either in or on a contaminated thing or an infectious host, such that the organism is likely but not certain to acquire an infection with the pathogen." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000111 "potentially infectious contact process" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "potentially infectious contact" xsd:string
@@ -3536,8 +3538,8 @@ name: contacted organism
 def: "An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process." []
 is_a: OBI:0100026 ! organism
 intersection_of: OBI:0100026 ! organism
-intersection_of: RO:0000053 APOLLO_SV:00000406 ! is bearer of potentially infectious contact role
-relationship: RO:0000053 APOLLO_SV:00000406 ! is bearer of potentially infectious contact role
+intersection_of: RO:0000053 APOLLO_SV:00000406 ! bearer of potentially infectious contact role
+relationship: RO:0000053 APOLLO_SV:00000406 ! bearer of potentially infectious contact role
 property_value: IAO:0000111 "potentially infectious contact organism" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "An organism that has been exposed to a pathogen by coming into close physical proximity with either an infectious host or a contaminated thing." xsd:string
@@ -3741,7 +3743,7 @@ property_value: IAO:0000600 "An epidemic simulator action specification that whe
 id: APOLLO_SV:00000428
 name: disease outcome with probability
 def: "A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism." []
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: APOLLO_SV:0000040 "DiseaseOutcomeWithProbability" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3801,7 +3803,7 @@ property_value: IAO:0000600 "A data item that specifies the largest numerical va
 id: APOLLO_SV:00000434
 name: statistical confidence
 def: "A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest." []
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: APOLLO_SV:0000040 "confidence" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -3809,7 +3811,7 @@ property_value: IAO:0000600 "A predicted data item that estimates how reliable s
 
 [Term]
 id: APOLLO_SV:00000435
-name: closure period
+name: obsolete closure period
 def: "A one-dimensional temporal region occupied by a place closure control strategy." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -4211,7 +4213,7 @@ property_value: IAO:0000600 "An epidemic simulator action specification that spe
 
 [Term]
 id: APOLLO_SV:00000475
-name: gonotrophic period duration
+name: obsolete gonotrophic period duration
 def: "A time measurement datum of the length of the temporal interval occupied by a gonotropic period." []
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -4252,7 +4254,7 @@ property_value: IAO:0000600 "A vector control strategy that has 1) an action spe
 id: APOLLO_SV:00000479
 name: ovisite carrying capacity
 def: "A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining." []
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining." xsd:string
@@ -4402,7 +4404,7 @@ property_value: IAO:0000600 "An identifier curated by the United States National
 
 [Term]
 id: APOLLO_SV:00000496
-name: ORCID
+name: obsolete ORCID
 def: "An identifier curated by ORCID, Inc. to denote some academic author." []
 property_value: APOLLO_SV:0000040 "orcId" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
@@ -4667,7 +4669,6 @@ id: APOLLO_SV:00000524
 name: compiling software
 def: "A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions." []
 comment: It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code".  Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
-comment: Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
 is_a: APOLLO_SV:00000008 ! software development
 property_value: IAO:0000111 "process of compiling software" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -4935,7 +4936,7 @@ id: APOLLO_SV:00000554
 name: disease surveillance data
 def: "A data set that is about some disease surveillance." []
 is_a: IAO:0000100 ! data set
-relationship: OBI:0000312 APOLLO_SV:00000545 ! is_specified_output_of disease surveillance
+relationship: OBI:0000312 APOLLO_SV:00000545 ! is specified output of disease surveillance
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "A data set that is about some disease surveillance." xsd:string
@@ -4985,7 +4986,7 @@ id: APOLLO_SV:00000559
 name: case series data set
 def: "A data set that is the output of a case series investigation." []
 is_a: IAO:0000100 ! data set
-relationship: OBI:0000312 APOLLO_SV:00000558 ! is_specified_output_of case series
+relationship: OBI:0000312 APOLLO_SV:00000558 ! is specified output of case series
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000600 "A data set that is the output of a case series investigation." xsd:string
@@ -5077,7 +5078,7 @@ id: APOLLO_SV:00000569
 name: total disease cases
 def: "A count of the total number of diseased indivduals in a population during a particular time interval." []
 is_a: APOLLO_SV:00000617 ! population count
-relationship: OBI:0000312 APOLLO_SV:00000155 ! is_specified_output_of population infection survey
+relationship: OBI:0000312 APOLLO_SV:00000155 ! is specified output of population infection survey
 property_value: APOLLO_SV:0000040 "totalCaseCount" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5153,7 +5154,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string
 id: APOLLO_SV:00000577
 name: epidemic peak intensity
 def: "A predicted data item that is about some aggregate of cases in an epidemic and whose value specification contains the maximum value in a data set that is about the epidemic." []
-is_a: OBI:0302867 ! predicted data item
+is_a: OBI:0302867 ! calculated datum
 property_value: IAO:0000117 "Amanda Hicks" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5313,7 +5314,6 @@ property_value: IAO:0000111 "census of treatment facility" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "census of treatment facilities" xsd:string
 property_value: IAO:0000118 "treatment facilities census" xsd:string
-property_value: IAO:0000118 "treatment facility census" xsd:string
 property_value: IAO:0000600 "A census that counts the number of treatment facilities of some kind in a particular geographical region." xsd:string
 
 [Term]
@@ -5548,8 +5548,8 @@ def: "A monkeypox disease inhering in a human being." []
 comment: requested by MIDAS CC
 is_a: DOID:3292 ! monkeypox
 intersection_of: DOID:3292 ! monkeypox
-intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
-relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
+intersection_of: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
+relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
 property_value: dc:date "2022-09-18T18:51:00" xsd:dateTime
 property_value: IAO:0000111 "monkeypox disease inhering in a human being" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5620,7 +5620,6 @@ id: APOLLO_SV:00000623
 name: incident epidemic case count
 def: "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." []
 comment: Incident case counts are measured according to regular intervals, typically day or week.
-comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin.
 is_a: APOLLO_SV:00000498 ! count of cases in an epidemic
 is_a: APOLLO_SV:00000649 ! incident case count
 property_value: IAO:0000117 "William R. Hogan" xsd:string
@@ -5843,7 +5842,7 @@ property_value: IAO:0000600 "The intent of a guardian to have a ward under their
 id: APOLLO_SV:00000651
 name: reproduction
 def: "The process by which new organisms are created from existing ones." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 union_of: GO:0019058 ! viral life cycle
 union_of: GO:0019953 ! sexual reproduction
 union_of: GO:0019954 ! asexual reproduction
@@ -5885,10 +5884,11 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string
 id: APOLLO_SV:00000796
 name: dataset creating
 def: "A planned process that has a data set as its specified output." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 intersection_of: OBI:0000011 ! planned process
-intersection_of: OBI:0000299 IAO:0000100 ! has_specified_output data set
-relationship: OBI:0000299 IAO:0000100 ! has_specified_output data set
+intersection_of: OBI:0000299 IAO:0000100 ! has specified output data set
+relationship: OBI:0000299 IAO:0000100 ! has specified output data set
 property_value: IAO:0000111 "creating a data set" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "data set creation" xsd:string
@@ -5899,10 +5899,11 @@ id: APOLLO_SV:00000797
 name: creating a copyright license
 def: "A planned process that has a copyright license as its specified output." []
 comment: Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time.
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 intersection_of: OBI:0000011 ! planned process
-intersection_of: OBI:0000299 APOLLO_SV:00000798 ! has_specified_output copyright license
-relationship: OBI:0000299 APOLLO_SV:00000798 ! has_specified_output copyright license
+intersection_of: OBI:0000299 APOLLO_SV:00000798 ! has specified output copyright license
+relationship: OBI:0000299 APOLLO_SV:00000798 ! has specified output copyright license
 property_value: IAO:0000111 "creating a copyright license" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 property_value: IAO:0000118 "copyright license creation" xsd:string
@@ -6024,11 +6025,10 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 id: BFO:0000004
 name: independent continuant
 def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
-def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
 comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
 is_a: BFO:0000002 ! continuant
-disjoint_from: BFO:0000020 ! characteristic
-disjoint_from: BFO:0000020 ! characteristic
+disjoint_from: BFO:0000020 ! specifically dependent continuant
+disjoint_from: BFO:0000020 ! specifically dependent continuant
 disjoint_from: BFO:0000031 ! generically dependent continuant
 relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant
 property_value: BFO:0000179 "ic" xsd:string
@@ -6125,7 +6125,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 id: BFO:0000015
 name: process
 def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
-def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
 comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
 is_a: BFO:0000003 ! occurrent
 property_value: BFO:0000179 "process" xsd:string
@@ -6161,10 +6160,9 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 
 [Term]
 id: BFO:0000017
-name: realizable
 name: realizable entity
 def: "A specifically dependent continuant  that inheres in continuant  entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." []
-is_a: BFO:0000020 ! characteristic
+is_a: BFO:0000020 ! specifically dependent continuant
 disjoint_from: BFO:0000019 ! quality
 relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity
 property_value: BFO:0000179 "realizable" xsd:string
@@ -6194,7 +6192,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 [Term]
 id: BFO:0000019
 name: quality
-is_a: BFO:0000020 ! characteristic
+is_a: BFO:0000020 ! specifically dependent continuant
 relationship: part_of BFO:0000019 {all_only="true"} ! quality
 property_value: BFO:0000179 "quality" xsd:string
 property_value: BFO:0000180 "Quality" xsd:string
@@ -6212,15 +6210,12 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 
 [Term]
 id: BFO:0000020
-name: characteristic
 name: specifically dependent continuant
 def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
-def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1  i &lt; j  n, ci  and cj share no common parts, are such that for each 1  i  n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"}
-def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
 comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
 is_a: BFO:0000002 ! continuant
 disjoint_from: BFO:0000031 ! generically dependent continuant
-relationship: part_of BFO:0000020 {all_only="true"} ! characteristic
+relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant
 property_value: BFO:0000179 "sdc" xsd:string
 property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string
 property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string
@@ -6235,11 +6230,8 @@ property_value: IAO:0000112 "the role of being a doctor" xsd:string
 property_value: IAO:0000112 "the shape of this hole." xsd:string
 property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string
 property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"}
-property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"}
 property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
 property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
-property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string
-property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string
 
 [Term]
 id: BFO:0000023
@@ -6263,7 +6255,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 [Term]
 id: BFO:0000024
 name: fiat object
-name: fiat object part
 is_a: BFO:0000040 ! material entity
 property_value: BFO:0000179 "fiat-object" xsd:string
 property_value: BFO:0000179 "fiat-object-part" xsd:string
@@ -6294,11 +6285,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 
 [Term]
 id: BFO:0000027
-name: object aggregate
 name: object_aggregate
 comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
-comment: Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
-comment: Synonyms: substance aggregate
 is_a: BFO:0000040 ! material entity
 property_value: BFO:0000179 "object-aggregate" xsd:string
 property_value: BFO:0000180 "ObjectAggregate" xsd:string
@@ -6316,6 +6304,7 @@ property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string
 property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string
 property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string
 property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"}
+property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011", IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"}
 property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"}
 property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string
 property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"}
@@ -6389,7 +6378,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 id: BFO:0000031
 name: generically dependent continuant
 def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." []
-def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
 comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
 is_a: BFO:0000002 ! continuant
 relationship: part_of BFO:0000031 {all_only="true"} ! generically dependent continuant
@@ -6465,6 +6453,7 @@ property_value: IAO:0000112 "the undetached arm of a human being" xsd:string
 property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string
 property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string
 property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string
+property_value: IAO:0000116 "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." xsd:string
 property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
 property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
 property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
@@ -6597,6 +6586,20 @@ name: antiviral drug
 comment: The usage or intended usage of a drug product to act against a viral infection of a host.
 is_a: BFO:0000023 ! role
 
+[Term]
+id: COB:0000022
+name: organism
+def: "A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome" []
+is_a: UBERON:0000465 ! material anatomical entity
+property_value: IAO:0000116 "'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'." xsd:string
+property_value: IAO:0000116 "Includes virus - we will later have a class for cellular organisms." xsd:string
+
+[Term]
+id: COB:0000035
+name: completely executed planned process
+is_a: BFO:0000015 ! process
+disjoint_from: GO:0008150 ! biological_process
+
 [Term]
 id: DOID:0060478
 name: Zika fever
@@ -6695,12 +6698,21 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/doid.owl" xsd:string
 
 [Term]
 id: DRON:00000005
-name: drug product
-def: "a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role" []
-is_a: BFO:0000030 ! object
-property_value: dc:creator "William Hogan" xsd:string
+name: clinical drug product
+def: "A drug product that is bearer of a clinical drug role." []
+comment: We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a "clinical drug role" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf "drug product", which also required changing the definition here.
+is_a: DRON:00000074 ! drug product
 property_value: IAO:0000117 "William Hogan" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/dron.owl" xsd:string
+
+[Term]
+id: DRON:00000074
+name: drug product
+def: "A material entity that (1) contains at least one scattered molecular aggregate as part and (2) is intended, when administered to an organism, to produce some therapeutic and/or psychoactive effect." []
+comment: The "intention" part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered.
+is_a: BFO:0000040 ! material entity
+property_value: IAO:0000117 "William R. Hogan" xsd:string
+property_value: terms:contributor https://orcid.org/0000-0001-6378-1703
+property_value: terms:contributor https://orcid.org/0000-0002-5039-2052
 
 [Term]
 id: EFO:0004600
@@ -6936,7 +6948,6 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string
 [Term]
 id: GEO:000000007
 name: aggregate of major administrative subdivisions
-name: group of major administrative subdivisions
 def: "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common." []
 comment: Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc.
 is_a: GEO:000000337 ! aggregate of governmental organizations
@@ -6946,7 +6957,6 @@ property_value: IAO:0000117 "Amanda Hicks" xsd:string
 [Term]
 id: GEO:000000008
 name: aggregate of dependencies
-name: group of dependencies
 def: "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." []
 comment: Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies.
 is_a: GEO:000000337 ! aggregate of governmental organizations
@@ -6994,9 +7004,6 @@ id: GEO:000000370
 name: geographical entity
 def: "A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface)." []
 comment: Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc.\n\nGenerally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought.  But the intent is definitely for this class to NOT subsume organism universally.  Human beings are contained within, but not part of, the Earth, for example.
-comment: Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc.
-comment: We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn).  So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities.
-comment: We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond.  \n\nThus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc.
 is_a: BFO:0000040 ! material entity
 property_value: IAO:0000111 "geographical entity of astronomical body" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
@@ -7013,7 +7020,6 @@ is_a: GEO:000000370 ! geographical entity
 id: GEO:000000372
 name: geographical region
 def: "A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface." []
-def: "A site designated by some relative spatial orientation." []
 is_a: GEO:000000370 ! geographical entity
 property_value: APOLLO_SV:0000040 "Location" xsd:string
 property_value: IAO:0000117 "François Modave" xsd:string
@@ -7048,7 +7054,7 @@ is_a: GEO:000000334 ! subcontinental land mass
 id: GEO:000000377
 name: aggregate of geographical entities
 def: "An object aggregate of geographical entities" []
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 relationship: BFO:0000075 GEO:000000370 ! is aggregate of geographical entity
 
 [Term]
@@ -7204,20 +7210,18 @@ property_value: IAO:0000118 "de jure state" xsd:string
 
 [Term]
 id: GO:0003674
-name: gene product or complex activity
 name: molecular_function
 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt]
-comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
-comment: This is the same as GO molecular function
+comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
 synonym: "molecular function" EXACT []
 is_a: BFO:0000015 ! process
-disjoint_from: GO:0008150 ! biological process
+property_value: IAO:0000116 "This is the same as GO molecular function" xsd:string
 
 [Term]
 id: GO:0006955
 name: immune response
 def: "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 
 [Term]
@@ -7245,18 +7249,13 @@ creation_date: 2012-09-20T14:06:08Z
 
 [Term]
 id: GO:0008150
-name: biological process
 name: biological_process
 namespace: biological_process
 alt_id: GO:0000004
 alt_id: GO:0007582
 alt_id: GO:0044699
 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
-def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." []
-def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." []
-comment: A biological process is an evolved process
 comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
-comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
 subset: goslim_candida
 subset: goslim_chembl
 subset: goslim_metagenomics
@@ -7270,8 +7269,6 @@ synonym: "single organism process" RELATED []
 synonym: "single-organism process" RELATED []
 xref: Wikipedia:Biological_process
 is_a: BFO:0000015 ! process
-disjoint_from: OBI:0000011 ! planned process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 created_by: jl
 creation_date: 2012-09-19T15:05:24Z
@@ -7289,8 +7286,9 @@ subset: goslim_virus
 synonym: "viral infection" RELATED []
 synonym: "virulence" RELATED []
 synonym: "virus process" EXACT [GOC:bf, GOC:jl]
+xref: Reactome:R-HSA-162906 "HIV Infection"
 xref: Wikipedia:Viral_life_cycle
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 
 [Term]
 id: GO:0016301
@@ -7313,6 +7311,9 @@ synonym: "lytic viral life cycle" RELATED []
 synonym: "viral assembly, maturation, egress, and release" NARROW [GOC:bf, GOC:jl]
 synonym: "viral infectious cycle" RELATED [GOC:bf, GOC:jl]
 synonym: "viral replication" RELATED [GOC:bf, GOC:jl]
+xref: Reactome:R-HSA-162588 "Budding and maturation of HIV virion"
+xref: Reactome:R-HSA-168255 "Influenza Infection"
+xref: Reactome:R-HSA-9609646 "HCMV Infection"
 is_a: APOLLO_SV:00000651 ! reproduction
 is_a: GO:0016032 ! viral process
 
@@ -7333,7 +7334,6 @@ is_a: GO:0007610 ! behavior
 is_a: GO:0048609 ! multicellular organismal reproductive process
 intersection_of: GO:0007610 ! behavior
 intersection_of: GO:0048609 ! multicellular organismal reproductive process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23491" xsd:anyURI
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 created_by: jl
 creation_date: 2012-09-19T16:01:37Z
@@ -7344,10 +7344,10 @@ name: sexual reproduction
 namespace: biological_process
 def: "A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid)." [Wikipedia:Sexual_reproduction]
 comment: Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
+subset: gocheck_do_not_annotate
 xref: Wikipedia:Sexual_reproduction
 is_a: APOLLO_SV:00000651 ! reproduction
 is_a: GO:0022414 ! reproductive process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI
 
 [Term]
 id: GO:0019954
@@ -7358,13 +7358,14 @@ synonym: "parthenogenesis" RELATED [Wikipedia:Parthenogenesis]
 xref: Wikipedia:Asexual_reproduction
 is_a: APOLLO_SV:00000651 ! reproduction
 is_a: GO:0022414 ! reproductive process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI
 
 [Term]
 id: GO:0022414
 name: reproductive process
 namespace: biological_process
+alt_id: GO:0019952
 alt_id: GO:0044702
+alt_id: GO:0050876
 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete]
 subset: gocheck_do_not_annotate
 subset: goslim_agr
@@ -7376,8 +7377,7 @@ subset: goslim_plant
 subset: goslim_plant_ribbon
 synonym: "single organism reproductive process" RELATED []
 xref: Wikipedia:Reproduction
-is_a: GO:0008150 ! biological process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI
+is_a: GO:0008150 ! biological_process
 created_by: jl
 creation_date: 2012-09-19T15:56:06Z
 
@@ -7393,21 +7393,10 @@ subset: gocheck_do_not_annotate
 subset: goslim_pir
 synonym: "organismal physiological process" EXACT []
 synonym: "single-multicellular organism process" RELATED []
-is_a: GO:0008150 ! biological process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI
+is_a: GO:0008150 ! biological_process
 created_by: jl
 creation_date: 2012-09-19T16:07:47Z
 
-[Term]
-id: GO:0032504
-name: obsolete multicellular organism reproduction
-namespace: biological_process
-def: "OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:isa_complete, GOC:jid]
-comment: The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process.
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI
-is_obsolete: true
-replaced_by: GO:0048609
-
 [Term]
 id: GO:0044403
 name: biological process involved in symbiotic interaction
@@ -7429,13 +7418,10 @@ synonym: "symbiotic interaction between organisms" RELATED []
 synonym: "symbiotic interaction between species" RELATED []
 synonym: "symbiotic process" RELATED []
 is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14807" xsd:anyURI
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI
 
 [Term]
 id: GO:0044409
 name: entry into host
-name: symbiont entry into host
 namespace: biological_process
 alt_id: GO:0030260
 alt_id: GO:0044411
@@ -7446,7 +7432,6 @@ alt_id: GO:0075052
 alt_id: GO:0085027
 alt_id: GO:0085028
 def: "Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:vw]
-def: "Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." []
 subset: goslim_virus
 synonym: "entry into cell of other organism during symbiotic interaction" NARROW [GOC:tb]
 synonym: "entry into cell of other organism involved in symbiotic interaction" RELATED []
@@ -7469,9 +7454,9 @@ synonym: "other organism invasion" RELATED []
 synonym: "penetration into host" EXACT [GOC:vw]
 synonym: "penetration into host via a specialized structure" NARROW [GOC:vw]
 synonym: "penetration into host via a specialized structure during symbiotic interaction" NARROW [GOC:vw]
+xref: Reactome:R-HSA-173107 "Binding and entry of HIV virion"
 is_a: GO:0051701 ! biological process involved in interaction with host
 is_a: GO:0051704 ! multi-organism process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/18563" xsd:anyURI
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 
 [Term]
@@ -7486,8 +7471,8 @@ synonym: "interaction with another species" EXACT []
 synonym: "interspecies interaction" EXACT []
 synonym: "interspecies interaction between organisms" EXACT []
 synonym: "interspecies interaction with other organisms" EXACT []
-is_a: GO:0008150 ! biological process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI
+xref: Reactome:R-HSA-9824443 "Parasitic Infection Pathways"
+is_a: GO:0008150 ! biological_process
 
 [Term]
 id: GO:0048609
@@ -7498,14 +7483,14 @@ subset: gocheck_do_not_annotate
 subset: goslim_drosophila
 synonym: "organismal reproductive process" BROAD []
 synonym: "reproductive process in a multicellular organism" EXACT []
+xref: Reactome:R-HSA-1474165 "Reproduction"
 is_a: GO:0022414 ! reproductive process
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI
 
 [Term]
 id: GO:0051234
 name: establishment of localization
 def: "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000412 "Gene Ontology: http://purl.obolibrary.org/obo/go.owl" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 
@@ -7526,14 +7511,15 @@ synonym: "growth of symbiont in host cell" NARROW []
 synonym: "growth of symbiont in host organelle" NARROW []
 synonym: "growth of symbiont in host vacuole" NARROW []
 synonym: "interaction with host" EXACT []
+xref: Reactome:R-HSA-9635486 "Infection with Mycobacterium tuberculosis"
+xref: Reactome:R-HSA-9658195 "Leishmania infection"
 is_a: GO:0044403 ! biological process involved in symbiotic interaction
-property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI
 
 [Term]
 id: GO:0051704
 name: multi-organism process
 def: "A biological process which involves another organism of the same or different species." []
-is_a: GO:0008150 ! biological process
+is_a: GO:0008150 ! biological_process
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl
 
 [Term]
@@ -7551,8 +7537,7 @@ property_value: IAO:0000119 "OBI_0000349" xsd:string
 id: IAO:0000003
 name: measurement unit label
 def: "A data item label that denotes a unit of measure." []
-def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." []
-is_a: IAO:0000009 ! datum label
+is_a: IAO:0000009 ! data item label
 property_value: IAO:0000111 "measurement unit label" xsd:string
 property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string
 property_value: IAO:0000114 IAO:0000122
@@ -7616,9 +7601,7 @@ is_obsolete: true
 [Term]
 id: IAO:0000009
 name: data item label
-name: datum label
 def: "A label is a symbol that is part of some other datum and is used to either partially define  the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" []
-def: "An information content entity that is part of some data item and is used to partially define the denotation of that data item." []
 is_a: IAO:0000030 ! information content entity
 property_value: IAO:0000111 "data item label" xsd:string
 property_value: IAO:0000111 "datum label" xsd:string
@@ -7663,8 +7646,8 @@ name: journal article
 def: "A report that is published in a journal." []
 is_a: IAO:0000088 ! report
 is_a: IAO:0000311 ! publication
-relationship: OBI:0000312 IAO:0000444 {all_only="true"} ! is_specified_output_of publishing process
-relationship: OBI:0000312 IAO:0000444 ! is_specified_output_of publishing process
+relationship: OBI:0000312 IAO:0000444 {all_only="true"} ! is specified output of publishing process
+relationship: OBI:0000312 IAO:0000444 ! is specified output of publishing process
 property_value: IAO:0000111 "journal article" xsd:string
 property_value: IAO:0000112 "Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g.  Authors, Title of article, Journal name, date or year of publication, volume and page number." xsd:string
 property_value: IAO:0000114 IAO:0000120
@@ -7815,7 +7798,6 @@ property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
 id: IAO:0000032
 name: scalar measurement datum
 def: "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." []
-def: "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." []
 is_a: IAO:0000109 ! measurement datum
 property_value: IAO:0000111 "scalar measurement datum" xsd:string
 property_value: IAO:0000112 "10 feet. 3 ml." xsd:string
@@ -8128,7 +8110,6 @@ property_value: IAO:0000119 "OBI_0000030" xsd:string
 id: IAO:0000102
 name: data about an ontology part
 def: "Data about an ontology part is a data item about a part of an ontology, for example a term" []
-def: "data about an ontology part is a data item about a part of an ontology, for example a term" []
 is_a: IAO:0000027 ! data item
 property_value: IAO:0000111 "data about an ontology part" xsd:string
 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
@@ -8494,7 +8475,7 @@ def: "A document that is the output of a publishing process." []
 comment: Revisit the term in Octorber 2020. Improve the defintion.
 is_a: IAO:0000310 ! document
 intersection_of: IAO:0000310 ! document
-intersection_of: OBI:0000312 IAO:0000444 {all_only="true"} ! is_specified_output_of publishing process
+intersection_of: OBI:0000312 IAO:0000444 {all_only="true"} ! is specified output of publishing process
 property_value: IAO:0000111 "publication" xsd:string
 property_value: IAO:0000112 "journal article, newspaper story, book, etc." xsd:string
 property_value: IAO:0000114 IAO:0000120
@@ -8879,9 +8860,10 @@ property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
 id: IAO:0000443
 name: data item extraction from journal article
 def: "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000013 ! has_specified_input journal article
-relationship: OBI:0000299 IAO:0000027 ! has_specified_output data item
+relationship: OBI:0000299 IAO:0000027 ! has specified output data item
 property_value: IAO:0000114 IAO:0000120
 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
 
@@ -8911,9 +8893,10 @@ property_value: IAO:0000234 "VEuPathDB" xsd:string
 id: IAO:0000572
 name: documenting
 def: "A planned process in which a document is created or added to by including the specified input in it." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity
-relationship: OBI:0000299 IAO:0000310 ! has_specified_output document
+relationship: OBI:0000299 IAO:0000310 ! has specified output document
 property_value: IAO:0000112 "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database." xsd:string
 property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000116 "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape" xsd:string
@@ -8937,9 +8920,10 @@ property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Line_chart" xsd:s
 id: IAO:0000574
 name: assigning a centrally registered identifier
 def: "A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity" []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
-relationship: OBI:0000299 IAO:0000577 ! has_specified_output centrally registered identifier symbol
-relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
+relationship: OBI:0000299 IAO:0000577 ! has specified output centrally registered identifier symbol
+relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry
 property_value: IAO:0000112 "A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned." xsd:string
 property_value: IAO:0000114 IAO:0000120
 property_value: IAO:0000116 "2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry." xsd:string
@@ -8954,7 +8938,7 @@ name: associating information with a centrally registered identifier in its regi
 def: "A planned process in which a CRID registry associates an information content entity with a CRID symbol" []
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol
-relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
+relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry
 property_value: IAO:0000112 "Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. " xsd:string
 property_value: IAO:0000114 IAO:0000120
 property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string
@@ -9022,10 +9006,11 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 id: IAO:0000580
 name: looking up a centrally registered identifier
 def: "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol
-relationship: OBI:0000299 IAO:0000030 ! has_specified_output information content entity
-relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
+relationship: OBI:0000299 IAO:0000030 ! has specified output information content entity
+relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry
 property_value: IAO:0000112 "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. " xsd:string
 property_value: IAO:0000114 IAO:0000120
 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
@@ -9677,9 +9662,10 @@ property_value: IAO:0000118 "ZIP code" xsd:string
 id: IAO:0000650
 name: database extract, transform, and load process
 def: "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity
-relationship: OBI:0000299 IAO:0000030 ! has_specified_output information content entity
+relationship: OBI:0000299 IAO:0000030 ! has specified output information content entity
 property_value: foaf:page https://en.wikipedia.org/wiki/Extract,_transform,_load
 property_value: IAO:0000111 "database extract, transform, and load process" xsd:string
 property_value: IAO:0000116 "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second" xsd:string
@@ -9805,22 +9791,18 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 [Term]
 id: IAO:0020000
 name: identifier
-def: "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." []
 def: "An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." []
 comment: Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
 is_a: IAO:0000030 ! information content entity
 intersection_of: IAO:0000030 ! information content entity
 intersection_of: IAO:0000219 BFO:0000001 ! denotes entity
-intersection_of: IAO:0000219 BFO:0000001 ! denotes entity
-intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output_of identifier creating process
-intersection_of: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process
+intersection_of: OBI:0000312 IAO:0020010 ! is specified output of identifier creating process
 relationship: IAO:0000219 BFO:0000001 ! denotes entity
-relationship: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process
+relationship: OBI:0000312 IAO:0020010 ! is specified output of identifier creating process
 property_value: dc:creator "Mathias Brochhausen" xsd:string
 property_value: IAO:0000111 "identifier" xsd:string
 property_value: IAO:0000117 "Justin Whorton" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "proper name" xsd:string
 property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string
 
@@ -9840,15 +9822,14 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 id: IAO:0020010
 name: identifier creating process
 def: "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." []
-def: "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 intersection_of: OBI:0000011 ! planned process
-intersection_of: OBI:0000299 IAO:0020000 ! has_specified_output identifier
-relationship: OBI:0000299 IAO:0020000 ! has_specified_output identifier
+intersection_of: OBI:0000299 IAO:0020000 ! has specified output identifier
+relationship: OBI:0000299 IAO:0020000 ! has specified output identifier
 property_value: dc:creator "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "Justin Whorton" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "dubbing process" xsd:string
 property_value: IAO:0000118 "naming" xsd:string
 property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string
@@ -9856,17 +9837,11 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 [Term]
 id: IAO:0020015
 name: personal name
-def: "A personal name is a proper name identifying an individual person." []
 def: "An identifier referring to an individual entity that is ascribed personhood by the user of the identifier." []
 comment: Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
-comment: Personal names to not include names of fictional characters, e.g. Sherlock Holmes.
-comment: Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)
 is_a: IAO:0020000 ! identifier
-intersection_of: IAO:0020000 ! identifier
-intersection_of: IAO:0000219 NCBITaxon:9606 {all_only="true"} ! denotes Homo sapiens
 property_value: IAO:0000117 "Justin Whorton" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Personal_name" xsd:string
 property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string
 
@@ -9896,16 +9871,8 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA
 [Term]
 id: IAO:0020020
 name: code set
-def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate." []
 def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things." []
 comment: Code sets might include non-entities/things (e.g. missing thumbs).
-comment: Does not imply absence vs. presence of any taxonomy.
-comment: Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
-comment: Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
-comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
-comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
-comment: Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
-comment: The information content entities do not denote each other.
 is_a: IAO:0000030 ! information content entity
 relationship: has_part IAO:0020000 ! identifier
 property_value: dc:contributor "Alan Ruttenberg" xsd:string
@@ -9916,7 +9883,6 @@ property_value: dc:contributor "William R. Hogan" xsd:string
 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
 property_value: IAO:0000117 "Justin Whorton" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
-property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "code map" xsd:string
 property_value: IAO:0000118 "code system" xsd:string
 property_value: IAO:0000118 "codeset" xsd:string
@@ -9929,7 +9895,7 @@ id: IAO:0021003
 name: social act
 def: "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived." []
 comment: The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).\nReinach clearly does not imply that a command that does not fulfill its prupose would not be a command.\nThanks to W.R. Hogan for finding the Reinach quote.
-is_a: OBI:0000011 ! planned process
+is_a: COB:0000035 ! completely executed planned process
 property_value: IAO:0000112 "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
@@ -10112,7 +10078,6 @@ id: IDO:0000406
 name: opportunistic infectious disposition
 def: "An infectious disposition to become part of a disorder only in organisms whose defenses are compromised." []
 comment: The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.
-comment: This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin).
 is_a: IDO:0000452 ! infectious disposition
 disjoint_from: IDO:0000407 ! primary infectious disposition
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
@@ -10125,7 +10090,6 @@ id: IDO:0000407
 name: primary infectious disposition
 def: "An infectious disposition to become part of a disorder in organisms that have intact defenses." []
 comment: A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
-comment: A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms.  ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease.  ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease."
 is_a: IDO:0000452 ! infectious disposition
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
@@ -10136,10 +10100,10 @@ id: IDO:0000450
 name: pathogenic disposition
 def: "A disposition to initiate processes that result in a disorder." []
 comment: A pathogenic disposition is realized in processes that create a disorder.
-comment: The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition.  By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.
 is_a: BFO:0000016 ! disposition
 disjoint_from: IDO:0000618 ! immunocompetence
 disjoint_from: OGMS:0000031 ! disease
+relationship: RO:0000052 BFO:0000040 ! characteristic of material entity
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10151,6 +10115,7 @@ name: infectious disposition
 def: "A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder." []
 comment: The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder.  The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder.
 is_a: IDO:0000450 ! pathogenic disposition
+relationship: RO:0000052 OBI:0100026 ! characteristic of organism
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10194,7 +10159,7 @@ def: "A quality that inheres in an infectious agent and is the likelihood that t
 comment: The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.
 is_a: BFO:0000019 ! quality
 disjoint_from: IDO:0000464 ! infectivity
-relationship: RO:0000052 IDO:0000596 ! inheres in infectious agent
+relationship: RO:0000052 IDO:0000596 ! characteristic of infectious agent
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10205,7 +10170,7 @@ name: infectivity
 def: "A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism." []
 comment: This quality is measured by the proportion of exposed who become infected.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10216,7 +10181,7 @@ name: virulence
 def: "A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal. " []
 comment: This quality is measured by the proportion of clinically apparent cases that are severe or fatal.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000596 ! inheres in infectious agent
+relationship: RO:0000052 IDO:0000596 ! characteristic of infectious agent
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10227,7 +10192,7 @@ name: susceptibility
 def: "A quality that inheres in an entity and is the degree to which it can be harmed by another entity." []
 comment: Low susceptibility is often referred to as resistance.  In this sense, resistance is a quality.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 BFO:0000040 ! inheres in material entity
+relationship: RO:0000052 BFO:0000040 ! characteristic of material entity
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10238,7 +10203,7 @@ name: infectious disease incidence
 def: "A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time." []
 comment: A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time.  Incidence is used as a measure of risk.  Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location.  Other constraints may include population demographics.  These constraints will vary with the context of the incidence measure.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10249,7 +10214,7 @@ name: infection incidence
 def: "A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time." []
 comment: A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time.  Incidence is used as a measure of risk.  Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location.  Other constraints may include population demographics.  These constraints will vary with the context of the incidence measure.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10260,7 +10225,7 @@ name: infectious disease incidence proportion
 def: "A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time. " []
 comment: An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10272,7 +10237,7 @@ name: infection incidence proportion
 def: "A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. " []
 comment: An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10284,7 +10249,7 @@ name: infectious disease incidence rate
 def: "A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time." []
 comment: An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10295,7 +10260,7 @@ name: infection incidence rate
 def: "A quality that inheres in an organism population and is the infection incidence proportion per unit time." []
 comment: An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10306,7 +10271,7 @@ name: infectious disease prevalence
 def: "A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time." []
 comment: Prevalence is sometimes defined as a proportion with total population size in the denominator.  A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time.  Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location.  Other constraints may include population demographics.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10317,7 +10282,7 @@ name: infection prevalence
 def: "A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time." []
 comment: Prevalence is sometimes defined as a proportion with total population size in the denominator.  A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time.  Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location.  Other constraints may include population demographics.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10328,7 +10293,7 @@ name: infectious disease lifetime prevalence
 def: "A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease." []
 comment: Prevalence is sometimes defined as a proportion with total population size in the denominator.  A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population.  Actual measures of prevalence are based only on reported cases and usually specify a geographic location.  Other constraints may include population demographics.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10339,7 +10304,7 @@ name: infectious agent seroprevalence
 def: "A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time." []
 comment: Prevalence is sometimes defined as a proportion with total population size in the denominator.  A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population.  Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location.  Other constraints may include population demographics.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10350,7 +10315,7 @@ name: infectious disease mortality rate
 def: "A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time." []
 comment: A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population.  Actual measures of mortality rate are based only on reported cases and usually specify a geographic location.  Other constraints may include population demographics.  Mortality rate is typically expressed in units of deaths per 1000 individuals per year.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10361,7 +10326,7 @@ name: infectious disease endemicity
 def: "A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir." []
 comment: A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population.  The population may be specified by temporal, geographic, or demographic constraints.  Infectious diseases that are typical or common to a particular population are referred to as endemic.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10372,7 +10337,7 @@ name: infectious disease sporadicity
 def: "A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence." []
 comment: Sporadic quality of infectious disease is relational to previous prevalence of the disease.
 is_a: BFO:0000019 ! quality
-relationship: RO:0000052 IDO:0000509 ! inheres in organism population
+relationship: RO:0000052 IDO:0000509 ! characteristic of organism population
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10382,7 +10347,7 @@ id: IDO:0000509
 name: organism population
 def: "An aggregate of organisms of the same Species." []
 comment: The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10457,7 +10422,8 @@ comment: The disposition inheres in a bearer in virtue of the fact that the bear
 is_a: BFO:0000016 ! disposition
 disjoint_from: OGMS:0000031 ! disease
 relationship: BFO:0000054 GO:0006955 ! is realized by immune response
-relationship: RO:0000052 OBI:0100026 ! inheres in organism
+relationship: RO:0000052 OBI:0100026 ! characteristic of organism
+relationship: RO:0000052 OBI:0100026 ! characteristic of organism
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10498,7 +10464,7 @@ property_value: IAO:0000117 "Lindsay Cowell" xsd:string
 id: IDO:0000629
 name: host role
 def: "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." []
-is_a: OMRSE:00000049 ! organism role
+is_a: BFO:0000023 ! role
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000117 "Alexander Diehl" xsd:string
 property_value: IAO:0000117 "Lindsay Cowell" xsd:string
@@ -10561,7 +10527,6 @@ property_value: IAO:0000118 "House mouse" xsd:string
 
 [Term]
 id: NCBITaxon:10239
-name: Virus
 name: Viruses
 is_a: OBI:0100026 ! organism
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl
@@ -10569,7 +10534,7 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl
 [Term]
 id: NCBITaxon:10240
 name: Poxviridae
-is_a: NCBITaxon:35237 ! dsDNA virus, no RNA stage
+is_a: NCBITaxon:35237 ! dsDNA viruses, no RNA stage
 
 [Term]
 id: NCBITaxon:10241
@@ -11547,6 +11512,12 @@ property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string
 property_value: IAO:0000118 "Diplococcus pneumoniae" xsd:string
 property_value: IAO:0000118 "Micrococcus pneumoniae" xsd:string
 
+[Term]
+id: NCBITaxon:131567
+name: cellular organisms
+xref: GC_ID:1
+is_a: COB:0000022 ! organism
+
 [Term]
 id: NCBITaxon:1329799
 name: Archelosauria
@@ -12493,6 +12464,10 @@ property_value: has_rank NCBITaxon:family
 [Term]
 id: NCBITaxon:2759
 name: Eukaryota
+xref: GC_ID:1
+xref: PMID:23020233
+xref: PMID:30257078
+is_a: NCBITaxon:131567 ! cellular organisms
 is_a: OBI:0100026 ! organism
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl
 
@@ -12933,16 +12908,15 @@ property_value: has_rank NCBITaxon:family
 
 [Term]
 id: NCBITaxon:35237
-name: dsDNA virus, no RNA stage
 name: dsDNA viruses, no RNA stage
 namespace: ncbi_taxonomy
 xref: GC_ID:1
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 
 [Term]
 id: NCBITaxon:35268
 name: Retro-transcribing viruses
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 property_value: IAO:0000118 "Retroid viruses" xsd:string
 
 [Term]
@@ -12972,7 +12946,7 @@ is_a: NCBITaxon:1933264 ! California encephalitis orthobunyavirus
 [Term]
 id: NCBITaxon:35325
 name: dsRNA viruses
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string
 property_value: IAO:0000118 "dsRNA nonenveloped viruses" xsd:string
 
@@ -13113,7 +13087,7 @@ property_value: has_rank NCBITaxon:genus
 [Term]
 id: NCBITaxon:39759
 name: Deltavirus
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string
 
 [Term]
@@ -13140,6 +13114,7 @@ property_value: has_rank NCBITaxon:subgenus
 [Term]
 id: NCBITaxon:40674
 name: Mammalia
+xref: GC_ID:1
 is_a: NCBITaxon:32524 ! Amniota
 property_value: IAO:0000118 "mammals" xsd:string
 
@@ -13234,7 +13209,7 @@ is_a: NCBITaxon:7157 ! Culicidae
 [Term]
 id: NCBITaxon:439488
 name: ssRNA virus
-is_a: NCBITaxon:10239 ! Virus
+is_a: NCBITaxon:10239 ! Viruses
 
 [Term]
 id: NCBITaxon:44025
@@ -13671,7 +13646,7 @@ id: NCBITaxon:548681
 name: Herpesvirales
 namespace: ncbi_taxonomy
 xref: GC_ID:1
-is_a: NCBITaxon:35237 ! dsDNA virus, no RNA stage
+is_a: NCBITaxon:35237 ! dsDNA viruses, no RNA stage
 property_value: has_rank NCBITaxon:order
 
 [Term]
@@ -14951,6 +14926,7 @@ property_value: has_rank NCBITaxon:genus
 [Term]
 id: NCBITaxon:9443
 name: Primates
+xref: GC_ID:1
 is_a: NCBITaxon:314146 ! Euarchontoglires
 property_value: IAO:0000118 "Primata" xsd:string
 property_value: IAO:0000118 "primate" xsd:string
@@ -15048,9 +15024,8 @@ property_value: IAO:0000118 "rhesus monkeys" xsd:string
 [Term]
 id: NCBITaxon:9606
 name: Homo sapiens
-is_a: NCBITaxon:2759 ! Eukaryota
-property_value: IAO:0000111 "Homo sapiens" xsd:string
-property_value: IAO:0000118 "human being" xsd:string
+xref: GC_ID:1
+is_a: NCBITaxon:9443 ! Primates
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl
 
 [Term]
@@ -15276,19 +15251,14 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/dideo/dev/dideo.owl"
 id: OBI:0000011
 name: planned process
 def: "A process that realizes a plan which is the concretization of a plan specification." []
-def: "A processual entity that realizes a plan which is the concretization of a plan specification." []
 is_a: BFO:0000015 ! process
 property_value: IAO:0000111 "planned process" xsd:string
-property_value: IAO:0000111 "planned process" xsd:string
 property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string
 property_value: IAO:0000114 IAO:0000122
 property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string
 property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \n  objectives is a planned process." xsd:string
-property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string
 property_value: IAO:0000117 "Bjoern Peters" xsd:string
 property_value: IAO:0000119 "branch derived" xsd:string
-property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string
-property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 
 [Term]
@@ -15338,7 +15308,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 id: OBI:0000245
 name: organization
 def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." []
-def: "An organization is a continuant entity which can play roles,  has members, and has a set of organization rules.  Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." []
 is_a: BFO:0000040 ! material entity
 property_value: IAO:0000111 "organization" xsd:string
 property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string
@@ -15375,7 +15344,7 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 id: OBI:0000576
 name: scattered molecular aggregate
 def: "a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates" []
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 property_value: IAO:0000111 "scattered molecular aggregate" xsd:string
 property_value: IAO:0000112 "the sodium and chloride ions in a glass of salt water" xsd:string
 property_value: IAO:0000114 IAO:0000123
@@ -15420,8 +15389,8 @@ name: average value
 def: "A  data item that is produced as the output of an averaging data transformation and represents the average value of the input data." []
 is_a: IAO:0000027 ! data item
 intersection_of: IAO:0000027 ! data item
-intersection_of: OBI:0000312 OBI:0200170 ! is_specified_output_of averaging data transformation
-relationship: OBI:0000312 OBI:0200170 ! is_specified_output_of averaging data transformation
+intersection_of: OBI:0000312 OBI:0200170 ! is specified output of averaging data transformation
+relationship: OBI:0000312 OBI:0200170 ! is specified output of averaging data transformation
 property_value: APOLLO_SV:0000040 "mean" xsd:string
 property_value: IAO:0000111 "average value" xsd:string
 property_value: IAO:0000114 IAO:0000125
@@ -15450,20 +15419,15 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 id: OBI:0000968
 name: device
 def: "A device is a processed material which is designed to perform some function or functions" []
-def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." []
 comment: would include reagents
 is_a: OBI:0000047 ! processed material
 property_value: IAO:0000111 "device" xsd:string
 property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string
-property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string
-property_value: IAO:0000114 IAO:0000122
 property_value: IAO:0000114 IAO:0000123
-property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions.  Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear.  For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component.  This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running  box  is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it.  This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation).  In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string
 property_value: IAO:0000116 "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only" xsd:string
 property_value: IAO:0000116 "if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of  the definition. device was needed, but couldn't define in Philadelphia. If we decide  that in addition to function there are also capabilities for which a device is created we will include these in the definition." xsd:string
 property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string
 property_value: IAO:0000118 "instrument" xsd:string
-property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string
 property_value: IAO:0000119 "OBI Vancouver workshop 2010" xsd:string
 
 [Term]
@@ -15670,30 +15634,21 @@ id: OBI:0100026
 name: organism
 def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." []
 is_a: BFO:0000040 ! material entity
-union_of: NCBITaxon:10239 ! Virus
+union_of: NCBITaxon:10239 ! Viruses
 union_of: NCBITaxon:2 ! Bacteria
 union_of: NCBITaxon:2157 ! Archaea
 union_of: NCBITaxon:2759 ! Eukaryota
 disjoint_from: OGMS:0000045 ! disorder
 property_value: APOLLO_SV:0000040 "Individual" xsd:string
 property_value: IAO:0000111 "organism" xsd:string
-property_value: IAO:0000112 "animal" xsd:string
-property_value: IAO:0000112 "fungus" xsd:string
-property_value: IAO:0000112 "plant" xsd:string
-property_value: IAO:0000112 "virus" xsd:string
 property_value: IAO:0000114 IAO:0000121
-property_value: IAO:0000114 IAO:0000122
-property_value: IAO:0000116 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string
-property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string
-property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string
-property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 
 [Term]
 id: OBI:0200000
 name: data transformation
-def: "A data transformation is a process which produces output data from input data" []
-def: "A planned process that produces output data from input data." []
+def: "A completely executed planned process that produces output data from input data." []
+is_a: COB:0000035 ! completely executed planned process
 is_a: OBI:0000011 ! planned process
 relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective
 property_value: IAO:0000111 "data transformation" xsd:string
@@ -15752,7 +15707,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 [Term]
 id: OBI:0302867
 name: calculated datum
-name: predicted data item
 def: "A data item that was generated on the basis of a calculation or logical reasoning" []
 comment: APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class.
 is_a: IAO:0000109 ! measurement datum
@@ -15837,22 +15791,19 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/OBIws.owl" xsd:strin
 id: OGMS:0000014
 name: clinical finding
 def: "A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof." []
-is_a: IAO:0000027 ! data item
+is_a: IAO:0000030 ! information content entity
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2010-07-19T10:18:02Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000018
 name: laboratory finding
 def: "A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient." []
 is_a: OGMS:0000014 ! clinical finding
-property_value: APOLLO_SV:0000040 "result" xsd:string
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T10:21:58Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000023
@@ -15862,7 +15813,6 @@ is_a: BFO:0000019 ! quality
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2010-07-19T11:13:49Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000027
@@ -15872,14 +15822,12 @@ is_a: OGMS:0000023 ! phenotype
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:18:05Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000031
 name: disease
 def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." []
 is_a: BFO:0000016 ! disposition
-property_value: APOLLO_SV:0000040 "disease" xsd:string
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:21:20Z" xsd:string
@@ -15888,15 +15836,9 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl
 [Term]
 id: OGMS:0000032
 name: homeostasis
-def: "A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning." []
 is_a: BFO:0000016 ! disposition
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
-property_value: IAO:0000117 "Barry Smith" xsd:string
-property_value: IAO:0000117 "Richard H. Scheuermann" xsd:string
-property_value: IAO:0000117 "Werner Ceusters" xsd:string
-property_value: IAO:0000119 "Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. \n\nLink: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:22:01Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000045
@@ -15907,7 +15849,6 @@ property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:39:44Z" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000060
@@ -15923,89 +15864,78 @@ id: OGMS:0000063
 name: disease course
 def: "The totality of all processes through which a given disease instance is realized." []
 is_a: BFO:0000015 ! process
-property_value: IAO:0000111 "disease course" xsd:string
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string
 property_value: IAO:0000232 "creation date: 2009-06-23T11:55:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000087
 name: extended organism
 def: "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism." []
 comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=3" xsd:string
 property_value: IAO:0000232 "creation date: 2010-01-25T04:51:11Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl
 
 [Term]
 id: OGMS:0000090
 name: treatment
-def: "A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder" []
-comment: Apollo-SV currently defines two subclasses of treatment.\nSee vaccination and antiviral treatment.  \n
-is_a: OBI:0000011 ! planned process
-property_value: APOLLO_SV:0000040 "Treatment" xsd:string
+def: "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process" []
+is_a: OGMS:0000096 ! health care process
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=35" xsd:string
 property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000092
 name: life course
-def: "A processual entity which has as parts all the processes in which a given organism is participant." []
-is_a: BFO:0000182 ! history
-property_value: APOLLO_SV:0000040 "LifeCycle" xsd:string
-property_value: IAO:0000117 "Albert Goldfain" xsd:string
+def: "A process which has as parts all the processes in which a given organism is participant." []
+is_a: BFO:0000015 ! process
+property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string
 property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=38" xsd:string
-property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
-property_value: IAO:0000600 "A processual entity which has as parts all the processes in which a given organism is participant." xsd:string
+property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z\n\nEDIT: 10 NOV 2015" xsd:string
 
 [Term]
 id: OGMS:0000096
 name: health care process
-def: "A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process" []
-is_a: BFO:0000015 ! process
-property_value: IAO:0000117 "Albert Goldfain" xsd:string
+def: "A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient" []
+is_a: COB:0000035 ! completely executed planned process
+is_a: OBI:0000011 ! planned process
+property_value: IAO:0000117 "Albert Goldfain\nSagar Jain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
-property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
+property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z\neditor date: 2017-04-18" xsd:string
 
 [Term]
 id: OGMS:0000097
 name: health care encounter
 def: "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role.  The health care provider role and patient are realized during the health care encounter" []
-is_a: OBI:0000011 ! planned process
+synonym: "healthcare encounter" EXACT []
 is_a: OGMS:0000096 ! health care process
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000098
 name: hospitalization
-is_a: OGMS:0000097 ! health care encounter
-property_value: APOLLO_SV:0000040 "hospitalization" xsd:string
+def: "TODO" []
+comment: 09/16/2020\nIs this same as admission? \nIs this the same as inpatient encounter?
+is_a: OGMS:0000096 ! health care process
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000099
 name: outpatient encounter
+def: "TODO" []
 is_a: OGMS:0000097 ! health care encounter
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000100
@@ -16015,25 +15945,26 @@ is_a: OGMS:0000097 ! health care encounter
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000101
-name: ED encounter
+name: emergency department encounter
+def: "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention." []
 is_a: OGMS:0000097 ! health care encounter
 property_value: IAO:0000117 "Albert Goldfain" xsd:string
 property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string
 property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OGMS:0000105
 name: relapse
-def: "A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course." []
+def: "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease." []
 is_a: BFO:0000015 ! process
-property_value: IAO:0000117 "Albert Goldfain" xsd:string
+property_value: dc:date "10 NOV 2015" xsd:string
+property_value: IAO:0000116 "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course." xsd:string
+property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string
+property_value: IAO:0000118 "recurrent" xsd:string
 property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=73" xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string
 
 [Term]
 id: OMIABIS:0000019
@@ -16051,27 +15982,27 @@ id: OMRSE:00000001
 name: human social role
 def: "A social role inhering in a human being." []
 is_a: OMRSE:00000026 ! organism social role
-is_a: OMRSE:00000050 ! Homo sapiens role
+relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
 
 [Term]
 id: OMRSE:00000010
-name: human health care role
+name: health care role
 def: "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis." []
+synonym: "healthcare role" EXACT []
 is_a: OMRSE:00002072 ! role in human social processes
 relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "William R. Hogan" xsd:string
-property_value: IAO:0000118 "health care role" xsd:string
 
 [Term]
 id: OMRSE:00000011
 name: patient role
-def: "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." []
+def: "A health care role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." []
 comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.
-is_a: OMRSE:00000010 ! human health care role
-is_a: OMRSE:00000049 ! organism role
+is_a: OMRSE:00000010 ! health care role
+relationship: RO:0000052 COB:0000022 ! characteristic of organism
 property_value: IAO:0000117 "Amanda Hicks" xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000118 "patient" xsd:string
@@ -16081,6 +16012,7 @@ property_value: IAO:0000119 "CAFE domain expert working group." xsd:string
 id: OMRSE:00000015
 name: health care provider organization role
 def: "A role that inheres in an organization and that is realized by the providing of services in a health care encounter." []
+synonym: "healthcare provider organization role" EXACT []
 is_a: OMRSE:00000027 ! organization health care role
 relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter
 property_value: dc:contributor "Mathias Brochhausen" xsd:string
@@ -16091,7 +16023,7 @@ id: OMRSE:00000022
 name: aggregate of objectual organisms
 def: "An object aggregate of objectual organisms." []
 comment: Any arbitrary collection of organisms.  They need not be of the same taxonomic class.  
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 
 [Term]
 id: OMRSE:00000023
@@ -16114,10 +16046,8 @@ id: OMRSE:00000026
 name: organism social role
 def: "A role in human social processes that inheres in an organism." []
 comment: Defined class that we will ultimately move to an application ontology.  We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants.
-comment: Includes animals as well as humans.  For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc.  Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
-comment: Previous definition: A role in human social processes played by an organism.
-is_a: OMRSE:00000049 ! organism role
 is_a: OMRSE:00002072 ! role in human social processes
+relationship: RO:0000052 COB:0000022 ! characteristic of organism
 property_value: IAO:0000117 "William R. Hogan\nMathias Brochhausen" xsd:string
 
 [Term]
@@ -16125,6 +16055,7 @@ id: OMRSE:00000027
 name: organization health care role
 def: "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process" []
 comment: Previous definition: An organization social role played by an organization in health care processes.
+synonym: "organization healthcare role" EXACT []
 is_a: OMRSE:00000025 ! organization social role
 
 [Term]
@@ -16132,9 +16063,9 @@ id: OMRSE:00000030
 name: human patient role
 def: "A patient role that inheres in a human being." []
 is_a: OMRSE:00000011 ! patient role
-is_a: OMRSE:00000050 ! Homo sapiens role
 intersection_of: OMRSE:00000011 ! patient role
-intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
+intersection_of: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
+relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens
 
 [Term]
 id: OMRSE:00000033
@@ -16145,41 +16076,14 @@ is_a: BFO:0000040 ! material entity
 relationship: RO:0002351 OBI:0000245 ! has member organization
 property_value: IAO:0000117 "William R. Hogan\nAmanda Hicks" xsd:string
 
-[Term]
-id: OMRSE:00000048
-name: material entity role
-is_a: BFO:0000023 ! role
-intersection_of: BFO:0000023 ! role
-intersection_of: RO:0000052 BFO:0000040 ! inheres in material entity
-relationship: RO:0000052 BFO:0000040 {all_only="true"} ! inheres in material entity
-relationship: RO:0000052 BFO:0000040 ! inheres in material entity
-
-[Term]
-id: OMRSE:00000049
-name: organism role
-is_a: OMRSE:00000048 ! material entity role
-intersection_of: OMRSE:00000048 ! material entity role
-intersection_of: RO:0000052 OBI:0100026 ! inheres in organism
-relationship: RO:0000052 OBI:0100026 {all_only="true"} ! inheres in organism
-relationship: RO:0000052 OBI:0100026 ! inheres in organism
-
-[Term]
-id: OMRSE:00000050
-name: Homo sapiens role
-is_a: OMRSE:00000049 ! organism role
-intersection_of: OMRSE:00000049 ! organism role
-intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
-relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
-relationship: RO:0000052 NCBITaxon:9606 {all_only="true"} ! inheres in Homo sapiens
-
 [Term]
 id: OMRSE:00000051
 name: organization role
-is_a: OMRSE:00000048 ! material entity role
+is_a: BFO:0000023 ! role
 intersection_of: BFO:0000023 ! role
-intersection_of: RO:0000052 OBI:0000245 ! inheres in organization
-relationship: RO:0000052 OBI:0000245 ! inheres in organization
-relationship: RO:0000052 OBI:0000245 {all_only="true"} ! inheres in organization
+intersection_of: RO:0000052 OBI:0000245 ! characteristic of organization
+relationship: RO:0000052 OBI:0000245 ! characteristic of organization
+relationship: RO:0000052 OBI:0000245 {all_only="true"} ! characteristic of organization
 
 [Term]
 id: OMRSE:00000053
@@ -16208,8 +16112,8 @@ name: hospital organization
 def: "An organization that is the bearer of a hospital role." []
 is_a: OBI:0000245 ! organization
 intersection_of: OBI:0000245 ! organization
-intersection_of: RO:0000053 OMRSE:00000054 ! is bearer of hospital role
-relationship: RO:0000053 OMRSE:00000054 ! is bearer of hospital role
+intersection_of: RO:0000053 OMRSE:00000054 ! bearer of hospital role
+relationship: RO:0000053 OMRSE:00000054 ! bearer of hospital role
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -16218,8 +16122,8 @@ name: school organization
 def: "An organization that is the bearer of a school role." []
 is_a: OBI:0000245 ! organization
 intersection_of: OBI:0000245 ! organization
-intersection_of: RO:0000053 OMRSE:00000055 ! is bearer of school role
-relationship: RO:0000053 OMRSE:00000055 ! is bearer of school role
+intersection_of: RO:0000053 OMRSE:00000055 ! bearer of school role
+relationship: RO:0000053 OMRSE:00000055 ! bearer of school role
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -16245,7 +16149,6 @@ id: OMRSE:00000061
 name: architectural structure
 def: "A material entity that is a human made strcuture with firm connection between its foundation and the ground." []
 comment: "Building" is a subclass of this. 
-comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".
 is_a: BFO:0000040 ! material entity
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000119 "http://de.wikipedia.org/wiki/Bauwerk" xsd:string
@@ -16256,9 +16159,9 @@ name: facility
 def: "An architectural structure that bears some function." []
 is_a: OMRSE:00000061 ! architectural structure
 intersection_of: OMRSE:00000061 ! architectural structure
-intersection_of: RO:0000053 BFO:0000034 ! is bearer of function
-relationship: OMRSE:00000068 OBI:0000245 {owl:versionInfo="09/09/2017"} ! is administered by organization
-relationship: RO:0000053 BFO:0000034 ! is bearer of function
+intersection_of: RO:0000053 BFO:0000034 ! bearer of function
+relationship: OMRSE:00000068 OBI:0000245 ! is administered by organization
+relationship: RO:0000053 BFO:0000034 ! bearer of function
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -16266,7 +16169,7 @@ id: OMRSE:00000064
 name: school facility
 def: "A facility that is run by a school organization and is the bearer of a school function." []
 is_a: OMRSE:00000062 ! facility
-relationship: RO:0000053 OMRSE:00000053 ! is bearer of school function
+relationship: RO:0000053 OMRSE:00000053 ! bearer of school function
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 
 [Term]
@@ -16297,6 +16200,7 @@ property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/issues/79" xsd:anyUR
 [Term]
 id: OMRSE:00000172
 name: health care function
+synonym: "healthcare function" EXACT []
 is_a: BFO:0000034 ! function
 intersection_of: BFO:0000034 ! function
 intersection_of: BFO:0000054 OGMS:0000097 ! is realized by health care encounter
@@ -16307,8 +16211,9 @@ id: OMRSE:00002072
 name: role in human social processes
 def: "A role that inheres in some entity that is realized in a social act." []
 comment: Previous definition: A role played by an entity in human social processes.
-is_a: OMRSE:00000048 ! material entity role
-relationship: RO:0000052 BFO:0000040 {all_only="true"} ! inheres in material entity
+is_a: BFO:0000023 ! role
+relationship: RO:0000052 BFO:0000040 ! characteristic of material entity
+relationship: RO:0000052 BFO:0000040 {all_only="true"} ! characteristic of material entity
 property_value: dc:contributor "Mathias Brochhausen" xsd:string
 property_value: IAO:0000117 "Matthew Diller" xsd:string
 
@@ -16316,7 +16221,7 @@ property_value: IAO:0000117 "Matthew Diller" xsd:string
 id: PATO:0000001
 name: quality
 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG]
-is_a: BFO:0000020 ! characteristic
+is_a: BFO:0000020 ! specifically dependent continuant
 
 [Term]
 id: PATO:0000040
@@ -16513,7 +16418,7 @@ id: PCO:0000000
 name: PCO:collection of organisms
 def: "A material entity that consists of two or more organisms, viruses, or viroids." []
 comment: May be of the same or different species.
-is_a: BFO:0000027 ! object aggregate
+is_a: BFO:0000027 ! object_aggregate
 property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string
 property_value: IAO:0000118 "group of organisms" xsd:string
 property_value: IAO:0000118 "organism collection" xsd:string
@@ -16677,10 +16582,11 @@ property_value: IAO:0000412 "Transmission Ontology: http://purl.obolibrary.org/o
 [Term]
 id: UBERON:0000061
 name: anatomical structure
-namespace: uberon
-def: "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome." []
 def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003]
 subset: common_anatomy
+subset: human_reference_atlas
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 synonym: "biological structure" EXACT []
 synonym: "connected biological structure" EXACT [CARO:0000003]
@@ -16690,40 +16596,72 @@ xref: BILA:0000003
 xref: CARO:0000003
 xref: EHDAA2:0003003
 xref: EMAPA:0
-xref: FBbt:00007001
+xref: FAO:0000001
 xref: FMA:305751
 xref: FMA:67135
 xref: GAID:781
 xref: HAO:0000003
 xref: http://dbpedia.org/ontology/AnatomicalStructure
 xref: MA:0003000
-xref: MESH:A13
 xref: MESH:D000825
 xref: SCTID:362889002
 xref: TAO:0000037
 xref: TGMA:0001823
 xref: VHOG:0001759
-xref: WBbt:0000100
 xref: XAO:0003000
 xref: ZFA:0000037
 is_a: UBERON:0000465 ! material anatomical entity
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: RO:0002175 NCBITaxon:33090
-property_value: RO:0002175 NCBITaxon:4751
+
+[Term]
+id: UBERON:0000071
+name: death stage
+def: "End of the life of an organism." [XAO:0000437]
+subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
+synonym: "death" RELATED []
+xref: XAO:0000437
+xref: XtroDO:0000085
+is_a: UBERON:0000105 ! life cycle stage
+
+[Term]
+id: UBERON:0000105
+name: life cycle stage
+def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165]
+subset: common_anatomy
+subset: efo_slim
+subset: human_subset
+subset: mouse_subset
+subset: upper_level
+synonym: "developmental stage" NARROW []
+synonym: "stage" NARROW []
+xref: BILS:0000105
+xref: EFO:0000399
+xref: FBdv:00007012
+xref: FMA:24120
+xref: MESH:D008018
+xref: ncithesaurus:Developmental_Stage
+xref: PdumDv:0000090
+xref: WBls:0000002
+xref: XAO:1000000
+xref: ZFS:0000000
+xref: ZFS:0100000
+is_a: BFO:0000015 ! process
+property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string
 
 [Term]
 id: UBERON:0000465
 name: material anatomical entity
-namespace: uberon
 def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737]
 subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 xref: AAO:0010264
 xref: AEO:0000006
 xref: BILA:0000006
 xref: CARO:0000006
 xref: EHDAA2:0003006
-xref: FBbt:00007016
 xref: FMA:67165
 xref: HAO:0000006
 xref: TAO:0001836
@@ -16731,23 +16669,27 @@ xref: TGMA:0001826
 xref: VHOG:0001721
 is_a: BFO:0000040 ! material entity
 is_a: UBERON:0001062 ! anatomical entity
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: RO:0002175 NCBITaxon:33090
-property_value: RO:0002175 NCBITaxon:4751
 
 [Term]
 id: UBERON:0000467
 name: anatomical system
-namespace: uberon
-def: "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]." []
+def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [CARO:0000011]
+subset: common_anatomy
+subset: human_reference_atlas
+subset: human_subset
+subset: mouse_subset
+subset: pheno_slim
 subset: uberon_slim
 subset: upper_level
-synonym: "body system" EXACT []
+synonym: "anatomical systems" RELATED OMO:0003004 [ZFA:0001439]
+synonym: "body system" EXACT [BIRNLEX:14]
+synonym: "connected anatomical system" EXACT [CARO:0000011]
 synonym: "organ system" EXACT []
-synonym: "system" BROAD []
+synonym: "system" BROAD [GO:0048731]
 xref: AAO:0000007
 xref: AEO:0000011
 xref: BILA:0000011
+xref: BIRNLEX:14
 xref: BSA:0000049
 xref: CALOHA:TS-2088
 xref: CARO:0000011
@@ -16755,71 +16697,65 @@ xref: EHDAA2:0003011
 xref: EHDAA:392
 xref: EMAPA:16103
 xref: EV:0100000
-xref: FBbt:00004856
 xref: FMA:7149
 xref: galen:AnatomicalSystem
 xref: HAO:0000011
 xref: MA:0000003
-xref: ncithesaurus:Organ_System
-xref: NIF_GrossAnatomy:birnlex_14
-xref: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
+xref: NCIT:C12919
 xref: SCTID:278195005
 xref: TAO:0001439
 xref: TGMA:0001831
-xref: UMLS:C0460002
 xref: VHOG:0001725
 xref: WBbt:0005746
 xref: WBbt:0005763
 xref: Wikipedia:Organ_system
 xref: XAO:0003002
 xref: ZFA:0001439
-is_a: UBERON:0000480 ! anatomical group
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: seeAlso EHDAA2:0001330
-property_value: UBPROP:0000001 "Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]" xsd:string
-property_value: UBPROP:0000001 "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]" xsd:string
-property_value: UBPROP:0000001 "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]" xsd:string
+is_a: UBERON:0000061 ! anatomical structure
 
 [Term]
 id: UBERON:0000479
 name: tissue
-namespace: uberon
-def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." []
-comment: Editor note: changed label and definition to reflect CARO2
+def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [CARO:0000043]
+subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
+subset: pheno_slim
 subset: upper_level
-synonym: "portion of tissue" EXACT []
-synonym: "simple tissue" NARROW []
+synonym: "portion of tissue" EXACT [CARO:0000043]
+synonym: "simple tissue" NARROW [AEO:0000043]
 synonym: "tissue portion" EXACT []
 xref: AAO:0000607
 xref: AAO:0010054
 xref: AEO:0000043
 xref: BILA:0000043
+xref: BIRNLEX:19
 xref: CALOHA:TS-2090
 xref: CARO:0000043
 xref: EHDAA2:0003043
-xref: FBbt:00007003
+xref: EMAPA:35868
 xref: FMA:9637
 xref: galen:Tissue
 xref: HAO:0000043
 xref: MA:0003002
-xref: MESH:A10
-xref: ncithesaurus:Tissue
-xref: NIF_GrossAnatomy:birnlex_19
+xref: MESH:D014024
+xref: NCIT:C12801
 xref: TAO:0001477
 xref: TGMA:0001844
-xref: UMLS:C0040300
 xref: VHOG:0001757
 xref: WBbt:0005729
 xref: XAO:0003040
 xref: ZFA:0001477
 is_a: UBERON:0010000 ! multicellular anatomical structure
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
+property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string
 
 [Term]
 id: UBERON:0000480
 name: anatomical group
-namespace: uberon
-def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." []
+def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." [CARO:0000054, http://orcid.org/0000-0001-9114-8737]
+subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 xref: AAO:0010008
 xref: AEO:0000054
@@ -16833,13 +16769,15 @@ xref: VHOG:0001724
 xref: XAO:0003001
 xref: ZFA:0001512
 is_a: UBERON:0000061 ! anatomical structure
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
+property_value: IAO:0000116 "Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]" xsd:string
 
 [Term]
 id: UBERON:0001062
 name: anatomical entity
 def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737]
 subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 xref: AAO:0010841
 xref: AEO:0000000
@@ -16854,78 +16792,58 @@ xref: MA:0000001
 xref: NCIT:C12219
 xref: TAO:0100000
 xref: TGMA:0001822
-xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"}
 xref: WBbt:0000100
 xref: XAO:0000000
 xref: ZFA:0100000
 is_a: BFO:0000004 ! independent continuant
-property_value: RO:0002175 NCBITaxon:33090
-property_value: RO:0002175 NCBITaxon:4751
 
 [Term]
 id: UBERON:0002405
 name: immune system
-namespace: uberon
-def: "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." []
-comment: This class was created automatically from a combination of ontologies
+def: "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." [Wikipedia:Immune_system]
+subset: human_reference_atlas
+subset: human_subset
+subset: mouse_subset
+subset: pheno_slim
 subset: uberon_slim
 subset: vertebrate_core
 xref: AAO:0011003
 xref: BILA:0000104
+xref: BTO:0005810
 xref: FMA:9825
 xref: GAID:328
 xref: MA:0002711
-xref: MESH:A15.382
-xref: ncithesaurus:Immune_System
-xref: OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA
+xref: MESH:D007107
+xref: NCIT:C12735
 xref: SCTID:362590003
 xref: TAO:0001159
-xref: UMLS:C0020962
 xref: VHOG:0001247
 xref: Wikipedia:Immune_system
 xref: XAO:0003152
 xref: ZFA:0001159
-is_a: UBERON:0000467 ! anatomical system
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string
+is_a: UBERON:0000465 ! material anatomical entity
 
 [Term]
 id: UBERON:0010000
 name: multicellular anatomical structure
-namespace: uberon
 def: "An anatomical structure that has more than one cell as a part." [CARO:0010000]
 subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
 synonym: "multicellular structure" EXACT [FBbt:00100313]
 xref: CARO:0010000
-xref: FBbt:00100313
 is_a: UBERON:0000061 ! anatomical structure
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: RO:0002175 NCBITaxon:33090
-property_value: RO:0002175 NCBITaxon:4751
 
 [Term]
 id: UBERON:0035943
 name: life cycle temporal boundary
-namespace: uberon
-def: "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity." []
+def: "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity." [https://orcid.org/0000-0002-6601-2165]
+subset: common_anatomy
+subset: human_subset
+subset: mouse_subset
 subset: upper_level
-is_a: BFO:0000015 ! process
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-
-[Term]
-id: UBERON:0035944
-name: life-death temporal boundary
-namespace: uberon
-def: "A life cycle temporal boundary that marks the end of the life cycle of the organism." []
-synonym: "death" RELATED []
-synonym: "end of life" RELATED []
-synonym: "end of life cycle" EXACT []
-synonym: "moment of death" EXACT []
-synonym: "time of death" EXACT []
-is_a: UBERON:0035943 ! life cycle temporal boundary
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
-property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
+is_a: BFO:0000035 ! process boundary
 
 [Term]
 id: UO:0000000
@@ -17022,7 +16940,7 @@ id: VO:0000001
 name: vaccine
 def: "A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine." []
 is_a: OBI:0000047 ! processed material
-relationship: OBI:0000312 VO:0000590 ! is_specified_output_of vaccine preparation
+relationship: OBI:0000312 VO:0000590 ! is specified output of vaccine preparation
 property_value: APOLLO_SV:0000040 "Vaccine" xsd:string
 property_value: IAO:0000116 "Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy." xsd:string
 property_value: IAO:0000117 "a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo." xsd:string
@@ -17062,7 +16980,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/vo.owl" xsd:string
 [Term]
 id: oboInOwl:ObsoleteClass
 name: Obsolete Class
-name: obsolete_class
 property_value: IAO:0000412 "http://www.geneontology.org/formats/oboInOwl" xsd:string
 
 [Term]
@@ -17071,14 +16988,14 @@ is_a: IAO:0000102 ! data about an ontology part
 
 [Typedef]
 id: APOLLO_SV:00000004
-name: basis of
+name: obsolete basis of
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
 is_obsolete: true
 
 [Typedef]
 id: APOLLO_SV:00000028
 name: obsolete is based on
-comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. 
+comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption.
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
 is_obsolete: true
 
@@ -17093,7 +17010,7 @@ is_asymmetric: true
 [Typedef]
 id: APOLLO_SV:00000057
 name: instantiates
-def: "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. " []
+def: "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times." []
 comment: Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.
 domain: BFO:0000001 ! entity
 is_asymmetric: true
@@ -17108,7 +17025,7 @@ is_asymmetric: true
 
 [Typedef]
 id: APOLLO_SV:00000116
-name: causally_precedes
+name: obsolete causally_precedes
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
 is_obsolete: true
@@ -17132,12 +17049,8 @@ range: BFO:0000019 ! quality
 [Typedef]
 id: BFO:0000054
 name: is realized by
-name: realized in
 def: "Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]" []
 comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
-property_value: ace_lexicon:TV_pl "BFO_0000054" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000054s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000054ed" xsd:string
 property_value: IAO:0000111 "obsolete_is_realized_by" xsd:string
 property_value: IAO:0000111 "realized in" xsd:string
 property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string
@@ -17165,10 +17078,8 @@ inverse_of: BFO:0000055 ! realizes
 [Typedef]
 id: BFO:0000055
 name: realizes
+def: "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" []
 comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
-property_value: ace_lexicon:TV_pl "BFO_0000055" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000055s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000055ed" xsd:string
 property_value: IAO:0000111 "realizes" xsd:string
 property_value: IAO:0000112 "this disease course realizes this disease" xsd:string
 property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string
@@ -17189,7 +17100,6 @@ property_value: IAO:0000116 "An example is: translation preceded_by transcriptio
 property_value: IAO:0000118 "is preceded by" xsd:string
 property_value: IAO:0000118 "preceded_by" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string
-property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string
 domain: BFO:0000003 ! occurrent
 range: BFO:0000003 ! occurrent
 holds_over_chain: part_of BFO:0000062
@@ -17213,7 +17123,6 @@ is_a: RO:0002222 ! temporal relation
 [Typedef]
 id: BFO:0000067
 name: contains process
-def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
 def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001" []
 comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
 property_value: BFO:0000179 "contains-process" xsd:string
@@ -17259,10 +17168,6 @@ name: exists at
 id: BFO:0000110
 name: has continuant part at all times
 def: "[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)" []
-def: "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])" []
-property_value: ace_lexicon:TV_pl "BFO_0000110" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000110s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000110ed" xsd:string
 property_value: BFO:0000179 "c-has-part_at" xsd:string
 property_value: BFO:0000180 "hasContinuantPartAt" xsd:string
 property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'" xsd:string
@@ -17276,9 +17181,6 @@ is_transitive: true
 id: BFO:0000111
 name: has proper continuant part at all times
 def: "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001" []
-property_value: ace_lexicon:TV_pl "BFO_0000111" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000111s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000111ed" xsd:string
 property_value: BFO:0000179 "c-has-ppart_at" xsd:string
 property_value: BFO:0000180 "hasProperContinuantPartAt" xsd:string
 property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'." xsd:string
@@ -17304,9 +17206,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 id: BFO:0000117
 name: has occurrent part
 def: "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" []
-property_value: ace_lexicon:TV_pl "BFO_0000117" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000117s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000117ed" xsd:string
 property_value: BFO:0000179 "o-has-part" xsd:string
 property_value: BFO:0000180 "hasOccurrentPart" xsd:string
 property_value: IAO:0000112 "[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life" xsd:string
@@ -17325,10 +17224,6 @@ inverse_of: BFO:0000132 ! part of occurrent
 id: BFO:0000118
 name: has proper occurrent part
 def: "[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])" []
-def: "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" []
-property_value: ace_lexicon:TV_pl "BFO_0000118" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000118s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000118ed" xsd:string
 property_value: BFO:0000179 "o-has-ppart" xsd:string
 property_value: BFO:0000180 "hasProperOccurrentPart" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string
@@ -17340,7 +17235,6 @@ is_a: BFO:0000117 ! has occurrent part
 id: BFO:0000121
 name: has temporal part
 def: "[copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])" []
-def: "[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t  & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" []
 property_value: BFO:0000179 "has-t-part" xsd:string
 property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" xsd:string
 property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life." xsd:string
@@ -17365,9 +17259,6 @@ range: BFO:0000004 ! independent continuant
 id: BFO:0000132
 name: part of occurrent
 def: "[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" []
-property_value: ace_lexicon:TV_pl "BFO_0000132" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000132s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000132ed" xsd:string
 property_value: BFO:0000179 "o-part-of" xsd:string
 property_value: BFO:0000180 "occurrentPartOf" xsd:string
 property_value: IAO:0000112 "Mary’s 5th birthday occurrent_part_of Mary’s life" xsd:string
@@ -17418,7 +17309,6 @@ inverse_of: BFO:0000187 ! has continuant part at all times that part exists
 id: BFO:0000138
 name: proper part of occurrent
 def: "[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" []
-def: "b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])" []
 property_value: BFO:0000179 "o-ppart-of" xsd:string
 property_value: BFO:0000180 "properOccurrentPartOf" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string
@@ -17430,7 +17320,6 @@ is_a: BFO:0000132 ! part of occurrent
 id: BFO:0000139
 name: temporal part of
 def: "b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])" []
-def: "b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t  & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" []
 property_value: BFO:0000179 "t-part-of" xsd:string
 property_value: BFO:0000180 "temporalPartOf" xsd:string
 property_value: IAO:0000112 "the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" xsd:string
@@ -17475,9 +17364,6 @@ name: during which exists
 [Typedef]
 id: BFO:0000167
 name: has participant at all times
-property_value: ace_lexicon:TV_pl "BFO_0000167" xsd:string
-property_value: ace_lexicon:TV_sg "BFO_0000167s" xsd:string
-property_value: ace_lexicon:TV_vbg "BFO_0000167ed" xsd:string
 
 [Typedef]
 id: BFO:0000169
@@ -17607,8 +17493,6 @@ range: GEO:000000400 ! governmental organization
 [Typedef]
 id: GEO:000000336
 name: has jurisdiction in
-comment: a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories.
-comment: if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b.
 comment: It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c.\n\nin other words, it is perfectly fine to say:\na disjoint b\nc has_jurisdiction_in a\nc has_jurisdiction_in b\n\notherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc.  We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc.  Seems like an unnecessary duplication of entities.
 domain: GEO:000000400 ! governmental organization
 range: GEO:000000375 ! land mass
@@ -17642,7 +17526,6 @@ is_obsolete: true
 id: IAO:0000136
 name: is about
 def: "A (currently) primitive relation that relates an information artifact to an entity." []
-def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." []
 property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string
 property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string
@@ -17816,7 +17699,7 @@ property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 domain: OBI:0000011 ! planned process
-is_a: RO:0000057 ! has_participant
+is_a: RO:0000057 ! has participant
 
 [Typedef]
 id: OBI:0000295
@@ -17831,8 +17714,9 @@ is_a: RO:0000056 ! participates in
 
 [Typedef]
 id: OBI:0000299
-name: has_specified_output
-def: "The inverse property of is_specified_output_of" []
+name: has specified output
+def: "The inverse property of is specified output of" []
+property_value: IAO:0000111 "has specified output" xsd:string
 property_value: IAO:0000111 "has_specified_output" xsd:string
 property_value: IAO:0000111 "has_specified_output" xsd:string
 property_value: IAO:0000114 IAO:0000122
@@ -17842,9 +17726,10 @@ property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string
 property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
+domain: COB:0000035 ! completely executed planned process
 domain: OBI:0000011 ! planned process
-is_a: RO:0000057 ! has_participant
-inverse_of: OBI:0000312 ! is_specified_output_of
+is_a: RO:0000057 ! has participant
+inverse_of: OBI:0000312 ! is specified output of
 
 [Typedef]
 id: OBI:0000308
@@ -17853,8 +17738,9 @@ is_obsolete: true
 
 [Typedef]
 id: OBI:0000312
-name: is_specified_output_of
-def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." []
+name: is specified output of
+def: "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." []
+property_value: IAO:0000111 "is specified output of" xsd:string
 property_value: IAO:0000111 "is_specified_output_of" xsd:string
 property_value: IAO:0000111 "is_specified_output_of" xsd:string
 property_value: IAO:0000114 IAO:0000122
@@ -17862,6 +17748,7 @@ property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string
 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
+range: COB:0000035 ! completely executed planned process
 range: OBI:0000011 ! planned process
 is_a: RO:0000056 ! participates in
 
@@ -17889,6 +17776,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 [Typedef]
 id: OBIB:0000732
 name: owns
+property_value: dc:source "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal." xsd:string
 inverse_of: OBIB:0000735 ! is owned by
@@ -17904,18 +17792,15 @@ is_asymmetric: true
 [Typedef]
 id: OMIABIS:0000008
 name: obsolete owns
-name: owns
 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
 property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string
 property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. " xsd:string
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
-is_obsolete: true
 replaced_by: OBIB:0000732
 
 [Typedef]
 id: OMIABIS:0000048
-name: is owned by
 name: obsolete is owned by
 def: "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." []
 property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string
@@ -17942,9 +17827,7 @@ range: OMRSE:00000056 ! hospital organization
 [Typedef]
 id: RO:0000052
 name: characteristic of
-name: inheres in
 def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
-def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" []
 comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
 property_value: IAO:0000111 "inheres in" xsd:string
 property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string
@@ -17956,15 +17839,11 @@ property_value: IAO:0000118 "inheres_in" xsd:string
 property_value: RO:0001900 RO:0001901
 is_functional: true
 is_a: RO:0002314 ! characteristic of part of
-inverse_of: RO:0000053 ! is bearer of
+inverse_of: RO:0000053 ! bearer of
 
 [Typedef]
 id: RO:0000053
 name: bearer of
-name: bearer_of
-name: has characteristic
-name: is bearer of
-def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" []
 def: "Inverse of characteristic_of" []
 property_value: IAO:0000111 "bearer of" xsd:string
 property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
@@ -17975,7 +17854,7 @@ property_value: IAO:0000118 "bearer_of" xsd:string
 property_value: IAO:0000118 "is bearer of" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string
 property_value: RO:0001900 RO:0001901
-range: BFO:0000020 ! characteristic
+range: BFO:0000020 ! specifically dependent continuant
 is_inverse_functional: true
 
 [Typedef]
@@ -17990,12 +17869,11 @@ property_value: IAO:0000118 "participates_in" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 domain: BFO:0000002 ! continuant
 range: BFO:0000003 ! occurrent
-inverse_of: RO:0000057 ! has_participant
+inverse_of: RO:0000057 ! has participant
 
 [Typedef]
 id: RO:0000057
 name: has participant
-name: has_participant
 def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
 property_value: dc:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string
 property_value: IAO:0000111 "has participant" xsd:string
@@ -18014,25 +17892,21 @@ holds_over_chain: has_part RO:0000057
 [Typedef]
 id: RO:0000058
 name: is concretized as
-def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." []
-property_value: IAO:0000111 "is concretized as" xsd:string
+def: "A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes." []
 property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string
 property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 domain: BFO:0000031 ! generically dependent continuant
-range: BFO:0000020 ! characteristic
+range: BFO:0000020 ! specifically dependent continuant
 inverse_of: RO:0000059 ! concretizes
 
 [Typedef]
 id: RO:0000059
 name: concretizes
 def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." []
-property_value: IAO:0000111 "concretizes" xsd:string
 property_value: IAO:0000111 "is_concretization_of" xsd:string
 property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string
 property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string
-property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
-domain: BFO:0000020 ! characteristic
+domain: BFO:0000020 ! specifically dependent continuant
 range: BFO:0000031 ! generically dependent continuant
 
 [Typedef]
@@ -18045,7 +17919,7 @@ property_value: IAO:0000116 "A function inheres in its bearer at all times for w
 property_value: IAO:0000118 "function_of" xsd:string
 property_value: IAO:0000118 "is function of" xsd:string
 domain: BFO:0000034 ! function
-is_a: RO:0000052 ! inheres in
+is_a: RO:0000052 ! characteristic of
 inverse_of: RO:0000085 ! has function
 
 [Typedef]
@@ -18057,7 +17931,7 @@ property_value: IAO:0000112 "this red color is a quality of this apple" xsd:stri
 property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string
 property_value: IAO:0000118 "is quality of" xsd:string
 property_value: IAO:0000118 "quality_of" xsd:string
-is_a: RO:0000052 ! inheres in
+is_a: RO:0000052 ! characteristic of
 inverse_of: RO:0000086 ! has quality
 
 [Typedef]
@@ -18069,7 +17943,7 @@ property_value: IAO:0000112 "this investigator role is a role of this person" xs
 property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string
 property_value: IAO:0000118 "is role of" xsd:string
 property_value: IAO:0000118 "role_of" xsd:string
-is_a: RO:0000052 ! inheres in
+is_a: RO:0000052 ! characteristic of
 inverse_of: RO:0000087 ! has role
 
 [Typedef]
@@ -18081,7 +17955,7 @@ property_value: IAO:0000116 "A bearer can have many functions, and its functions
 property_value: IAO:0000118 "has_function" xsd:string
 domain: BFO:0000004 ! independent continuant
 range: BFO:0000034 ! function
-is_a: RO:0000053 ! is bearer of
+is_a: RO:0000053 ! bearer of
 
 [Typedef]
 id: RO:0000086
@@ -18091,7 +17965,7 @@ property_value: IAO:0000112 "this apple has quality this red color" xsd:string
 property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
 property_value: IAO:0000118 "has_quality" xsd:string
 range: BFO:0000019 ! quality
-is_a: RO:0000053 ! is bearer of
+is_a: RO:0000053 ! bearer of
 
 [Typedef]
 id: RO:0000087
@@ -18102,7 +17976,7 @@ property_value: IAO:0000116 "A bearer can have many roles, and its roles can exi
 property_value: IAO:0000118 "has_role" xsd:string
 domain: BFO:0000004 ! independent continuant
 range: BFO:0000023 ! role
-is_a: RO:0000053 ! is bearer of
+is_a: RO:0000053 ! bearer of
 
 [Typedef]
 id: RO:0000091
@@ -18110,7 +17984,7 @@ name: has disposition
 def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" []
 domain: BFO:0000004 ! independent continuant
 range: BFO:0000016 ! disposition
-is_a: RO:0000053 ! is bearer of
+is_a: RO:0000053 ! bearer of
 inverse_of: RO:0000092 ! disposition of
 
 [Typedef]
@@ -18119,7 +17993,7 @@ name: disposition of
 def: "inverse of has disposition" []
 comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
 subset: RO:0002259
-is_a: RO:0000052 ! inheres in
+is_a: RO:0000052 ! characteristic of
 
 [Typedef]
 id: RO:0001000
@@ -18170,12 +18044,11 @@ property_value: IAO:0000116 "Most location relations will only hold at certain t
 property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
 property_value: IAO:0000118 "located_in" xsd:string
 property_value: RO:0001900 RO:0001901
-property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI
 property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string
 domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
 range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
 is_transitive: true
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 
 [Typedef]
 id: RO:0002000
@@ -18293,7 +18166,7 @@ id: RO:0002084
 name: during which ends
 comment: Previously had ID  http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point.  No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line.  Official ID now chosen from DOS ID range.
 subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
+property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 is_a: RO:0002222 ! temporal relation
 inverse_of: ends_during ! ends during
 
@@ -18302,7 +18175,7 @@ id: RO:0002086
 name: ends after
 comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
 subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
+property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 holds_over_chain: ends_during BFO:0000062
 is_transitive: true
 is_a: RO:0002222 ! temporal relation
@@ -18310,14 +18183,11 @@ is_a: RO:0002222 ! temporal relation
 [Typedef]
 id: RO:0002090
 name: immediately precedes
-name: immediately_precedes
 comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
 subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 property_value: IAO:0000118 "ends_at_start_of" xsd:string
 property_value: IAO:0000118 "meets" xsd:string
-property_value: RO:0002575 BFO:0000063
 holds_over_chain: RO:0002230 RO:0002224
 is_a: BFO:0000063 ! precedes
 
@@ -18330,12 +18200,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam
 subset: ro-eco
 property_value: IAO:0000114 IAO:0000125
 property_value: RO:0001900 RO:0001901
-holds_over_chain: has_part part_of {RO:0002582="true"}
 holds_over_chain: has_part RO:0002131
 holds_over_chain: part_of part_of
 is_symmetric: true
 is_a: RO:0002323 ! mereotopologically related to
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []
 
 [Typedef]
@@ -18352,7 +18221,6 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" xsd:string
 property_value: RO:0001900 RO:0001901
-property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI
 is_a: RO:0002323 ! mereotopologically related to
 expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" []
 
@@ -18365,7 +18233,6 @@ property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string
 property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string
 property_value: RO:0001900 RO:0001901
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency
 is_a: has_part ! has part
 
 [Typedef]
@@ -18390,17 +18257,13 @@ name: capable of part of
 def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "has function in" xsd:string
-property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
-holds_over_chain: RO:0002215 part_of {RO:0002582="true"}
 is_a: RO:0002328 ! functionally related to
 is_a: RO:0002500 ! causal agent in process
 
 [Typedef]
 id: RO:0002218
-name: has active participant
 name: obsolete has active participant
 def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" []
-def: "x has participant y if and only if x realizes some active role that inheres in y" []
 subset: ro-eco
 property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string
 property_value: IAO:0000114 IAO:0000125
@@ -18409,8 +18272,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "has agent" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string
-is_a: RO:0000057 ! has_participant
-is_obsolete: true
+is_a: RO:0000057 ! has participant
 replaced_by: RO:0002500
 
 [Typedef]
@@ -18420,7 +18282,7 @@ def: "x adjacent to y if and only if x and y share a boundary." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
-property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"}
+property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string
 property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string
 property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string
 property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string
@@ -18438,7 +18300,6 @@ is_a: RO:0002163 ! spatially disjoint from
 [Typedef]
 id: RO:0002222
 name: temporal relation
-name: temporally related to
 comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
 subset: ro-eco
 property_value: IAO:0000114 IAO:0000125
@@ -18448,7 +18309,6 @@ property_value: IAO:0000119 "Allen" xsd:string
 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
-property_value: terms:source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI
 domain: BFO:0000003 ! occurrent
 range: BFO:0000003 ! occurrent
 
@@ -18458,10 +18318,9 @@ name: starts
 def: "inverse of starts with" []
 subset: ro-eco
 property_value: IAO:0000114 IAO:0000125
-property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000119 "Allen" xsd:string
-is_a: part_of ! part_of
+is_a: part_of ! part of
 is_a: RO:0002222 ! temporal relation
 inverse_of: RO:0002224 ! starts with
 
@@ -18472,7 +18331,6 @@ def: "x starts with y if and only if x has part y and the time point at which x
 subset: ro-eco
 property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string
 property_value: IAO:0000114 IAO:0000125
-property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "started by" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
@@ -18487,9 +18345,8 @@ def: "inverse of ends with" []
 subset: ro-eco
 property_value: dc:source "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl" xsd:string
 property_value: IAO:0000114 IAO:0000125
-property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-is_a: part_of ! part_of
+is_a: part_of ! part of
 is_a: RO:0002222 ! temporal relation
 inverse_of: RO:0002230 ! ends with
 
@@ -18500,7 +18357,6 @@ def: "x ends with y if and only if x has part y and the time point at which x en
 subset: ro-eco
 property_value: dc:source "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl" xsd:string
 property_value: IAO:0000114 IAO:0000125
-property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "finished by" xsd:string
 property_value: IAO:0000118 "finished with" xsd:string
@@ -18545,17 +18401,15 @@ subset: ro-eco
 property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "consumes" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI
 domain: BFO:0000015 ! process
 holds_over_chain: RO:0002224 RO:0002233
-is_a: RO:0000057 ! has_participant
+is_a: RO:0000057 ! has participant
 inverse_of: RO:0002352 ! input of
 
 [Typedef]
 id: RO:0002234
 name: has output
 def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." []
-def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
@@ -18564,9 +18418,8 @@ property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "produces" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI
 holds_over_chain: RO:0002230 RO:0002234
-is_a: RO:0000057 ! has_participant
+is_a: RO:0000057 ! has participant
 inverse_of: RO:0002353 ! output of
 
 [Typedef]
@@ -18575,7 +18428,6 @@ name: acts upstream of
 def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
 property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
-property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
 holds_over_chain: RO:0002327 RO:0002411
 is_a: RO:0002264 ! acts upstream of or within
 
@@ -18586,7 +18438,6 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
 synonym: "affects" RELATED []
 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0002418
 is_a: RO:0002500 ! causal agent in process
 
@@ -18597,9 +18448,6 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of
 comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
-property_value: RO:0004049 RO:0002411
-property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect
-property_value: terms:creator https://orcid.org/0000-0002-6601-2165
 is_a: RO:0002411 ! causally upstream of
 is_a: RO:0004047 ! causally upstream of or within, positive effect
 
@@ -18609,9 +18457,6 @@ name: causally upstream of, negative effect
 def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
-property_value: RO:0004050 RO:0002411
-property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect
-property_value: terms:creator https://orcid.org/0000-0002-6601-2165
 is_a: RO:0002411 ! causally upstream of
 is_a: RO:0004046 ! causally upstream of or within, negative effect
 
@@ -18624,10 +18469,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "inheres in part of" xsd:string
 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
 property_value: RO:0001900 RO:0001901
-property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
-holds_over_chain: RO:0000052 part_of {RO:0002582="true"}
 is_a: RO:0002502 ! depends on
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 
 [Typedef]
 id: RO:0002323
@@ -18666,7 +18509,6 @@ property_value: IAO:0000118 "has" xsd:string
 property_value: IAO:0000118 "is catalyzing" xsd:string
 property_value: IAO:0000118 "is executing" xsd:string
 property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI
 is_a: RO:0002215 ! capable of
 inverse_of: RO:0002333 ! enabled by
 transitive_over: has_part ! has part
@@ -18685,7 +18527,6 @@ name: part of structure that is capable of
 def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "false" xsd:boolean
-holds_over_chain: part_of RO:0002215 {RO:0002581="true"}
 is_a: RO:0002328 ! functionally related to
 
 [Typedef]
@@ -18695,11 +18536,10 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "actively involved in" xsd:string
 property_value: IAO:0000118 "enables part of" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI
 holds_over_chain: RO:0002327 part_of
 is_a: RO:0000056 ! participates in
 is_a: RO:0002431 ! involved in or involved in regulation of
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 
 [Typedef]
 id: RO:0002333
@@ -18707,8 +18547,7 @@ name: enabled by
 def: "inverse of enables" []
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI
-is_a: RO:0000057 ! has_participant
+is_a: RO:0000057 ! has participant
 is_a: RO:0002328 ! functionally related to
 
 [Typedef]
@@ -18748,7 +18587,7 @@ property_value: IAO:0000118 "is member of" xsd:string
 property_value: IAO:0000118 "member part of" xsd:string
 property_value: IAO:0000119 "SIO" xsd:string
 property_value: RO:0001900 RO:0001901
-is_a: part_of ! part_of
+is_a: part_of ! part of
 inverse_of: RO:0002351 ! has member
 
 [Typedef]
@@ -18806,7 +18645,7 @@ id: RO:0002405
 name: immediately causally downstream of
 property_value: IAO:0000114 IAO:0000428
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-is_a: immediately_preceded_by ! immediately preceded by
+is_a: immediately_preceded_by ! immediately_preceded_by
 is_a: RO:0002404 ! causally downstream of
 inverse_of: RO:0002412 ! immediately causally upstream of
 
@@ -18816,8 +18655,6 @@ name: indirectly positively regulates
 def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "indirectly activates" xsd:string
-property_value: RO:0002579 RO:0002213
-property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI
 holds_over_chain: RO:0002409 RO:0002409
 holds_over_chain: RO:0002629 RO:0002407
 holds_over_chain: RO:0002629 RO:0002629
@@ -18832,8 +18669,6 @@ name: indirectly negatively regulates
 def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "indirectly inhibits" xsd:string
-property_value: RO:0002579 RO:0002212
-property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI
 holds_over_chain: RO:0002630 RO:0002409
 holds_over_chain: RO:0002630 RO:0002630
 is_transitive: true
@@ -18853,7 +18688,6 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a
 id: RO:0002411
 name: causally upstream of
 def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" []
-def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000114 IAO:0000428
@@ -18870,10 +18704,34 @@ id: RO:0002412
 name: immediately causally upstream of
 def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: RO:0002575 RO:0002411
 is_a: RO:0002090 ! immediately precedes
 is_a: RO:0002411 ! causally upstream of
 
+[Typedef]
+id: RO:0002413
+name: provides input for
+def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." []
+property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
+property_value: IAO:0000118 "directly provides input for" xsd:string
+property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
+property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string
+holds_over_chain: RO:0002234 RO:0002233
+is_a: RO:0002412 ! immediately causally upstream of
+is_a: RO:0002414 ! transitively provides input for
+
+[Typedef]
+id: RO:0002414
+name: transitively provides input for
+def: "transitive form of directly_provides_input_for" []
+property_value: IAO:0000114 IAO:0000428
+property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
+property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string
+property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string
+domain: BFO:0000015 ! process
+range: BFO:0000015 ! process
+is_transitive: true
+is_a: RO:0004047 ! causally upstream of or within, positive effect
+
 [Typedef]
 id: RO:0002418
 name: causally upstream of or within
@@ -18885,6 +18743,7 @@ property_value: IAO:0000118 "influences (processual)" xsd:string
 is_transitive: true
 is_a: RO:0002501 ! causal relation between processes
 inverse_of: RO:0002427 ! causally downstream of or within
+transitive_over: part_of ! part of
 
 [Typedef]
 id: RO:0002427
@@ -18911,7 +18770,6 @@ id: RO:0002429
 name: involved in positive regulation of
 def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: RO:0004049 RO:0002428
 holds_over_chain: RO:0002327 positively_regulates
 holds_over_chain: RO:0002331 positively_regulates
 is_a: RO:0002428 ! involved in regulation of
@@ -18921,7 +18779,6 @@ id: RO:0002430
 name: involved in negative regulation of
 def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: RO:0004050 RO:0002428
 holds_over_chain: RO:0002327 negatively_regulates
 holds_over_chain: RO:0002331 negatively_regulates
 is_a: RO:0002428 ! involved in regulation of
@@ -18945,8 +18802,6 @@ synonym: "enables activity in" EXACT []
 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "executes activity in" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI
-holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"}
 is_a: RO:0002131 ! overlaps
 is_a: RO:0002328 ! functionally related to
 
@@ -18960,8 +18815,6 @@ property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'
 property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string
-property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI
-property_value: skos:closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI
 domain: BFO:0000040 ! material entity
 range: BFO:0000040 ! material entity
 is_symmetric: true
@@ -18973,8 +18826,6 @@ def: "An interaction relationship in which the two partners are molecular entiti
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000118 "binds" xsd:string
 property_value: IAO:0000118 "molecularly binds with" xsd:string
-property_value: seeAlso ECO:0000353
-property_value: skos:closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI
 is_symmetric: true
 is_a: RO:0002434 ! interacts with
 
@@ -19036,7 +18887,6 @@ subset: ro-eco
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 domain: BFO:0000003 ! occurrent
 range: BFO:0000004 ! independent continuant
-holds_over_chain: has_part occurs_in {RO:0002581="true"}
 
 [Typedef]
 id: RO:0002481
@@ -19056,7 +18906,6 @@ inverse_of: RO:0002608 ! process has causal agent
 id: RO:0002501
 name: causal relation between processes
 def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." []
-def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." []
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
@@ -19070,7 +18919,6 @@ is_a: RO:0002410 ! causally related to
 id: RO:0002502
 name: depends on
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: seeAlso BFO:0000169
 
 [Typedef]
 id: RO:0002506
@@ -19096,8 +18944,6 @@ inverse_of: RO:0002566 ! causally influences
 id: RO:0002563
 name: interaction relation helper property
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29
-property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI
 is_a: RO:0002464 ! helper property (not for use in curation)
 
 [Typedef]
@@ -19128,7 +18974,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
 property_value: IAO:0000589 "directly regulates (processual)" xsd:string
-property_value: RO:0002575 RO:0002211
 is_a: regulates ! regulates
 is_a: RO:0002412 ! immediately causally upstream of
 
@@ -19195,8 +19040,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
 property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string
-property_value: RO:0004049 RO:0002578
-property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI
 is_a: positively_regulates ! positively regulates
 is_a: RO:0002578 ! directly regulates
 
@@ -19209,8 +19052,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
 property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string
-property_value: RO:0004050 RO:0002578
-property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI
 is_a: negatively_regulates ! negatively regulates
 is_a: RO:0002578 ! directly regulates
 
@@ -19260,8 +19101,6 @@ creation_date: 2018-01-25T23:20:13Z
 id: RO:0004032
 name: acts upstream of or within, positive effect
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
-property_value: RO:0004049 RO:0002264
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0004047
 is_a: RO:0002264 ! acts upstream of or within
 created_by: https://orcid.org/0000-0002-6601-2165
@@ -19271,8 +19110,6 @@ creation_date: 2018-01-26T23:49:30Z
 id: RO:0004033
 name: acts upstream of or within, negative effect
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
-property_value: RO:0004050 RO:0002264
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0004046
 is_a: RO:0002264 ! acts upstream of or within
 created_by: https://orcid.org/0000-0002-6601-2165
@@ -19283,8 +19120,6 @@ id: RO:0004034
 name: acts upstream of, positive effect
 def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
-property_value: RO:0004049 RO:0002263
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0002304
 is_a: RO:0002263 ! acts upstream of
 is_a: RO:0004032 ! acts upstream of or within, positive effect
@@ -19296,8 +19131,6 @@ id: RO:0004035
 name: acts upstream of, negative effect
 def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
-property_value: RO:0004050 RO:0002263
-property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI
 holds_over_chain: RO:0002327 RO:0002305
 is_a: RO:0002263 ! acts upstream of
 is_a: RO:0004033 ! acts upstream of or within, negative effect
@@ -19307,8 +19140,6 @@ creation_date: 2018-01-26T23:53:22Z
 [Typedef]
 id: RO:0004046
 name: causally upstream of or within, negative effect
-property_value: RO:0004050 RO:0002418
-property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI
 is_a: RO:0002418 ! causally upstream of or within
 created_by: https://orcid.org/0000-0002-6601-2165
 creation_date: 2018-03-13T23:55:05Z
@@ -19316,8 +19147,6 @@ creation_date: 2018-03-13T23:55:05Z
 [Typedef]
 id: RO:0004047
 name: causally upstream of or within, positive effect
-property_value: RO:0004049 RO:0002418
-property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect
 is_a: RO:0002418 ! causally upstream of or within
 created_by: https://orcid.org/0000-0002-6601-2165
 creation_date: 2018-03-13T23:55:19Z
@@ -19341,7 +19170,6 @@ synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165]
 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string
 property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string
 property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string
-property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI
 property_value: terms:contributor https://orcid.org/0000-0001-6996-0040
 property_value: terms:contributor https://orcid.org/0000-0002-6601-2165
 property_value: terms:contributor https://orcid.org/0000-0002-7073-9172
@@ -19445,6 +19273,13 @@ holds_over_chain: negatively_regulates RO:0019001
 holds_over_chain: positively_regulates RO:0019002
 is_a: RO:0019000 ! regulates characteristic
 
+[Typedef]
+id: RO:0020105
+name: is anatomical entity
+def: "This property only applies to anatomical entities." []
+property_value: terms:contributor https://orcid.org/0000-0001-6677-8489
+domain: UBERON:0001062 ! anatomical entity
+
 [Typedef]
 id: bearer_of
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
@@ -19458,6 +19293,7 @@ comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND
 subset: ro-eco
 xref: RO:0002093
 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
+property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 property_value: IAO:0000118 "o" xsd:string
 property_value: IAO:0000118 "overlaps" xsd:string
 is_a: RO:0002222 ! temporal relation
@@ -19501,7 +19337,6 @@ is_obsolete: true
 
 [Typedef]
 id: immediately_preceded_by
-name: immediately preceded by
 name: immediately_preceded_by
 namespace: uberon
 def: "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" []
@@ -19512,7 +19347,7 @@ synonym: "is immediately preceded by" EXACT []
 synonym: "starts_at_end_of" EXACT []
 xref: http://semanticscience.org/resource/SIO_000251
 xref: RO:0002087
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
+property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
 property_value: IAO:0000118 "starts_at_end_of" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string
 property_value: UBPROP:0000001 "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." xsd:string
@@ -19537,7 +19372,6 @@ name: negatively_regulates
 namespace: external
 namespace: relationship
 def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." []
-def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
@@ -19549,7 +19383,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string
 property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
-property_value: RO:0004050 RO:0002211
 holds_over_chain: RO:0002230 negatively_regulates
 is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
 is_a: regulates ! regulates
@@ -19564,12 +19397,10 @@ name: ObsoleteProperty
 [Typedef]
 id: occurs_in
 name: occurs in
-name: unfolds_in
 namespace: external
 namespace: relationship
 def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
 comment: Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
-comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
@@ -19581,17 +19412,15 @@ property_value: IAO:0000118 "unfolds_in" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string
 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string
 property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
-property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI
 domain: BFO:0000003 ! occurrent
 range: BFO:0000004 ! independent continuant
 holds_over_chain: part_of occurs_in
 inverse_of: BFO:0000067 ! contains process
-transitive_over: part_of ! part_of
+transitive_over: part_of ! part of
 
 [Typedef]
 id: part_of
 name: part of
-name: part_of
 namespace: external
 def: "a core relation that holds between a part and its whole" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
@@ -19609,17 +19438,7 @@ property_value: IAO:0000116 "Occurrents are not subject to change and so parthoo
 property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
 property_value: IAO:0000118 "part_of" xsd:string
 property_value: RO:0001900 RO:0001901
-property_value: RO:0040042 BFO:0000002
-property_value: RO:0040042 BFO:0000003
-property_value: RO:0040042 BFO:0000004
-property_value: RO:0040042 BFO:0000017
-property_value: RO:0040042 BFO:0000019
-property_value: RO:0040042 BFO:0000020
-property_value: RO:0040042 BFO:0000031
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
 property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI
 is_reflexive: true
 is_transitive: true
 is_a: RO:0002131 ! overlaps
@@ -19637,7 +19456,6 @@ xref: RO:0002213
 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
 property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
-property_value: RO:0004049 RO:0002211
 holds_over_chain: negatively_regulates negatively_regulates
 holds_over_chain: RO:0002230 positively_regulates
 is_transitive: true
@@ -19667,7 +19485,6 @@ name: regulates
 namespace: external
 namespace: relationship
 def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." []
-def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
diff --git a/apollo_sv.owl b/apollo_sv.owl
index 0dac2c8..c8384fd 100644
--- a/apollo_sv.owl
+++ b/apollo_sv.owl
@@ -27,7 +27,7 @@
      xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"
      xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/apollo_sv.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv.owl"/>
         <dc:contributor>Amanda Hicks</dc:contributor>
         <dc:contributor>John Levander</dc:contributor>
         <dc:contributor>Josh Hanna</dc:contributor>
@@ -43,7 +43,7 @@
         <www:RTS_00000001>C87985BA-6A8A-483A-A6B6-63975101F672</www:RTS_00000001>
         <www:RTS_00000002>082D5D78-D916-457E-B4FD-365F86F45B30</www:RTS_00000002>
         <rdfs:comment xml:lang="en">When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl.  When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component&apos;s Uniform Resource Identifier (URI).</rdfs:comment>
-        <owl:versionInfo>2024-12-24</owl:versionInfo>
+        <owl:versionInfo>2026-03-13</owl:versionInfo>
     </owl:Ontology>
     
 
@@ -59,24 +59,6 @@
     
 
 
-    <!-- http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl -->
-
-    <owl:AnnotationProperty rdf:about="http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl"/>
-    
-
-
-    <!-- http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg -->
-
-    <owl:AnnotationProperty rdf:about="http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg"/>
-    
-
-
-    <!-- http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg -->
-
-    <owl:AnnotationProperty rdf:about="http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg"/>
-    
-
-
     <!-- http://protege.stanford.edu/plugins/owl/protege#defaultLanguage -->
 
     <owl:AnnotationProperty rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
@@ -86,8 +68,7 @@
     <!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000319 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000319">
-        <obo:IAO_0000118 xml:lang="en">National Library of Medicine Identifier
-</obo:IAO_0000118>
+        <obo:IAO_0000118 xml:lang="en">National Library of Medicine Identifier</obo:IAO_0000118>
         <rdfs:comment xml:lang="en">This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed.</rdfs:comment>
         <rdfs:label xml:lang="en">NLM ID</rdfs:label>
     </owl:AnnotationProperty>
@@ -481,7 +462,6 @@ We also have the outstanding issue of how to aim different definitions to differ
         <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
         <rdfs:comment>Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).</rdfs:comment>
-        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
         <rdfs:label xml:lang="en">alternative label</rdfs:label>
         <rdfs:label xml:lang="en">alternative term</rdfs:label>
     </owl:AnnotationProperty>
@@ -913,24 +893,25 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
+    <!-- http://purl.obolibrary.org/obo/OMO_0003004 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0003004">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/RO_0001900 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001900">
         <obo:IAO_0000115>An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.</obo:IAO_0000115>
         <rdfs:label>temporal interpretation</rdfs:label>
         <rdfs:label xml:lang="en">temporal interpretation</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"/>
         <foaf:page rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/oborel/obo-relations/wiki/ROAndTime</foaf:page>
     </owl:AnnotationProperty>
     
 
 
-    <!-- http://purl.obolibrary.org/obo/RO_0002175 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002175"/>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/RO_0002259 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002259">
@@ -939,54 +920,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://purl.obolibrary.org/obo/RO_0002575 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002575"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0002579 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002579"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0002581 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002581">
-        <obo:IAO_0000115>If R &lt;- P o Q is a defining property chain axiom, then it also holds that R -&gt; P o Q. Note that this cannot be expressed directly in OWL</obo:IAO_0000115>
-        <rdfs:label>is a defining property chain axiom</rdfs:label>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0002582 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002582">
-        <obo:IAO_0000115>If R &lt;- P o Q is a defining property chain axiom, then (1) R -&gt; P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.</obo:IAO_0000115>
-        <rdfs:label>is a defining property chain axiom where second argument is reflexive</rdfs:label>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0004049 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0004049"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0004050 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0004050"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/RO_0040042 -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0040042"/>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/STATO_0000032 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000032">
@@ -1245,7 +1178,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/ro/subsets#ro-eco">
         <rdfs:label>eco subset</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/subsets/"/>
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
     </owl:AnnotationProperty>
     
@@ -1259,9 +1191,51 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
+    <!-- http://purl.obolibrary.org/obo/uberon/core#efo_slim -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#efo_slim">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/uberon/core#human_subset -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#human_subset">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/uberon/core#mouse_subset -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#mouse_subset">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/uberon/core#pheno_slim -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#pheno_slim">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/uberon/core#uberon_slim -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#uberon_slim"/>
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#uberon_slim">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
     
 
 
@@ -1275,7 +1249,9 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
     <!-- http://purl.obolibrary.org/obo/uberon/core#vertebrate_core -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#vertebrate_core"/>
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon/core#vertebrate_core">
+        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
+    </owl:AnnotationProperty>
     
 
 
@@ -1405,12 +1381,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://purl.org/dc/terms/creator -->
-
-    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/creator"/>
-    
-
-
     <!-- http://purl.org/dc/terms/description -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description"/>
@@ -1435,12 +1405,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled -->
-
-    <owl:AnnotationProperty rdf:about="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled"/>
-    
-
-
     <!-- http://usefulinc.com/ns/doap#bug-database -->
 
     <owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#bug-database"/>
@@ -1453,21 +1417,25 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
+    <!-- http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by"/>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#creation_date -->
+    <!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#creation_date"/>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by">
+        <rdfs:label>created by</rdfs:label>
+    </owl:AnnotationProperty>
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#default-namespace -->
+    <!-- http://www.geneontology.org/formats/oboInOwl#creation_date -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#default-namespace"/>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#creation_date">
+        <rdfs:label>creation date</rdfs:label>
+    </owl:AnnotationProperty>
     
 
 
@@ -1496,7 +1464,11 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
+        <obo:IAO_0000112>disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) &quot;NCIT:C41009&quot;^^xsd:string</obo:IAO_0000112>
+        <obo:IAO_0000115>An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.</obo:IAO_0000115>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label>database_cross_reference</rdfs:label>
+        <rdfs:label>has cross-reference</rdfs:label>
     </owl:AnnotationProperty>
     
 
@@ -1537,12 +1509,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion -->
-
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion"/>
-    
-
-
     <!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace">
@@ -1597,12 +1563,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#source -->
-
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#source"/>
-    
-
-
     <!-- http://www.referent-tracking.com/RTS_00000001 -->
 
     <owl:AnnotationProperty rdf:about="http://www.referent-tracking.com/RTS_00000001">
@@ -1648,12 +1608,6 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     
 
 
-    <!-- http://www.w3.org/2004/02/skos/core#closeMatch -->
-
-    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#closeMatch"/>
-    
-
-
     <!-- http://xmlns.com/foaf/0.1/homepage -->
 
     <owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
@@ -1687,7 +1641,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000004">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
-        <rdfs:label xml:lang="en">basis of</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete basis of</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
@@ -1697,7 +1651,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000028">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
-        <rdfs:comment xml:lang="en">p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. </rdfs:comment>
+        <rdfs:comment xml:lang="en">p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption.</rdfs:comment>
         <rdfs:label xml:lang="en">obsolete is based on</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
@@ -1740,7 +1694,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AsymmetricProperty"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#IrreflexiveProperty"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
-        <obo:IAO_0000115 xml:lang="en">A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times.</obo:IAO_0000115>
         <rdfs:comment>Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.</rdfs:comment>
         <rdfs:label xml:lang="en">instantiates</rdfs:label>
     </owl:ObjectProperty>
@@ -1765,7 +1719,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000116">
         <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
-        <rdfs:label xml:lang="en">causally_precedes</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete causally_precedes</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
@@ -1820,13 +1774,6 @@ For example, the disposition of a piece of glass to bend light and the lattice s
 A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An occurrent cannot be part of a continuant: use &apos;has participant&apos;. A material entity cannot be part of an immaterial entity: use &apos;has location&apos;. A specifically dependent continuant cannot be part of an independent continuant: use &apos;inheres in&apos;. An independent continuant cannot be part of a specifically dependent continuant: use &apos;bearer of&apos;.</obo:IAO_0000116>
         <obo:IAO_0000118 xml:lang="en">part_of</obo:IAO_0000118>
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
         <oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>external</oboInOwl:hasOBONamespace>
         <oboInOwl:id>part_of</oboInOwl:id>
@@ -1838,10 +1785,7 @@ A continuant cannot be part of an occurrent: use &apos;participates in&apos;. An
         <rdfs:label>part of</rdfs:label>
         <rdfs:label xml:lang="en">part of</rdfs:label>
         <rdfs:label xml:lang="en">part_of</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections"/>
-        <rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:PartOf"/>
         <rdfs:seeAlso>http://www.obofoundry.org/ro/#OBO_REL:part_of</rdfs:seeAlso>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Part_of</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -1886,9 +1830,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <ace_lexicon:TV_pl>BFO_0000054</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000054s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000054ed</ace_lexicon:TV_vbg>
         <obo:IAO_0000111 xml:lang="en">obsolete_is_realized_by</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">realized in</obo:IAO_0000111>
         <obo:IAO_0000112 xml:lang="en">this disease is realized in this disease course</obo:IAO_0000112>
@@ -1922,13 +1863,11 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000055">
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
-        <ace_lexicon:TV_pl>BFO_0000055</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000055s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000055ed</ace_lexicon:TV_vbg>
         <obo:IAO_0000111 xml:lang="en">realizes</obo:IAO_0000111>
         <obo:IAO_0000112 xml:lang="en">this disease course realizes this disease</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">this investigation realizes this investigator role</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">this shattering realizes this fragility</obo:IAO_0000112>
+        <obo:IAO_0000115 xml:lang="en">Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">to say that b realizes c at t is to assert that there is some material entity d &amp; b is a process which has participant d at t &amp; c is a disposition or role of which d is bearer_of at t&amp; the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])</obo:IAO_0000600>
         <rdfs:comment>Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</rdfs:comment>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
@@ -1957,7 +1896,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
         <obo:IAO_0000118 xml:lang="en">preceded_by</obo:IAO_0000118>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/ro.owl</obo:IAO_0000412>
         <dc:source>http://www.obofoundry.org/ro/#OBO_REL:preceded_by</dc:source>
-        <terms:source>http://www.obofoundry.org/ro/#OBO_REL:preceded_by</terms:source>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">preceded by</rdfs:label>
     </owl:ObjectProperty>
@@ -2020,7 +1958,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
         <rdfs:label>occurs in</rdfs:label>
         <rdfs:label xml:lang="en">occurs in</rdfs:label>
         <rdfs:label xml:lang="en">unfolds_in</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Occurs_in</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -2093,9 +2030,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000110">
         <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000110</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000110s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000110ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>c-has-part_at</obo:BFO_0000179>
         <obo:BFO_0000180>hasContinuantPartAt</obo:BFO_0000180>
         <obo:IAO_0000115>[copied from inverse property &apos;part of continuant at all times that whole exists&apos;] forall(t) exists_at(y,t) -&gt; exists_at(x,t) and &apos;part of continuant&apos;(x,y,t)</obo:IAO_0000115>
@@ -2115,9 +2049,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000111">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000110"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000111</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000111s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000111ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>c-has-ppart_at</obo:BFO_0000179>
         <obo:BFO_0000180>hasProperContinuantPartAt</obo:BFO_0000180>
         <obo:IAO_0000115 xml:lang="en">b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001</obo:IAO_0000115>
@@ -2153,9 +2084,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
         <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000132"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000117</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000117s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000117ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>o-has-part</obo:BFO_0000179>
         <obo:BFO_0000180>hasOccurrentPart</obo:BFO_0000180>
         <obo:IAO_0000112>[copied from inverse property &apos;part of occurrent&apos;] Mary’s 5th birthday occurrent_part_of Mary’s life</obo:IAO_0000112>
@@ -2178,9 +2106,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000118">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000117"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000118</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000118s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000118ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>o-has-ppart</obo:BFO_0000179>
         <obo:BFO_0000180>hasProperOccurrentPart</obo:BFO_0000180>
         <obo:IAO_0000115>[copied from inverse property &apos;proper part of occurrent&apos;] b proper_occurrent_part_of c =Def. b occurrent_part_of c &amp; b and c are not identical. (axiom label in BFO2 Reference: [005-001])</obo:IAO_0000115>
@@ -2230,9 +2155,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000132">
         <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <ace_lexicon:TV_pl>BFO_0000132</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000132s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000132ed</ace_lexicon:TV_vbg>
         <obo:BFO_0000179>o-part-of</obo:BFO_0000179>
         <obo:BFO_0000180>occurrentPartOf</obo:BFO_0000180>
         <obo:IAO_0000112 xml:lang="en">Mary’s 5th birthday occurrent_part_of Mary’s life</obo:IAO_0000112>
@@ -2373,9 +2295,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <!-- http://purl.obolibrary.org/obo/BFO_0000167 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000167">
-        <ace_lexicon:TV_pl>BFO_0000167</ace_lexicon:TV_pl>
-        <ace_lexicon:TV_sg>BFO_0000167s</ace_lexicon:TV_sg>
-        <ace_lexicon:TV_vbg>BFO_0000167ed</ace_lexicon:TV_vbg>
         <rdfs:label xml:lang="en">has participant at all times</rdfs:label>
     </owl:ObjectProperty>
     
@@ -2934,6 +2853,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AsymmetricProperty"/>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.</obo:IAO_0000600>
+        <dc:source>Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.</dc:source>
         <rdfs:label xml:lang="en">owns</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3001,12 +2921,14 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             </rdf:Description>
         </owl:equivalentProperty>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
-        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <obo:IAO_0000111>has specified output</obo:IAO_0000111>
         <obo:IAO_0000111>has_specified_output</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">has_specified_output</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115>The inverse property of is specified output of</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">The inverse property of is_specified_output_of</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000117>PERSON: Bjoern Peters</obo:IAO_0000117>
@@ -3014,6 +2936,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000117>PERSON: Melanie Courtot</obo:IAO_0000117>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
+        <rdfs:label xml:lang="en">has specified output</rdfs:label>
         <rdfs:label xml:lang="en">has_specified_output</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3032,16 +2955,19 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <obo:IAO_0000111>is specified output of</obo:IAO_0000111>
         <obo:IAO_0000111>is_specified_output_of</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">is_specified_output_of</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115 xml:lang="en">A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
-        <rdfs:label>is_specified_output_of</rdfs:label>
+        <rdfs:label xml:lang="en">is specified output of</rdfs:label>
         <rdfs:label xml:lang="en">is_specified_output_of</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3090,7 +3016,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/OBIB_0000732"/>
         <rdfs:label>obsolete owns</rdfs:label>
         <rdfs:label xml:lang="en">owns</rdfs:label>
-        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
 
@@ -3192,7 +3117,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/omrse.owl</obo:IAO_0000412>
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
         <rdfs:label xml:lang="en">bearer of</rdfs:label>
-        <rdfs:label xml:lang="en">bearer_of</rdfs:label>
         <rdfs:label xml:lang="en">has characteristic</rdfs:label>
         <rdfs:label xml:lang="en">is bearer of</rdfs:label>
     </owl:ObjectProperty>
@@ -3245,7 +3169,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <dc:source>http://www.obofoundry.org/ro/#OBO_REL:has_participant</dc:source>
         <terms:source>http://www.obofoundry.org/ro/#OBO_REL:has_participant</terms:source>
         <rdfs:label xml:lang="en">has participant</rdfs:label>
-        <rdfs:label>has_participant</rdfs:label>
         <rdfs:label xml:lang="en">has_participant</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3254,15 +3177,21 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
     <!-- http://purl.obolibrary.org/obo/RO_0000058 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
-        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <obo:IAO_0000111 xml:lang="en">is concretized as</obo:IAO_0000111>
+        <rdfs:range>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000020"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:range>
         <obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
+        <obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
         <rdfs:label xml:lang="en">is concretized as</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3271,15 +3200,21 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
     <!-- http://purl.obolibrary.org/obo/RO_0000059 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
-        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+        <rdfs:domain>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000020"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:domain>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
-        <obo:IAO_0000111 xml:lang="en">concretizes</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">is_concretization_of</obo:IAO_0000111>
         <obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
+        <obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.</obo:IAO_0000115>
         <rdfs:label xml:lang="en">concretizes</rdfs:label>
     </owl:ObjectProperty>
     
@@ -3493,7 +3428,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <terms:source>http://www.obofoundry.org/ro/#OBO_REL:located_in</terms:source>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label xml:lang="en">located in</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Located_in</rdfs:seeAlso>
     </owl:ObjectProperty>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
@@ -3694,7 +3628,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002084">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002093"/>
-        <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:comment>Previously had ID  http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point.  No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line.  Official ID now chosen from DOS ID range.</rdfs:comment>
         <rdfs:label xml:lang="en">during which ends</rdfs:label>
@@ -3711,7 +3645,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002093"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000062"/>
         </owl:propertyChainAxiom>
-        <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:comment xml:lang="en">X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)</rdfs:comment>
         <rdfs:label xml:lang="en">ends after</rdfs:label>
@@ -3729,7 +3663,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002230"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)</obo:IAO_0000115>
-        <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
         <obo:IAO_0000118>starts_at_end_of</obo:IAO_0000118>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
         <obo:UBPROP_0000001>A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].</obo:UBPROP_0000001>
@@ -3758,10 +3692,8 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002224"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
-        <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
         <obo:IAO_0000118>ends_at_start_of</obo:IAO_0000118>
         <obo:IAO_0000118>meets</obo:IAO_0000118>
-        <obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:comment xml:lang="en">X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)</rdfs:comment>
         <rdfs:label xml:lang="en">immediately precedes</rdfs:label>
@@ -3774,6 +3706,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002093">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-7073-9172"/>
         <obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
         <obo:IAO_0000118>o</obo:IAO_0000118>
         <obo:IAO_0000118>overlaps</obo:IAO_0000118>
@@ -3798,10 +3731,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
         </owl:propertyChainAxiom>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:propertyChainAxiom>
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002131"/>
@@ -3819,15 +3748,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">overlaps</rdfs:label>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002582 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002582>
-    </owl:Axiom>
     
 
 
@@ -3848,7 +3768,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label>spatially disjoint from</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern</rdfs:seeAlso>
         <foaf:page rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern</foaf:page>
     </owl:ObjectProperty>
     
@@ -3865,7 +3784,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">has component</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:Componency"/>
     </owl:ObjectProperty>
     
 
@@ -3937,7 +3855,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/ro.owl</obo:IAO_0000412>
         <obo:IAO_0000589>negatively regulates (process to process)</obo:IAO_0000589>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
         <oboInOwl:hasDbXref>RO:0002212</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>external</oboInOwl:hasOBONamespace>
         <oboInOwl:id>negatively_regulates</oboInOwl:id>
@@ -3970,7 +3887,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000589>positively regulates (process to process)</obo:IAO_0000589>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
         <oboInOwl:hasDbXref>RO:0002213</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>external</oboInOwl:hasOBONamespace>
         <oboInOwl:id>positively_regulates</oboInOwl:id>
@@ -4009,25 +3925,11 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002216">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002500"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:propertyChainAxiom>
         <obo:IAO_0000115>c stands in this relationship to p if and only if there exists some p&apos; such that c is capable_of p&apos;, and p&apos; is part_of p.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118>has function in</obo:IAO_0000118>
         <rdfs:label xml:lang="en">capable of part of</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/reflexivity/"/>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002216"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002582 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002582>
-    </owl:Axiom>
     
 
 
@@ -4048,7 +3950,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">has active participant</rdfs:label>
         <rdfs:label>obsolete has active participant</rdfs:label>
-        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:ObjectProperty>
     
 
@@ -4076,12 +3977,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdfs:label xml:lang="en">adjacent to</rdfs:label>
         <rdfs:seeAlso rdf:resource="https://github.com/jhpoelen/eol-globi-data/issues/225#issuecomment-218584934"/>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002220"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000112"/>
-        <owl:annotatedTarget>A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.</owl:annotatedTarget>
-        <rdfs:seeAlso rdf:resource="https://github.com/jhpoelen/eol-globi-data/issues/225#issuecomment-218584934"/>
-    </owl:Axiom>
     
 
 
@@ -4098,7 +3993,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000119>Allen</obo:IAO_0000119>
         <obo:IAO_0000232>Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.</obo:IAO_0000232>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
-        <terms:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1</terms:source>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:comment>A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.</rdfs:comment>
         <rdfs:label xml:lang="en">temporal relation</rdfs:label>
@@ -4116,7 +4010,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>inverse of starts with</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000119>Allen</obo:IAO_0000119>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">starts</rdfs:label>
@@ -4134,7 +4027,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) &lt; ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>started by</obo:IAO_0000118>
         <obo:IAO_0000412>http://purl.obolibrary.org/obo/obi.owl</obo:IAO_0000412>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
@@ -4153,7 +4045,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>inverse of ends with</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">inverse of ends with</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <dc:source>http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl</dc:source>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">ends</rdfs:label>
@@ -4171,7 +4062,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) &gt; α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) &gt; α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>finished by</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">finished with</obo:IAO_0000118>
         <dc:source xml:lang="en">http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl</dc:source>
@@ -4240,7 +4130,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">has input</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Has_input</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4265,7 +4154,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label xml:lang="en">has output</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Has_output</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4282,7 +4170,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>c acts upstream of p if and only if c enables some f that is involved in p&apos; and p&apos; occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p&apos; are processes.</obo:IAO_0000115>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://wiki.geneontology.org/index.php/Acts_upstream_of"/>
     </owl:ObjectProperty>
     
 
@@ -4300,7 +4187,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <oboInOwl:hasRelatedSynonym>affects</oboInOwl:hasRelatedSynonym>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of or within</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of_or_within</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4326,13 +4212,10 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0004047"/>
         <obo:IAO_0000115>p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.</obo:IAO_0000115>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
-        <terms:creator rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:comment>holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y</rdfs:comment>
         <rdfs:label>causally upstream of, positive effect</rdfs:label>
-        <rdfs:seeAlso rdf:resource="https://wiki.geneontology.org/Causally_upstream_of,_positive_effect"/>
     </owl:ObjectProperty>
     
 
@@ -4343,12 +4226,9 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0004046"/>
         <obo:IAO_0000115>p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.</obo:IAO_0000115>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
-        <terms:creator rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:label>causally upstream of, negative effect</rdfs:label>
-        <rdfs:seeAlso rdf:resource="https://wiki.geneontology.org/Causally_upstream_of,_negative_effect"/>
     </owl:ObjectProperty>
     
 
@@ -4357,10 +4237,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002314">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002502"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000052"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:propertyChainAxiom>
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002314"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
@@ -4372,17 +4248,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/20064205"/>
         <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
         <rdfs:label xml:lang="en">characteristic of part of</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/reflexivity/"/>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002314"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000052"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002582 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002582>
-    </owl:Axiom>
     
 
 
@@ -4443,7 +4309,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000232>This relation differs from the parent relation &apos;capable of&apos; in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.</obo:IAO_0000232>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label xml:lang="en">enables</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Enables</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4463,24 +4328,11 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002329">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
-        </owl:propertyChainAxiom>
         <obo:IAO_0000115>this relation holds between c and p when c is part of some c&apos;, and c&apos; is capable of p.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</obo:IAO_0000118>
         <rdfs:label xml:lang="en">part of structure that is capable of</rdfs:label>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002329"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002581 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002581>
-    </owl:Axiom>
     
 
 
@@ -4502,7 +4354,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000118>actively involved in</obo:IAO_0000118>
         <obo:IAO_0000118>enables part of</obo:IAO_0000118>
         <rdfs:label xml:lang="en">involved in</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Involved_in</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4516,7 +4367,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:label xml:lang="en">enabled by</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Enabled_by</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4692,9 +4542,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118>indirectly activates</obo:IAO_0000118>
-        <obo:RO_0002579 rdf:resource="http://purl.obolibrary.org/obo/RO_0002213"/>
         <rdfs:label xml:lang="en">indirectly positively regulates</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Indirectly_positively_regulates</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4720,9 +4568,7 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <obo:IAO_0000115>p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118>indirectly inhibits</obo:IAO_0000118>
-        <obo:RO_0002579 rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
         <rdfs:label xml:lang="en">indirectly negatively regulates</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Indirectly_negatively_regulates</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -4786,18 +4632,57 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
         <obo:IAO_0000115>p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
         <rdfs:label xml:lang="en">immediately causally upstream of</rdfs:label>
     </owl:ObjectProperty>
     
 
 
+    <!-- http://purl.obolibrary.org/obo/RO_0002413 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002413">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002412"/>
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002414"/>
+        <owl:propertyChainAxiom rdf:parseType="Collection">
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002234"/>
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002233"/>
+        </owl:propertyChainAxiom>
+        <obo:IAO_0000115>p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
+        <obo:IAO_0000118>directly provides input for</obo:IAO_0000118>
+        <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
+        <obo:IAO_0000589>directly provides input for (process to process)</obo:IAO_0000589>
+        <rdfs:label xml:lang="en">provides input for</rdfs:label>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/RO_0002414 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002414">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0004047"/>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
+        <obo:IAO_0000115>transitive form of directly_provides_input_for</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
+        <obo:IAO_0000232>This is a grouping relation that should probably not be used in annotation. Consider instead the child relation &apos;provides input for&apos;.</obo:IAO_0000232>
+        <obo:IAO_0000589>transitively provides input for (process to process)</obo:IAO_0000589>
+        <rdfs:label xml:lang="en">transitively provides input for</rdfs:label>
+    </owl:ObjectProperty>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/RO_0002418 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002418">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002501"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002427"/>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+        <owl:propertyChainAxiom rdf:parseType="Collection">
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002418"/>
+            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
+        </owl:propertyChainAxiom>
         <obo:IAO_0000115>p is &apos;causally upstream or within&apos; q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.</obo:IAO_0000115>
         <obo:IAO_0000116>We would like to make this disjoint with &apos;preceded by&apos;, but this is prohibited in OWL2</obo:IAO_0000116>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
@@ -4856,7 +4741,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; positively regulates some p</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
         <rdfs:label>involved in positive regulation of</rdfs:label>
     </owl:ObjectProperty>
     
@@ -4876,7 +4760,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; negatively regulates some p</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
         <rdfs:label>involved in negative regulation of</rdfs:label>
     </owl:ObjectProperty>
     
@@ -4902,28 +4785,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002432">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
-        </owl:propertyChainAxiom>
         <obo:IAO_0000112>A protein that enables activity in a cytosol.</obo:IAO_0000112>
         <obo:IAO_0000115>c executes activity in d if and only if c enables p and p occurs_in d.  Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000118>executes activity in</obo:IAO_0000118>
         <oboInOwl:hasExactSynonym>enables activity in</oboInOwl:hasExactSynonym>
-        <rdfs:comment></rdfs:comment>
         <rdfs:label>is active in</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Is_active_in</rdfs:seeAlso>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002432"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002581 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002581>
-    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002432"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
@@ -4948,8 +4816,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         <oboInOwl:hasExactSynonym>in pairwise interaction with</oboInOwl:hasExactSynonym>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label>interacts with</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/ro/docs/interaction-relations/</rdfs:seeAlso>
-        <skos:closeMatch rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/MI_0914</skos:closeMatch>
     </owl:ObjectProperty>
     
 
@@ -4964,8 +4830,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
         <obo:IAO_0000118>binds</obo:IAO_0000118>
         <obo:IAO_0000118>molecularly binds with</obo:IAO_0000118>
         <rdfs:label>molecularly interacts with</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ECO_0000353"/>
-        <skos:closeMatch rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/MI_0915</skos:closeMatch>
     </owl:ObjectProperty>
     
 
@@ -5064,24 +4928,11 @@ For example, A and B may be gene products and binding of B by A positively regul
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002479">
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
-        </owl:propertyChainAxiom>
         <obo:IAO_0000115>p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
         <rdfs:label>has part that occurs in</rdfs:label>
     </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002479"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
-        <owl:annotatedTarget rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
-            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
-        </owl:annotatedTarget>
-        <obo:RO_0002581 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:RO_0002581>
-    </owl:Axiom>
     
 
 
@@ -5131,7 +4982,6 @@ For example, A and B may be gene products and binding of B by A positively regul
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002502">
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <rdfs:label>depends on</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/BFO_0000169"/>
     </owl:ObjectProperty>
     
 
@@ -5170,8 +5020,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002464"/>
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <rdfs:label>interaction relation helper property</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29"/>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/ro/docs/interaction-relations/</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5221,7 +5069,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000589>directly regulates (processual)</obo:IAO_0000589>
-        <obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
@@ -5328,12 +5175,10 @@ For example, A and B may be gene products and binding of B by A positively regul
         <obo:IAO_0000115>p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.</obo:IAO_0000115>
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000589>directly positively regulates (process to process)</obo:IAO_0000589>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:label>directly positively regulates</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Directly_positively_regulates</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5346,12 +5191,10 @@ For example, A and B may be gene products and binding of B by A positively regul
         <obo:IAO_0000115>p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.</obo:IAO_0000115>
         <obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
         <obo:IAO_0000589>directly negatively regulates (process to process)</obo:IAO_0000589>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
         <rdfs:label>directly negatively regulates</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Directly_negatively_regulates</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5434,12 +5277,10 @@ For example, A and B may be gene products and binding of B by A positively regul
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0004047"/>
         </owl:propertyChainAxiom>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002264"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-01-26T23:49:30Z</oboInOwl:creation_date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of or within, positive effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5452,12 +5293,10 @@ For example, A and B may be gene products and binding of B by A positively regul
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0004046"/>
         </owl:propertyChainAxiom>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002264"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-01-26T23:49:51Z</oboInOwl:creation_date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of or within, negative effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5472,12 +5311,10 @@ For example, A and B may be gene products and binding of B by A positively regul
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002304"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>c &apos;acts upstream of, positive effect&apos; p if c is enables f, and f is causally upstream of p, and the direction of f is positive</obo:IAO_0000115>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002263"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-01-26T23:53:14Z</oboInOwl:creation_date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of, positive effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of,_positive_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5492,12 +5329,10 @@ For example, A and B may be gene products and binding of B by A positively regul
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002305"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000115>c &apos;acts upstream of, negative effect&apos; p if c is enables f, and f is causally upstream of p, and the direction of f is negative</obo:IAO_0000115>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002263"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-01-26T23:53:22Z</oboInOwl:creation_date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
         <rdfs:label>acts upstream of, negative effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Acts_upstream_of,_negative_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5506,11 +5341,9 @@ For example, A and B may be gene products and binding of B by A positively regul
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0004046">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
-        <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-03-13T23:55:05Z</oboInOwl:creation_date>
         <rdfs:label>causally upstream of or within, negative effect</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect</rdfs:seeAlso>
     </owl:ObjectProperty>
     
 
@@ -5519,11 +5352,9 @@ For example, A and B may be gene products and binding of B by A positively regul
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0004047">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
-        <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
         <oboInOwl:created_by rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-03-13T23:55:19Z</oboInOwl:creation_date>
         <rdfs:label>causally upstream of or within, positive effect</rdfs:label>
-        <rdfs:seeAlso rdf:resource="https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect"/>
     </owl:ObjectProperty>
     
 
@@ -5567,7 +5398,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <terms:contributor rdf:resource="https://orcid.org/0000-0002-8461-9745"/>
         <oboInOwl:hasExactSynonym>triggered by process</oboInOwl:hasExactSynonym>
         <rdfs:label xml:lang="en">realized in response to</rdfs:label>
-        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit</rdfs:seeAlso>
     </owl:ObjectProperty>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0009501"/>
@@ -5729,6 +5559,17 @@ For example, A and B may be gene products and binding of B by A positively regul
     
 
 
+    <!-- http://purl.obolibrary.org/obo/RO_0020105 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0020105">
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001062"/>
+        <obo:IAO_0000115>This property only applies to anatomical entities.</obo:IAO_0000115>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0001-6677-8489"/>
+        <rdfs:label>is anatomical entity</rdfs:label>
+    </owl:ObjectProperty>
+    
+
+
     <!-- http://purl.org/obo/owl/OBO_REL#has_disposition -->
 
     <owl:ObjectProperty rdf:about="http://purl.org/obo/owl/OBO_REL#has_disposition">
@@ -6127,6 +5968,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -6269,7 +6111,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
         <obo:IAO_0000115 xml:lang="en">A control strategy start time information item that is based on a condition that triggers the control strategy.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A control strategy start time information item that is based on a condition that triggers the control strategy.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">control strategy reactive start time information</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete control strategy reactive start time information</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -6280,10 +6122,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000012">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000029"/>
         <obo:IAO_0000115 xml:lang="en">A numeral that is part of a simulation time step action specification.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A number of time step units in a time step of a simulation.  
-
-For example, if the time step is 6 hours, then this value is 6.
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A number of time step units in a time step of a simulation.  For example, if the time step is 6 hours, then this value is 6.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>numberOfUnitsOfTimeInOneSimulatorStep</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation time step value</rdfs:label>
     </owl:Class>
@@ -6330,10 +6169,7 @@ For example, if the time step is 6 hours, then this value is 6.
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">The action specification that specifies the number of time steps a simulation is going to run.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The number of time steps in a simulator run.
-
-For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>runLength</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation run length</rdfs:label>
     </owl:Class>
@@ -6394,11 +6230,7 @@ Note that the susceptible and infectious organisms can be of different species.<
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
-        <obo:IAO_0000600 xml:lang="en">A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  
-
-Note that the susceptible and infected organisms can be of different species.
-
-</obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species.  Note that the susceptible and infected organisms can be of different species.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>latentPeriodDuration</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs</rdfs:comment>
         <rdfs:comment xml:lang="en">The duration of the period between when an organism becomes infected and when it becomes infectious.</rdfs:comment>
@@ -6463,11 +6295,10 @@ Note that the susceptible and infected organisms can be of different species.
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">The count of (simulated organisms) in a simulated population.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
-        <obo:IAO_0000600 xml:lang="en">The number of simulated organisms in a simulated population.  The number does not have to be an integer.  </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of simulated organisms in a simulated population.  The number does not have to be an integer.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">MW: I know this causes problems with our set-theoretic definition.  Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step.  
 
-Any ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’
-</rdfs:comment>
+Any ideas?  I’ve considered and rejected allowing individual organisms to be fractional.  Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’</rdfs:comment>
         <rdfs:label xml:lang="en">count of simulated population</rdfs:label>
     </owl:Class>
     
@@ -6478,7 +6309,7 @@ Any ideas?  I’ve considered and rejected allowing individual organisms to be f
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000023">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000084"/>
         <obo:IAO_0000115 xml:lang="en">An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">vaccination dose schedule</rdfs:label>
     </owl:Class>
     
@@ -6493,8 +6324,7 @@ Any ideas?  I’ve considered and rejected allowing individual organisms to be f
         <rdfs:comment xml:lang="en">MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class &quot;eligibility rule&quot; in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.</rdfs:comment>
         <rdfs:comment xml:lang="en">MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy”  and “control measure efficacy delay.”    We could then post-coordinate particular control measures such as vaccine.
 
-It is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.
-</rdfs:comment>
+It is worth noting that there are control measures such as closing schools that are not applied at the individual level.   We have not represented those control measures yet.</rdfs:comment>
         <rdfs:label xml:lang="en">vaccination compliance</rdfs:label>
     </owl:Class>
     
@@ -6626,8 +6456,8 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:someValuesFrom>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.  </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">infectious disease control strategy execution</rdfs:label>
     </owl:Class>
     
@@ -6753,6 +6583,7 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -6908,10 +6739,9 @@ can&apos;t recall whether we should use process or processual_entity for future
                 </owl:someValuesFrom>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A simulated organism in a simulated population that is not susceptible. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A simulated organism in a simulated population that is not susceptible.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. 
-Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.
-</obo:IAO_0000600>
+Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’  However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’  The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">simulation of recovered organism</rdfs:label>
     </owl:Class>
     
@@ -6980,7 +6810,7 @@ Note that the name for this concept, were it to be named based on its intent, wo
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">The number of susceptible organisms that each infected organism infects.  ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ReproductionNumber</apollo_sv:APOLLO_SV_0000040>
@@ -7090,8 +6920,8 @@ Preventable outcomes include but are not limited to infection, infectiousness, s
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000049">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000243"/>
-        <obo:IAO_0000115 xml:lang="en">The value of the time interval between an organism&apos;s taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">The value of the time interval between an organism&apos;s taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">antiviral efficacy delay</rdfs:label>
     </owl:Class>
     
@@ -7102,7 +6932,7 @@ Preventable outcomes include but are not limited to infection, infectiousness, s
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000050">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0302867"/>
         <obo:IAO_0000115 xml:lang="en">The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The fraction of individuals in a simulated population that will accept antiviral treatment if offered. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The fraction of individuals in a simulated population that will accept antiviral treatment if offered.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>antiviral cm compliance</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class &quot;eligibility rule&quot; in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.</rdfs:comment>
         <rdfs:comment xml:lang="en">MW: Since the estimates that modelers use are from real populations, I have two questions:
@@ -7119,7 +6949,7 @@ MB: This issue will need to be taken care of in the axiomatization of simulated
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000051">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000795"/>
-        <obo:IAO_0000115 xml:lang="en">An action specification giving the number of doses of an antiviral to be made available during a specific time interval. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">An action specification giving the number of doses of an antiviral to be made available during a specific time interval.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">Counts of antiviral doses that become available in a specific location per time step unit.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">antiviral supply schedule</rdfs:label>
     </owl:Class>
@@ -7274,13 +7104,12 @@ MB: This issue will need to be taken care of in the axiomatization of simulated
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000060">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000070"/>
-        <obo:IAO_0000115>The simulation of an antiviral control measure. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The simulation of an antiviral control measure.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>antiviral control measure</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn&apos;t able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).
 AND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.
-Maybe we need to discuss this.
-</rdfs:comment>
+Maybe we need to discuss this.</rdfs:comment>
         <rdfs:label xml:lang="en">simulation of antiviral control measure</rdfs:label>
     </owl:Class>
     
@@ -7405,8 +7234,7 @@ Maybe we need to discuss this.
 
 One property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.
 
-While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.
-</rdfs:comment>
+While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.</rdfs:comment>
         <rdfs:label xml:lang="en">simulation time series</rdfs:label>
     </owl:Class>
     
@@ -7468,6 +7296,12 @@ While in many pieces of fiction the order in which the purely intentional entiti
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000067"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000038"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates a temporal interval of pre-specified length.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates a temporal interval of pre-specified length.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>simulation time step</apollo_sv:APOLLO_SV_0000040>
@@ -7565,12 +7399,8 @@ The time step value and unit are specified using a scalar value specification.</
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates an entity and its properties.
-
-</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates an entity and its properties.
-
-</obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">A purely intentional entity that simulates an entity and its properties.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">A purely intentional entity that simulates an entity and its properties.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>simulation</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">simulation</rdfs:label>
     </owl:Class>
@@ -7701,7 +7531,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">the mean or expectation of a distribution</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>μ</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">μ</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete μ</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -7713,7 +7543,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">standard deviation</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>sigma</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">σ</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete σ</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -7735,7 +7565,7 @@ The time step value and unit are specified using a scalar value specification.</
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000079">
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated log normal distribution</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete log normal distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -7796,7 +7626,7 @@ The time step value and unit are specified using a scalar value specification.</
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism.</obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism.</obo:IAO_0000600>
         <rdfs:label xml:lang="en">control strategy dose schedule</rdfs:label>
     </owl:Class>
     
@@ -7838,6 +7668,33 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                                <owl:someValuesFrom>
+                                    <owl:Class>
+                                        <owl:intersectionOf rdf:parseType="Collection">
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000038"/>
+                                            <owl:Restriction>
+                                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000156"/>
+                                                <owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
+                                                <owl:onClass rdf:resource="http://purl.obolibrary.org/obo/BFO_0000182"/>
+                                            </owl:Restriction>
+                                        </owl:intersectionOf>
+                                    </owl:Class>
+                                </owl:someValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000111 xml:lang="en">age structure data set</obo:IAO_0000111>
         <obo:IAO_0000115>A data set consisting of measurements of age organized in age brackets.</obo:IAO_0000115>
         <obo:IAO_0000600>A data set consisting of measurements of age organized in age brackets.</obo:IAO_0000600>
@@ -7937,13 +7794,44 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000025"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/PCO_0000000"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
+                                <owl:allValuesFrom>
+                                    <owl:Class>
+                                        <owl:intersectionOf rdf:parseType="Collection">
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
+                                            <owl:Restriction>
+                                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000142"/>
+                                            </owl:Restriction>
+                                        </owl:intersectionOf>
+                                    </owl:Class>
+                                </owl:allValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A vaccination efficacy that results from a vaccination efficacy study.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>VaccinationEfficacyMeasured</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’
 
-2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.
-</rdfs:comment>
+2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.</rdfs:comment>
         <rdfs:label xml:lang="en">measured vaccination efficacy</rdfs:label>
     </owl:Class>
     
@@ -7967,6 +7855,7 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000471"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -8041,6 +7930,12 @@ The time step value and unit are specified using a scalar value specification.</
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PCO_0000001"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">Two or more distinct populations that are part of the same biotic ecosystem.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">Two or more distinct populations that are part of the same biotic ecosystem.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>community</apollo_sv:APOLLO_SV_0000040>
@@ -8056,7 +7951,7 @@ The time step value and unit are specified using a scalar value specification.</
         <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
         <obo:IAO_0000600 xml:lang="en">a probability distribution over a discrete random variable</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>discrete probability distribution</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label>deprecated discrete probability distribution</rdfs:label>
+        <rdfs:label>obsolete discrete probability distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -8076,8 +7971,8 @@ The time step value and unit are specified using a scalar value specification.</
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000097">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <obo:IAO_0000115 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region. </obo:IAO_0000115>
-        <obo:IAO_0000600 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region. </obo:IAO_0000600>
+        <obo:IAO_0000115 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region.</obo:IAO_0000115>
+        <obo:IAO_0000600 xml:lang="en">The sum of all biotic and abiotic entities in a geographical region.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>Ecosystem</apollo_sv:APOLLO_SV_0000040>
         <dc:creator xml:lang="en">William R. Hogan</dc:creator>
         <rdfs:label xml:lang="en">ecosystem</rdfs:label>
@@ -8537,19 +8432,16 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000114"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A process where a susceptible organism from a particular species becomes infected by a particular pathogen.  The infection is acquired from an infected organism of a particular species or from a contaminated thing.  
 
-Note that the susceptible and infectious organisms can be of different species.
-
-</obo:IAO_0000600>
+Note that the susceptible and infectious organisms can be of different species.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>InfectionAcquisition</apollo_sv:APOLLO_SV_0000040>
         <rdfs:comment xml:lang="en">Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use.  The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.
 The likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient.   
-An infection is acquired from an infectious organism or a contaminated thing. 
-</rdfs:comment>
-        <rdfs:comment xml:lang="en">Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing</rdfs:comment>
+An infection is acquired from an infectious organism or a contaminated thing.</rdfs:comment>
+        <rdfs:comment xml:lang="en">Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing.</rdfs:comment>
         <rdfs:label xml:lang="en">infection acquisition</rdfs:label>
     </owl:Class>
     
@@ -8720,7 +8612,7 @@ An infection is acquired from an infectious organism or a contaminated thing.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000125">
         <obo:IAO_0000600 xml:lang="en">The time steps that a school will be in session.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">school calendar</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete school calendar</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -8790,8 +8682,7 @@ An infection is acquired from an infectious organism or a contaminated thing.
         <obo:IAO_0000115 xml:lang="en">A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.
 
-The event could be infection acquisition, vaccination, antiviral treatment, etc.
-</obo:IAO_0000600>
+The event could be infection acquisition, vaccination, antiviral treatment, etc.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>reactiveControlMeasureThreshold</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">reactive control strategy threshold</rdfs:label>
     </owl:Class>
@@ -8896,7 +8787,7 @@ For example, once a vaccination control strategy starts, individual vaccinations
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000137">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000032"/>
-        <obo:IAO_0000600 xml:lang="en">the number of distinct antigenic strains in a vaccine product </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">The number of distinct antigenic strains in a vaccine product.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>valence</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">vaccine valence</rdfs:label>
     </owl:Class>
@@ -9149,7 +9040,7 @@ For example, once a vaccination control strategy starts, individual vaccinations
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000143">
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <rdfs:comment xml:lang="en">replaced with VO &apos;vaccine function&apos;</rdfs:comment>
-        <rdfs:label xml:lang="en">vaccine disposition</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete vaccine disposition</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9213,7 +9104,7 @@ Somehow, it&apos;s not innate and it&apos;s temporary, ie, the body will eventua
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000146">
         <obo:IAO_0000600 xml:lang="en">Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">it is the same thing as transmission coefficient</rdfs:comment>
-        <rdfs:label xml:lang="en">beta</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete beta</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9234,7 +9125,7 @@ Somehow, it&apos;s not innate and it&apos;s temporary, ie, the body will eventua
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000148">
         <obo:IAO_0000600 xml:lang="en">random number seed</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">random number seed</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete random number seed</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9689,7 +9580,7 @@ I checked because an infection and immunity census would involve two different c
         <obo:IAO_0000115 xml:lang="en">An ecosystem in which a population of hosts is undergoing at least one infection.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An ecosystem in which a population of hosts is undergoing at least one infection.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">MIDAS scenario</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete MIDAS scenario</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -9919,7 +9810,7 @@ I checked because an infection and immunity census would involve two different c
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An independent continuant that is the localization of a pathogen, but is not undergoing an infection.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ContaminatedThing</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:comment xml:lang="en">A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.    </rdfs:comment>
+        <rdfs:comment xml:lang="en">A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.</rdfs:comment>
         <rdfs:label xml:lang="en">contaminated thing</rdfs:label>
     </owl:Class>
     
@@ -10345,6 +10236,12 @@ I checked because an infection and immunity census would involve two different c
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000015"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>SimulatorTimeSpecification</apollo_sv:APOLLO_SV_0000040>
@@ -10462,7 +10359,7 @@ The infectious disease scenario typically also includes a lot of additional data
         <obo:IAO_0000115 xml:lang="en">A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.</obo:IAO_0000115>
         <obo:IAO_0000600 xml:lang="en">A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.</rdfs:comment>
-        <rdfs:comment xml:lang="en">This census should exclude infection, immunity, treatment, or contamination.  </rdfs:comment>
+        <rdfs:comment xml:lang="en">This census should exclude infection, immunity, treatment, or contamination.</rdfs:comment>
         <rdfs:label xml:lang="en">population and environment census</rdfs:label>
     </owl:Class>
     
@@ -10548,6 +10445,7 @@ Note that the infected and susceptible organisms may be of different species.</o
     <!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000194 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000194">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000086"/>
         <rdfs:subClassOf>
             <owl:Class>
                 <owl:intersectionOf rdf:parseType="Collection">
@@ -10574,6 +10472,27 @@ Note that the infected and susceptible organisms may be of different species.</o
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:someValuesFrom>
+                    <owl:Class>
+                        <owl:intersectionOf rdf:parseType="Collection">
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000007"/>
+                            <owl:Restriction>
+                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+                                <owl:someValuesFrom>
+                                    <owl:Restriction>
+                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
+                                        <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000090"/>
+                                    </owl:Restriction>
+                                </owl:someValuesFrom>
+                            </owl:Restriction>
+                        </owl:intersectionOf>
+                    </owl:Class>
+                </owl:someValuesFrom>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000112 xml:lang="en">vaccination control strategy, antiviral control strategy</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">An infectious disease control strategy that immediately targets individuals.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
@@ -10609,7 +10528,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000197">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000188"/>
-        <rdfs:comment xml:lang="en">An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved. </rdfs:comment>
+        <rdfs:comment xml:lang="en">An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved.</rdfs:comment>
         <rdfs:label xml:lang="en">agent level population and environment census</rdfs:label>
     </owl:Class>
     
@@ -10619,7 +10538,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000198">
         <rdfs:comment xml:lang="en">At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics.</rdfs:comment>
-        <rdfs:label xml:lang="en">agent model ecosystem census description</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete agent model ecosystem census description</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -10629,7 +10548,7 @@ Note that the infected and susceptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000199">
         <rdfs:comment xml:lang="en">The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census).</rdfs:comment>
-        <rdfs:label xml:lang="en">compartment model population and environment census</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete compartment model population and environment census</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -10662,7 +10581,7 @@ Note that the infected and susceptible organisms may be of different species.</o
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000202">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
         <apollo_sv:APOLLO_SV_0000040>ApolloIndexableItem</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:comment xml:lang="en">A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. </rdfs:comment>
+        <rdfs:comment xml:lang="en">A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved.</rdfs:comment>
         <rdfs:label xml:lang="en">indexable Apollo item</rdfs:label>
     </owl:Class>
     
@@ -10910,9 +10829,9 @@ Note that the infected and sucseptible organisms may be of different species.</o
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000215">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
-        <obo:IAO_0000115 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. </obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.</obo:IAO_0000115>
         <obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Probability_distribution</obo:IAO_0000119>
-        <obo:IAO_0000600 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. </obo:IAO_0000600>
+        <obo:IAO_0000600 xml:lang="en">An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>ProbabilityDistribution</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">probability distribution</rdfs:label>
     </owl:Class>
@@ -11496,7 +11415,7 @@ can&apos;t recall whether we should use process or processual_entity for future
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0100001>http://purl.obolibrary.org/obo/STATO_0000321</obo:IAO_0100001>
         <apollo_sv:APOLLO_SV_0000040>NonparametricProbabilityDistribution</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">nonparametric probability distribution</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete nonparametric probability distribution</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -11790,8 +11709,7 @@ For example, it may take time to communicate to workers to stop vaccinating and
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">An infection acquisition from an individual who is infectious.
 
-The individual acquiring the infection can be of a different species than the one who is infectious.
-</obo:IAO_0000600>
+The individual acquiring the infection can be of a different species than the one who is infectious.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>InfectionAcquisitionFromInfectedHost</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">infection acquisition from infectious host</rdfs:label>
     </owl:Class>
@@ -11833,8 +11751,7 @@ The individual acquiring the infection can be of a different species than the on
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time.
 
-In epidemic simulation, it can be &apos;simulator time&apos; where time zero is the starting point of an infectious disease scenario, or it can be &apos;control strategy time&apos; where time zero is the time at which the control strategy is initiated.
-</obo:IAO_0000600>
+In epidemic simulation, it can be &apos;simulator time&apos; where time zero is the starting point of an infectious disease scenario, or it can be &apos;control strategy time&apos; where time zero is the time at which the control strategy is initiated.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>timeScale</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">time scale name</rdfs:label>
     </owl:Class>
@@ -12151,8 +12068,7 @@ For example, the trigger could occur once the incidence or prevalence of the inf
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">The unit of measure for the supply schedule of an individual treatment.
 
-For example, &apos;daily dose&apos;.
-</obo:IAO_0000600>
+For example, &apos;daily dose&apos;.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>supplyScheduleUnits</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">individual treatment strategy supply schedule unit of measure</rdfs:label>
     </owl:Class>
@@ -12205,8 +12121,7 @@ For example, &apos;daily dose&apos;.</obo:IAO_0000600>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A specification of the criteria an organism must meet to be considered to be in some abnormal state.
 
-The abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.
-</obo:IAO_0000600>
+The abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.</obo:IAO_0000600>
         <apollo_sv:APOLLO_SV_0000040>CaseDefinition</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">case definition</rdfs:label>
     </owl:Class>
@@ -12536,7 +12451,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000651"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0032504"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0048609"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
@@ -13233,7 +13148,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -13256,7 +13171,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -13908,7 +13823,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -13931,7 +13846,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -13981,7 +13896,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:someValuesFrom>
                                             <owl:Class>
                                                 <owl:intersectionOf rdf:parseType="Collection">
-                                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                                     <owl:Restriction>
                                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
                                                         <owl:someValuesFrom>
@@ -14020,7 +13935,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:someValuesFrom>
                                     <owl:Class>
                                         <owl:intersectionOf rdf:parseType="Collection">
-                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
                                                 <owl:someValuesFrom>
@@ -14071,7 +13986,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                         <owl:complementOf>
                                             <owl:Restriction>
                                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                             </owl:Restriction>
                                         </owl:complementOf>
                                     </owl:Class>
@@ -14094,7 +14009,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                 <owl:complementOf>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:complementOf>
                             </owl:Class>
@@ -14256,7 +14171,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000371"/>
                                     <owl:Restriction>
                                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                                     </owl:Restriction>
                                 </owl:intersectionOf>
                             </owl:Class>
@@ -14275,7 +14190,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000371"/>
                             <owl:Restriction>
                                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035944"/>
+                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
                             </owl:Restriction>
                         </owl:intersectionOf>
                     </owl:Class>
@@ -14767,7 +14682,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated homeostasis</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete homeostasis</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -15181,7 +15096,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A count of individuals in a population who meet an infection case definition during a particular time interval.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">deprecated infection case count</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete infection case count</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -15737,7 +15652,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A one-dimensional temporal region occupied by a place closure control strategy.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">closure period</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete closure period</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -16299,7 +16214,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000117>Matthew Diller</obo:IAO_0000117>
         <obo:IAO_0000117>William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000600 xml:lang="en">A time measurement datum of the length of the temporal interval occupied by a gonotropic period.</obo:IAO_0000600>
-        <rdfs:label xml:lang="en">gonotrophic period duration</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete gonotrophic period duration</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -16572,7 +16487,7 @@ The constant rate may be zero.  The period of an epidemic may be defined using s
         <obo:IAO_0000600 xml:lang="en">An identifier curated by ORCID, Inc. to denote some academic author.</obo:IAO_0000600>
         <obo:IAO_0100001 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/IAO_0000708</obo:IAO_0100001>
         <apollo_sv:APOLLO_SV_0000040>orcId</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:label xml:lang="en">ORCID</rdfs:label>
+        <rdfs:label xml:lang="en">obsolete ORCID</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
     
@@ -18167,7 +18082,6 @@ has specified input some case definition.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">census of treatment facilities</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">treatment facilities census</obo:IAO_0000118>
-        <obo:IAO_0000118 xml:lang="en">treatment facility census</obo:IAO_0000118>
         <obo:IAO_0000600 xml:lang="en">A census that counts the number of treatment facilities of some kind in a particular geographical region.</obo:IAO_0000600>
         <rdfs:comment xml:lang="en">NOTE: this class counts the facilities themselves, not patients (people) in those facilities.  For example, how many hospitals in a state.  Not how many patients are in a hospital or hospitals in a state.</rdfs:comment>
         <rdfs:label xml:lang="en">treatment facility census</rdfs:label>
@@ -19291,6 +19205,7 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -19322,6 +19237,7 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -19995,7 +19911,6 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <obo:IAO_0000602>(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] </obo:IAO_0000602>
         <obo:IAO_0000602>(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] </obo:IAO_0000602>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
-        <rdfs:label xml:lang="en">realizable</rdfs:label>
         <rdfs:label xml:lang="en">realizable entity</rdfs:label>
     </owl:Class>
     <owl:Axiom>
@@ -20129,24 +20044,13 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <obo:IAO_0000112 xml:lang="en">the shape of this hole.</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">the smell of this portion of mozzarella</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.</obo:IAO_0000115>
-        <obo:IAO_0000115 xml:lang="en">b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &amp;gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1  i &amp;lt; j  n, ci  and cj share no common parts, are such that for each 1  i  n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant &amp; there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">Specifically dependent continuant doesn&apos;t have a closure axiom because the subclasses don&apos;t necessarily exhaust all possibilites. We&apos;re not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.</obo:IAO_0000116>
-        <obo:IAO_0000602>(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] </obo:IAO_0000602>
         <obo:IAO_0000602>(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] </obo:IAO_0000602>
         <rdfs:comment xml:lang="en">A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.</rdfs:comment>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
-        <rdfs:label xml:lang="en">characteristic</rdfs:label>
         <rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
-        <rdfs:seeAlso>https://github.com/OBOFoundry/COB/issues/65</rdfs:seeAlso>
-        <rdfs:seeAlso>https://github.com/oborel/obo-relations/pull/284</rdfs:seeAlso>
     </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget xml:lang="en">b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &amp;gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1  i &amp;lt; j  n, ci  and cj share no common parts, are such that for each 1  i  n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/131-004"/>
-    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
@@ -20160,12 +20064,6 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000005"/>
         <rdfs:comment>per discussion with Barry Smith</rdfs:comment>
     </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
-        <owl:annotatedTarget>(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/131-004"/>
-    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
@@ -20311,6 +20209,13 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <owl:annotatedTarget>An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects </owl:annotatedTarget>
         <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000011"/>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+        <owl:annotatedTarget>An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects </owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000011"/>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000301"/>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000027"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
@@ -20609,6 +20514,7 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60</obo:IAO_0000116>
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.</obo:IAO_0000116>
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.</obo:IAO_0000116>
         <obo:IAO_0000600 xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</obo:IAO_0000600>
         <obo:IAO_0000601 xml:lang="en">Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])</obo:IAO_0000601>
         <obo:IAO_0000601 xml:lang="en">every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])</obo:IAO_0000601>
@@ -20943,6 +20849,28 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
     
 
 
+    <!-- http://purl.obolibrary.org/obo/COB_0000022 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000115 xml:lang="en">A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">&apos;Maximal functionally integrated unit&apos; is intended to express unity, which Barry considers synonymous with BFO &apos;object&apos;.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">Includes virus - we will later have a class for cellular organisms.</obo:IAO_0000116>
+        <rdfs:label xml:lang="en">organism</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/COB_0000035 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000035">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
+        <rdfs:label xml:lang="en">completely executed planned process</rdfs:label>
+    </owl:Class>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/DOID_0060478 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_0060478">
@@ -21066,11 +20994,26 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si
     <!-- http://purl.obolibrary.org/obo/DRON_00000005 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_00000005">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000030"/>
-        <obo:IAO_0000115 xml:lang="en">a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role</obo:IAO_0000115>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DRON_00000074"/>
+        <obo:IAO_0000115 xml:lang="en">A drug product that is bearer of a clinical drug role.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">William Hogan</obo:IAO_0000117>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/dron.owl</obo:IAO_0000412>
-        <dc:creator xml:lang="en">William Hogan</dc:creator>
+        <rdfs:comment xml:lang="en">We changed the label to &apos;clinical drug product&apos; because it was clear that the part of the definition re: bearer of a &quot;clinical drug role&quot; made it such. Other drugs don&apos;t have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf &quot;drug product&quot;, which also required changing the definition here.</rdfs:comment>
+        <rdfs:label xml:lang="en">clinical drug product</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/DRON_00000074 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_00000074">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+        <obo:IAO_0000115 xml:lang="en">A material entity that (1) contains at least one scattered molecular aggregate as part and (2) is intended, when administered to an organism, to produce some therapeutic and/or psychoactive effect.</obo:IAO_0000115>
+        <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0001-6378-1703"/>
+        <terms:contributor rdf:resource="https://orcid.org/0000-0002-5039-2052"/>
+        <rdfs:comment xml:lang="en">The &quot;intention&quot; part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered.</rdfs:comment>
+        <rdfs:comment xml:lang="en">The psychoactive effect is added for illicit drugs such as crack cocaine.</rdfs:comment>
+        <rdfs:comment xml:lang="en">We are including prophylactic and diagnostic effects / usage under the more general heading of &apos;therapeutic&apos;.</rdfs:comment>
         <rdfs:label xml:lang="en">drug product</rdfs:label>
     </owl:Class>
     
@@ -22064,12 +22007,11 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003674">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">This is the same as GO molecular function</obo:IAO_0000116>
         <oboInOwl:hasExactSynonym>molecular function</oboInOwl:hasExactSynonym>
         <oboInOwl:id>GO:0003674</oboInOwl:id>
-        <rdfs:comment>Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code &apos;no data&apos; (ND), is used to indicate this. Despite its name, this is not a type of &apos;function&apos; in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.</rdfs:comment>
-        <rdfs:comment>This is the same as GO molecular function</rdfs:comment>
+        <rdfs:comment>Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code &apos;no data&apos; (ND), is used to indicate this. Despite its name, this is not a type of &apos;function&apos; in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.</rdfs:comment>
         <rdfs:label xml:lang="en">gene product or complex activity</rdfs:label>
         <rdfs:label>molecular_function</rdfs:label>
     </owl:Class>
@@ -22135,11 +22077,8 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0008150">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <obo:IAO_0000115>A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.</obo:IAO_0000115>
-        <obo:IAO_0000115>A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.</obo:IAO_0000115>
         <obo:IAO_0000115>Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/24968</obo:IAO_0000233>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
         <oboInOwl:created_by>jl</oboInOwl:created_by>
         <oboInOwl:creation_date>2012-09-19T15:05:24Z</oboInOwl:creation_date>
@@ -22160,9 +22099,7 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_plant"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_pombe"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_yeast"/>
-        <rdfs:comment>A biological process is an evolved process</rdfs:comment>
         <rdfs:comment>Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code &apos;no data&apos; (ND), is used to indicate this.</rdfs:comment>
-        <rdfs:comment>Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code &apos;no data&apos; (ND), is used to indicate this.</rdfs:comment>
         <rdfs:label xml:lang="en">biological process</rdfs:label>
         <rdfs:label>biological_process</rdfs:label>
     </owl:Class>
@@ -22181,6 +22118,7 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, &apos;complete&apos; its life cycle.</obo:IAO_0000115>
         <oboInOwl:hasAlternativeId>GO:0022415</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-162906</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>Wikipedia:Viral_life_cycle</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>virus process</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
@@ -22201,6 +22139,12 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:hasDbXref>GOC:jl</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:mah</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0016032"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-162906</owl:annotatedTarget>
+        <rdfs:label>HIV Infection</rdfs:label>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0016032"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
@@ -22257,6 +22201,9 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0016032"/>
         <obo:IAO_0000115>A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.</obo:IAO_0000115>
         <oboInOwl:hasAlternativeId>GO:0019067</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-162588</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-168255</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-9609646</oboInOwl:hasDbXref>
         <oboInOwl:hasNarrowSynonym>viral assembly, maturation, egress, and release</oboInOwl:hasNarrowSynonym>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:hasRelatedSynonym>lytic viral life cycle</oboInOwl:hasRelatedSynonym>
@@ -22272,6 +22219,24 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <owl:annotatedTarget>A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>ISBN:1555811272</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0019058"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-162588</owl:annotatedTarget>
+        <rdfs:label>Budding and maturation of HIV virion</rdfs:label>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0019058"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-168255</owl:annotatedTarget>
+        <rdfs:label>Influenza Infection</rdfs:label>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0019058"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-9609646</owl:annotatedTarget>
+        <rdfs:label>HCMV Infection</rdfs:label>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0019058"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
@@ -22310,7 +22275,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0007610"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0048609"/>
         <obo:IAO_0000115>The specific behavior of an organism that is associated with reproduction.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/23491</obo:IAO_0000233>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
         <oboInOwl:created_by>jl</oboInOwl:created_by>
         <oboInOwl:creation_date>2012-09-19T16:01:37Z</oboInOwl:creation_date>
@@ -22342,10 +22306,10 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000651"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0022414"/>
         <obo:IAO_0000115>A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/22929</obo:IAO_0000233>
         <oboInOwl:hasDbXref>Wikipedia:Sexual_reproduction</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:id>GO:0019953</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate"/>
         <rdfs:comment>Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.</rdfs:comment>
         <rdfs:label>sexual reproduction</rdfs:label>
     </owl:Class>
@@ -22364,7 +22328,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000651"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0022414"/>
         <obo:IAO_0000115>A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/22929</obo:IAO_0000233>
         <oboInOwl:hasDbXref>Wikipedia:Asexual_reproduction</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:hasRelatedSynonym>parthenogenesis</oboInOwl:hasRelatedSynonym>
@@ -22394,10 +22357,11 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0022414">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/27054</obo:IAO_0000233>
         <oboInOwl:created_by>jl</oboInOwl:created_by>
         <oboInOwl:creation_date>2012-09-19T15:56:06Z</oboInOwl:creation_date>
+        <oboInOwl:hasAlternativeId>GO:0019952</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044702</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasAlternativeId>GO:0050876</oboInOwl:hasAlternativeId>
         <oboInOwl:hasDbXref>Wikipedia:Reproduction</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:hasRelatedSynonym>single organism reproductive process</oboInOwl:hasRelatedSynonym>
@@ -22427,7 +22391,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0032501">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>Any biological process, occurring at the level of a multicellular organism, pertinent to its function.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/27189</obo:IAO_0000233>
         <oboInOwl:created_by>jl</oboInOwl:created_by>
         <oboInOwl:creation_date>2012-09-19T16:07:47Z</oboInOwl:creation_date>
         <oboInOwl:hasAlternativeId>GO:0044707</oboInOwl:hasAlternativeId>
@@ -22453,35 +22416,11 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     
 
 
-    <!-- http://purl.obolibrary.org/obo/GO_0032504 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0032504">
-        <obo:IAO_0000115>OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/27054</obo:IAO_0000233>
-        <obo:IAO_0100001>GO:0048609</obo:IAO_0100001>
-        <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
-        <oboInOwl:id>GO:0032504</oboInOwl:id>
-        <rdfs:comment>The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process.</rdfs:comment>
-        <rdfs:label>obsolete multicellular organism reproduction</rdfs:label>
-        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0032504"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref>GOC:isa_complete</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>GOC:jid</oboInOwl:hasDbXref>
-    </owl:Axiom>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/GO_0044403 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044403">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044419"/>
         <obo:IAO_0000115>A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/14807</obo:IAO_0000233>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/20191</obo:IAO_0000233>
         <oboInOwl:hasAlternativeId>GO:0043298</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044404</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0072519</oboInOwl:hasAlternativeId>
@@ -22518,7 +22457,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0051704"/>
         <obo:IAO_0000115>Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.</obo:IAO_0000115>
         <obo:IAO_0000115>Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/18563</obo:IAO_0000233>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
         <oboInOwl:hasAlternativeId>GO:0030260</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044411</oboInOwl:hasAlternativeId>
@@ -22528,6 +22466,7 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:hasAlternativeId>GO:0075052</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0085027</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0085028</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-173107</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>entry into host</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>host invasion</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>host penetration</oboInOwl:hasExactSynonym>
@@ -22561,6 +22500,12 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <owl:annotatedTarget>Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:vw</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0044409"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-173107</owl:annotatedTarget>
+        <rdfs:label>Binding and entry of HIV virion</rdfs:label>
+    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0044409"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
@@ -22605,7 +22550,7 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0044419">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000115>Any process evolved to enable an interaction with an organism of a different species.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/20191</obo:IAO_0000233>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-9824443</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>interaction with another species</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>interspecies interaction</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>interspecies interaction between organisms</oboInOwl:hasExactSynonym>
@@ -22623,6 +22568,12 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <owl:annotatedTarget>Any process evolved to enable an interaction with an organism of a different species.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:cc</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0044419"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-9824443</owl:annotatedTarget>
+        <rdfs:label>Parasitic Infection Pathways</rdfs:label>
+    </owl:Axiom>
     
 
 
@@ -22631,8 +22582,8 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0048609">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0022414"/>
         <obo:IAO_0000115>The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/27054</obo:IAO_0000233>
         <oboInOwl:hasBroadSynonym>organismal reproductive process</oboInOwl:hasBroadSynonym>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-1474165</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>reproductive process in a multicellular organism</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:id>GO:0048609</oboInOwl:id>
@@ -22648,6 +22599,12 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:hasDbXref>GOC:jid</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:tb</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0048609"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-1474165</owl:annotatedTarget>
+        <rdfs:label>Reproduction</rdfs:label>
+    </owl:Axiom>
     
 
 
@@ -22668,7 +22625,6 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0051701">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0044403"/>
         <obo:IAO_0000115>An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.</obo:IAO_0000115>
-        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/20191</obo:IAO_0000233>
         <oboInOwl:hasAlternativeId>GO:0044112</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044116</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044117</oboInOwl:hasAlternativeId>
@@ -22676,6 +22632,8 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <oboInOwl:hasAlternativeId>GO:0044121</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044123</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId>GO:0044125</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-9635486</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>Reactome:R-HSA-9658195</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>interaction with host</oboInOwl:hasExactSynonym>
         <oboInOwl:hasNarrowSynonym>growth of symbiont in host</oboInOwl:hasNarrowSynonym>
         <oboInOwl:hasNarrowSynonym>growth of symbiont in host cell</oboInOwl:hasNarrowSynonym>
@@ -22691,6 +22649,18 @@ Date accessed: 2015-04-13</obo:IAO_0000119>
         <owl:annotatedTarget>An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:cc</oboInOwl:hasDbXref>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0051701"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-9635486</owl:annotatedTarget>
+        <rdfs:label>Infection with Mycobacterium tuberculosis</rdfs:label>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0051701"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+        <owl:annotatedTarget>Reactome:R-HSA-9658195</owl:annotatedTarget>
+        <rdfs:label>Leishmania infection</rdfs:label>
+    </owl:Axiom>
     
 
 
@@ -23114,6 +23084,12 @@ Previous. An information content entity is a non-realizable information entity t
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000032">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
+                <owl:someValuesFrom rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
@@ -24585,6 +24561,12 @@ GO   gene ontology</obo:IAO_0000112>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000018"/>
             </owl:Restriction>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000407"/>
+                <owl:someValuesFrom rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000407"/>
@@ -24886,6 +24868,7 @@ GO   gene ontology</obo:IAO_0000112>
     <!-- http://purl.obolibrary.org/obo/IAO_0000443 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000443">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -24940,6 +24923,7 @@ GO   gene ontology</obo:IAO_0000112>
     <!-- http://purl.obolibrary.org/obo/IAO_0000572 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000572">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -24985,6 +24969,7 @@ points together with a line.</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/IAO_0000574 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000574">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -25135,6 +25120,7 @@ points together with a line.</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/IAO_0000580 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000580">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -26195,6 +26181,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
     <!-- http://purl.obolibrary.org/obo/IAO_0000650 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000650">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -26385,20 +26372,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
-                    </owl:Restriction>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
-                        <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0020010"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -26413,10 +26386,8 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000111 xml:lang="en">identifier</obo:IAO_0000111>
-        <obo:IAO_0000115 xml:lang="en">An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
-        <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">proper name</obo:IAO_0000118>
         <obo:IAO_0000233 xml:lang="en">https://github.com/information-artifact-ontology/IAO/issues/237</obo:IAO_0000233>
@@ -26457,12 +26428,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <owl:equivalentClass>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0020000"/>
-            </owl:Restriction>
-        </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -26471,9 +26437,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.</obo:IAO_0000115>
-        <obo:IAO_0000115 xml:lang="en">An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
-        <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">dubbing process</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">naming</obo:IAO_0000118>
@@ -26487,22 +26451,9 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
     <!-- http://purl.obolibrary.org/obo/IAO_0020015 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0020015">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0020000"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
-                        <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0020000"/>
-        <obo:IAO_0000115 xml:lang="en">A personal name is a proper name identifying an individual person.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">An identifier referring to an individual entity that is ascribed personhood by the user of the identifier.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
-        <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000119>http://en.wikipedia.org/wiki/Personal_name</obo:IAO_0000119>
         <obo:IAO_0000233 xml:lang="en">https://github.com/information-artifact-ontology/IAO/issues/237</obo:IAO_0000233>
@@ -26555,11 +26506,9 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0020000"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
-        <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">code map</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">code system</obo:IAO_0000118>
@@ -26590,7 +26539,7 @@ When there is no such string, it is almost always because the entities take the
     <!-- http://purl.obolibrary.org/obo/IAO_0021003 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0021003">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <obo:IAO_0000112 xml:lang="en">Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom</obo:IAO_0000112>
         <obo:IAO_0000115 xml:lang="en">A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
@@ -27023,6 +26972,12 @@ No imports</obo:IAO_0000115>
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/IDO_0000618"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000031"/>
         <obo:IAO_0000115 xml:lang="en">A disposition to initiate processes that result in a disorder.</obo:IAO_0000115>
@@ -27073,6 +27028,12 @@ No imports</obo:IAO_0000115>
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
@@ -27667,6 +27628,12 @@ No imports</obo:IAO_0000115>
                 </owl:intersectionOf>
             </owl:Class>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000031"/>
         <obo:IAO_0000115 xml:lang="en">A disposition that is the ability to mount a normal immune response.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
@@ -27776,7 +27743,7 @@ No imports</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/IDO_0000629 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000629">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
@@ -29935,6 +29902,16 @@ No imports</obo:IAO_0000115>
     
 
 
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_131567 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
+        <rdfs:label>cellular organisms</rdfs:label>
+    </owl:Class>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_1329799 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1329799">
@@ -31831,8 +31808,12 @@ No imports</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_2759 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2759">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:23020233</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PMID:30257078</oboInOwl:hasDbXref>
         <rdfs:label>Eukaryota</rdfs:label>
         <rdfs:label xml:lang="en">Eukaryota</rdfs:label>
     </owl:Class>
@@ -33277,6 +33258,8 @@ No imports</obo:IAO_0000115>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_40674">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_32524"/>
         <obo:IAO_0000118 xml:lang="en">mammals</obo:IAO_0000118>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
+        <rdfs:label>Mammalia</rdfs:label>
         <rdfs:label xml:lang="en">Mammalia</rdfs:label>
     </owl:Class>
     
@@ -36895,6 +36878,8 @@ No imports</obo:IAO_0000115>
         <obo:IAO_0000118 xml:lang="en">Primata</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">primate</obo:IAO_0000118>
         <obo:IAO_0000118 xml:lang="en">primates</obo:IAO_0000118>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
+        <rdfs:label>Primates</rdfs:label>
         <rdfs:label xml:lang="en">Primates</rdfs:label>
     </owl:Class>
     
@@ -37150,12 +37135,10 @@ No imports</obo:IAO_0000115>
     <!-- http://purl.obolibrary.org/obo/NCBITaxon_9606 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2759"/>
-        <obo:IAO_0000111 xml:lang="en">Homo sapiens</obo:IAO_0000111>
-        <obo:IAO_0000118>human being</obo:IAO_0000118>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9443"/>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
+        <oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
         <rdfs:label>Homo sapiens</rdfs:label>
-        <rdfs:label xml:lang="en">Homo sapiens</rdfs:label>
     </owl:Class>
     
 
@@ -37791,7 +37774,6 @@ No imports</obo:IAO_0000115>
                 </owl:someValuesFrom>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000111>planned process</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">planned process</obo:IAO_0000111>
         <obo:IAO_0000112>Injecting mice with a vaccine in order to test its efficacy</obo:IAO_0000112>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
@@ -37800,12 +37782,8 @@ No imports</obo:IAO_0000115>
         <obo:IAO_0000116>&apos;Plan&apos; includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn&apos;t have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)</obo:IAO_0000116>
         <obo:IAO_0000116>We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some 
   objectives is a planned process.</obo:IAO_0000116>
-        <obo:IAO_0000116>We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some 
-objectives is a planned process.</obo:IAO_0000116>
         <obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
         <obo:IAO_0000119>branch derived</obo:IAO_0000119>
-        <obo:IAO_0000232>6/11/9: Edited at workshop. Used to include: is initiated by an agent</obo:IAO_0000232>
-        <obo:IAO_0000232 xml:lang="en">This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
         <rdfs:label xml:lang="en">planned process</rdfs:label>
     </owl:Class>
@@ -38061,28 +38039,13 @@ for now.</obo:IAO_0000116>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
         <obo:IAO_0000111>device</obo:IAO_0000111>
         <obo:IAO_0000112>A voltmeter is a measurement device which is intended to perform some measure function.</obo:IAO_0000112>
-        <obo:IAO_0000112>An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.</obo:IAO_0000112>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
         <obo:IAO_0000115>A device is a processed material which is designed to perform some function or functions</obo:IAO_0000115>
-        <obo:IAO_0000115>A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.</obo:IAO_0000115>
-        <obo:IAO_0000116>2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of &quot;device&quot;, and are enumerating the types of roles that a reagent can perform.
-
-2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions.  Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear.  For example:
-
-(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component.  This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.
-
-(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.
-
-(3) A gel running  box  is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it.  This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.
-
-In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation).  In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.</obo:IAO_0000116>
         <obo:IAO_0000116>food should not classify as a device - counter example for using manufacturer and not device. macroscopic only</obo:IAO_0000116>
         <obo:IAO_0000116>if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn&apos;t work before as we had manufacturing as part of  the definition. device was needed, but couldn&apos;t define in Philadelphia. If we decide  that in addition to function there are also capabilities for which a device is created we will include these in the definition.</obo:IAO_0000116>
         <obo:IAO_0000117>PERSON: Helen Parkinson</obo:IAO_0000117>
         <obo:IAO_0000118>instrument</obo:IAO_0000118>
         <obo:IAO_0000119>OBI Vancouver workshop 2010</obo:IAO_0000119>
-        <obo:IAO_0000119>OBI development call 2012-12-17.</obo:IAO_0000119>
         <rdfs:comment>would include reagents</rdfs:comment>
         <rdfs:label>device</rdfs:label>
     </owl:Class>
@@ -38431,19 +38394,8 @@ https://www.doi.org/</obo:IAO_0000119>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000045"/>
         <obo:IAO_0000111 xml:lang="en">organism</obo:IAO_0000111>
-        <obo:IAO_0000112 xml:lang="en">animal</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">fungus</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">plant</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">virus</obo:IAO_0000112>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000121"/>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
         <obo:IAO_0000115 xml:lang="en">A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.</obo:IAO_0000115>
-        <obo:IAO_0000116>10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and &apos;other organisms&apos;)</obo:IAO_0000116>
-        <obo:IAO_0000116>13-02-2009:
-OBI doesn&apos;t take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus.
-This issue is outside the scope of OBI.</obo:IAO_0000116>
-        <obo:IAO_0000117>GROUP: OBI Biomaterial Branch</obo:IAO_0000117>
-        <obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/Organism</obo:IAO_0000119>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
         <apollo_sv:APOLLO_SV_0000040>Individual</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label xml:lang="en">organism</rdfs:label>
@@ -38454,6 +38406,7 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
     <!-- http://purl.obolibrary.org/obo/OBI_0200000 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200000">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -38465,6 +38418,7 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000112>The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.</obo:IAO_0000112>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+        <obo:IAO_0000115 xml:lang="en">A completely executed planned process that produces output data from input data.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">A data transformation is a process which produces output data from input data</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">A planned process that produces output data from input data.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
@@ -38661,12 +38615,11 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
     <!-- http://purl.obolibrary.org/obo/OGMS_0000014 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000014">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
         <obo:IAO_0000115 xml:lang="en">A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2010-07-19T10:18:02Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>clinical finding</rdfs:label>
     </owl:Class>
     
@@ -38680,8 +38633,6 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T10:21:58Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <apollo_sv:APOLLO_SV_0000040>result</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label>laboratory finding</rdfs:label>
     </owl:Class>
     
@@ -38695,7 +38646,6 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2010-07-19T11:13:49Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>phenotype</rdfs:label>
     </owl:Class>
     
@@ -38709,7 +38659,6 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:18:05Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>clinical phenotype</rdfs:label>
     </owl:Class>
     
@@ -38724,7 +38673,6 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:21:20Z</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
-        <apollo_sv:APOLLO_SV_0000040>disease</apollo_sv:APOLLO_SV_0000040>
         <rdfs:label>disease</rdfs:label>
     </owl:Class>
     
@@ -38734,16 +38682,8 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000032">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
-        <obo:IAO_0000115 xml:lang="en">A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
-        <obo:IAO_0000117 xml:lang="en">Barry Smith</obo:IAO_0000117>
-        <obo:IAO_0000117 xml:lang="en">Richard H. Scheuermann</obo:IAO_0000117>
-        <obo:IAO_0000117 xml:lang="en">Werner Ceusters</obo:IAO_0000117>
-        <obo:IAO_0000119 xml:lang="en">Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. 
-
-Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:22:01Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>homeostasis</rdfs:label>
     </owl:Class>
     
@@ -38758,7 +38698,6 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:39:44Z</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>disorder</rdfs:label>
     </owl:Class>
     
@@ -38786,14 +38725,11 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000063">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <obo:IAO_0000111>disease course</obo:IAO_0000111>
         <obo:IAO_0000115 xml:lang="en">The totality of all processes through which a given disease instance is realized.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2009-06-23T11:55:44Z</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ido.owl</obo:IAO_0000412>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>disease course</rdfs:label>
     </owl:Class>
     
@@ -38808,7 +38744,6 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
         <obo:IAO_0000119>http://code.google.com/p/ogms/issues/detail?id=3</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2010-01-25T04:51:11Z</obo:IAO_0000232>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:comment>From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087</rdfs:comment>
         <rdfs:label>extended organism</rdfs:label>
     </owl:Class>
@@ -38818,16 +38753,11 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/</obo:IAO_0000119>
     <!-- http://purl.obolibrary.org/obo/OGMS_0000090 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000090">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
-        <obo:IAO_0000115 xml:lang="en">A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder</obo:IAO_0000115>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000096"/>
+        <obo:IAO_0000115 xml:lang="en">A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://code.google.com/p/ogms/issues/detail?id=35</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2010-03-31T04:51:11Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <apollo_sv:APOLLO_SV_0000040>Treatment</apollo_sv:APOLLO_SV_0000040>
-        <rdfs:comment xml:lang="en">Apollo-SV currently defines two subclasses of treatment.
-See vaccination and antiviral treatment.  
-</rdfs:comment>
         <rdfs:label>treatment</rdfs:label>
     </owl:Class>
     
@@ -38836,14 +38766,15 @@ See vaccination and antiviral treatment.
     <!-- http://purl.obolibrary.org/obo/OGMS_0000092 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000092">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000182"/>
-        <obo:IAO_0000115 xml:lang="en">A processual entity which has as parts all the processes in which a given organism is participant.</obo:IAO_0000115>
-        <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <obo:IAO_0000115 xml:lang="en">A process which has as parts all the processes in which a given organism is participant.</obo:IAO_0000115>
+        <obo:IAO_0000117>Albert Goldfain
+Richard Scheuermann
+Sagar Jain</obo:IAO_0000117>
         <obo:IAO_0000119>http://code.google.com/p/ogms/issues/detail?id=38</obo:IAO_0000119>
-        <obo:IAO_0000232>creation date: 2010-03-31T04:51:11Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <obo:IAO_0000600 xml:lang="en">A processual entity which has as parts all the processes in which a given organism is participant.</obo:IAO_0000600>
-        <apollo_sv:APOLLO_SV_0000040>LifeCycle</apollo_sv:APOLLO_SV_0000040>
+        <obo:IAO_0000232>creation date: 2010-03-31T04:51:11Z
+
+EDIT: 10 NOV 2015</obo:IAO_0000232>
         <rdfs:label>life course</rdfs:label>
     </owl:Class>
     
@@ -38852,12 +38783,14 @@ See vaccination and antiviral treatment.
     <!-- http://purl.obolibrary.org/obo/OGMS_0000096 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000096">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <obo:IAO_0000115 xml:lang="en">A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process</obo:IAO_0000115>
-        <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000035"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <obo:IAO_0000115 xml:lang="en">A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient</obo:IAO_0000115>
+        <obo:IAO_0000117>Albert Goldfain
+Sagar Jain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
-        <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
+        <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z
+editor date: 2017-04-18</obo:IAO_0000232>
         <rdfs:label>health care process</rdfs:label>
     </owl:Class>
     
@@ -38866,13 +38799,12 @@ See vaccination and antiviral treatment.
     <!-- http://purl.obolibrary.org/obo/OGMS_0000097 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000097">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000096"/>
         <obo:IAO_0000115 xml:lang="en">A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role.  The health care provider role and patient are realized during the health care encounter</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
+        <oboInOwl:hasExactSynonym xml:lang="en">healthcare encounter</oboInOwl:hasExactSynonym>
         <rdfs:label>health care encounter</rdfs:label>
     </owl:Class>
     
@@ -38881,12 +38813,14 @@ See vaccination and antiviral treatment.
     <!-- http://purl.obolibrary.org/obo/OGMS_0000098 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000098">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000097"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000096"/>
+        <obo:IAO_0000115 xml:lang="en">TODO</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <apollo_sv:APOLLO_SV_0000040>hospitalization</apollo_sv:APOLLO_SV_0000040>
+        <rdfs:comment>09/16/2020
+Is this same as admission? 
+Is this the same as inpatient encounter?</rdfs:comment>
         <rdfs:label>hospitalization</rdfs:label>
     </owl:Class>
     
@@ -38896,10 +38830,10 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000099">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000097"/>
+        <obo:IAO_0000115 xml:lang="en">TODO</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>outpatient encounter</rdfs:label>
     </owl:Class>
     
@@ -38913,7 +38847,6 @@ See vaccination and antiviral treatment.
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
         <rdfs:label>inpatient encounter</rdfs:label>
     </owl:Class>
     
@@ -38923,11 +38856,11 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000101">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000097"/>
+        <obo:IAO_0000115 xml:lang="en">A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention.</obo:IAO_0000115>
         <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
         <obo:IAO_0000119>http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6</obo:IAO_0000119>
         <obo:IAO_0000232>creation date: 2011-02-21T09:57:44Z</obo:IAO_0000232>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
-        <rdfs:label>ED encounter</rdfs:label>
+        <rdfs:label>emergency department encounter</rdfs:label>
     </owl:Class>
     
 
@@ -38936,10 +38869,14 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000105">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
-        <obo:IAO_0000115 xml:lang="en">A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course.</obo:IAO_0000115>
-        <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+        <obo:IAO_0000115>A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course.</obo:IAO_0000116>
+        <obo:IAO_0000117>Albert Goldfain
+Richard Scheuermann
+Sagar Jain</obo:IAO_0000117>
+        <obo:IAO_0000118>recurrent</obo:IAO_0000118>
         <obo:IAO_0000119>http://code.google.com/p/ogms/issues/detail?id=73</obo:IAO_0000119>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/ogms.owl</obo:IAO_0000412>
+        <dc:date>10 NOV 2015</dc:date>
         <rdfs:label xml:lang="en">relapse</rdfs:label>
     </owl:Class>
     
@@ -38964,7 +38901,12 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000001">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000026"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000050"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A social role inhering in a human being.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
@@ -38986,8 +38928,8 @@ See vaccination and antiviral treatment.
         <obo:IAO_0000115 xml:lang="en">A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.</obo:IAO_0000115>
         <obo:IAO_0000117>Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan</obo:IAO_0000117>
-        <obo:IAO_0000118 xml:lang="en">health care role</obo:IAO_0000118>
-        <rdfs:label xml:lang="en">human health care role</rdfs:label>
+        <oboInOwl:hasExactSynonym xml:lang="en">healthcare role</oboInOwl:hasExactSynonym>
+        <rdfs:label xml:lang="en">health care role</rdfs:label>
     </owl:Class>
     
 
@@ -38996,8 +38938,13 @@ See vaccination and antiviral treatment.
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000011">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000010"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
-        <obo:IAO_0000115 xml:lang="en">A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.</obo:IAO_0000115>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <obo:IAO_0000115 xml:lang="en">A health care role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Amanda Hicks</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <obo:IAO_0000118 xml:lang="en">patient</obo:IAO_0000118>
@@ -39021,6 +38968,7 @@ See vaccination and antiviral treatment.
         <obo:IAO_0000115 xml:lang="en">A role that inheres in an organization and that is realized by the providing of services in a health care encounter.</obo:IAO_0000115>
         <dc:contributor>Mathias Brochhausen</dc:contributor>
         <dc:creator>Amanda Hicks</dc:creator>
+        <oboInOwl:hasExactSynonym xml:lang="en">healthcare provider organization role</oboInOwl:hasExactSynonym>
         <rdfs:label xml:lang="en">health care provider organization role</rdfs:label>
     </owl:Class>
     
@@ -39037,7 +38985,7 @@ See vaccination and antiviral treatment.
                     <owl:Class>
                         <owl:intersectionOf rdf:parseType="Collection">
                             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000030"/>
-                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
+                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000022"/>
                         </owl:intersectionOf>
                     </owl:Class>
                 </owl:allValuesFrom>
@@ -39084,8 +39032,13 @@ Ditto for its current descendants.</rdfs:comment>
     <!-- http://purl.obolibrary.org/obo/OMRSE_00000026 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000026">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00002072"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A role in human social processes that inheres in an organism.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">William R. Hogan
 Mathias Brochhausen</obo:IAO_0000117>
@@ -39104,6 +39057,7 @@ Ditto for its current descendants.</rdfs:comment>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000027">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000025"/>
         <obo:IAO_0000115 xml:lang="en">An organization social role that, if realized, is realized by either a health care process or an ancillary health care process</obo:IAO_0000115>
+        <oboInOwl:hasExactSynonym xml:lang="en">organization healthcare role</oboInOwl:hasExactSynonym>
         <rdfs:comment xml:lang="en">Previous definition: An organization social role played by an organization in health care processes.</rdfs:comment>
         <rdfs:label xml:lang="en">organization health care role</rdfs:label>
     </owl:Class>
@@ -39125,7 +39079,12 @@ Ditto for its current descendants.</rdfs:comment>
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000011"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000050"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 xml:lang="en">A patient role that inheres in a human being.</obo:IAO_0000115>
         <rdfs:label xml:lang="en">human patient role</rdfs:label>
     </owl:Class>
@@ -39169,102 +39128,6 @@ Amanda Hicks</obo:IAO_0000117>
     
 
 
-    <!-- http://purl.obolibrary.org/obo/OMRSE_00000048 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000048">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000023"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:label xml:lang="en">material entity role</rdfs:label>
-    </owl:Class>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/OMRSE_00000049 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000049">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000048"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:label xml:lang="en">organism role</rdfs:label>
-    </owl:Class>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/OMRSE_00000050 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000050">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000049"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
-                <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:label xml:lang="en">Homo sapiens role</rdfs:label>
-    </owl:Class>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/OMRSE_00000051 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00000051">
@@ -39279,7 +39142,7 @@ Amanda Hicks</obo:IAO_0000117>
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000048"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
@@ -39466,7 +39329,12 @@ Amanda Hicks</obo:IAO_0000117>
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000061"/>
-        <rdfs:subClassOf rdf:nodeID="genid3146"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000068"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000245"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
@@ -39477,16 +39345,6 @@ Amanda Hicks</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
         <rdfs:label xml:lang="en">facility</rdfs:label>
     </owl:Class>
-    <owl:Restriction rdf:nodeID="genid3146">
-        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000068"/>
-        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000245"/>
-    </owl:Restriction>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000062"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
-        <owl:annotatedTarget rdf:nodeID="genid3146"/>
-        <owl:versionInfo>09/09/2017</owl:versionInfo>
-    </owl:Axiom>
     
 
 
@@ -39630,6 +39488,7 @@ Amanda Hicks</obo:IAO_0000117>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000097"/>
             </owl:Restriction>
         </rdfs:subClassOf>
+        <oboInOwl:hasExactSynonym xml:lang="en">healthcare function</oboInOwl:hasExactSynonym>
         <rdfs:label xml:lang="en">health care function</rdfs:label>
     </owl:Class>
     
@@ -39638,7 +39497,13 @@ Amanda Hicks</obo:IAO_0000117>
     <!-- http://purl.obolibrary.org/obo/OMRSE_00002072 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OMRSE_00002072">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OMRSE_00000048"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
@@ -40180,38 +40045,34 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000061">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
-        <obo:IAO_0000115>Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism&apos;s own genome.</obo:IAO_0000115>
         <obo:IAO_0000115>Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism&apos;s own genome.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_4751"/>
         <oboInOwl:hasDbXref>AAO:0010825</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CARO:0000003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EHDAA2:0003003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EMAPA:0</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00007001</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FAO:0000001</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:305751</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:67135</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GAID:781</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>HAO:0000003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MA:0003000</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>MESH:A13</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MESH:D000825</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>SCTID:362889002</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0000037</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001823</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001759</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WBbt:0000100</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0003000</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0000037</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>http://dbpedia.org/ontology/AnatomicalStructure</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>biological structure</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>connected biological structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0000061</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>anatomical structure</rdfs:label>
     </owl:Class>
@@ -40230,29 +40091,85 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000071 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000071">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
+        <obo:IAO_0000115>End of the life of an organism.</obo:IAO_0000115>
+        <oboInOwl:hasDbXref>XAO:0000437</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>XtroDO:0000085</oboInOwl:hasDbXref>
+        <oboInOwl:hasRelatedSynonym>death</oboInOwl:hasRelatedSynonym>
+        <oboInOwl:id>UBERON:0000071</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <rdfs:label>death stage</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000071"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>End of the life of an organism.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>XAO:0000437</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000105 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000105">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <obo:IAO_0000115>A spatiotemporal region encompassing some part of the life cycle of an organism.</obo:IAO_0000115>
+        <obo:IAO_0000116>this class represents a proper part of the life cycle of an organism. The class &apos;life cycle&apos; should not be placed here</obo:IAO_0000116>
+        <oboInOwl:hasDbXref>BILS:0000105</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>EFO:0000399</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FBdv:00007012</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>FMA:24120</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>MESH:D008018</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PdumDv:0000090</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>WBls:0000002</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>XAO:1000000</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>ZFS:0000000</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>ZFS:0100000</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>ncithesaurus:Developmental_Stage</oboInOwl:hasDbXref>
+        <oboInOwl:hasNarrowSynonym>developmental stage</oboInOwl:hasNarrowSynonym>
+        <oboInOwl:hasNarrowSynonym>stage</oboInOwl:hasNarrowSynonym>
+        <oboInOwl:id>UBERON:0000105</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#efo_slim"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
+        <rdfs:label>life cycle stage</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A spatiotemporal region encompassing some part of the life cycle of an organism.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>https://orcid.org/0000-0002-6601-2165</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0000465 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000465">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001062"/>
         <obo:IAO_0000115>Anatomical entity that has mass.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_4751"/>
         <oboInOwl:hasDbXref>AAO:0010264</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000006</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000006</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CARO:0000006</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EHDAA2:0003006</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00007016</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:67165</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>HAO:0000006</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0001836</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001826</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001721</oboInOwl:hasDbXref>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0000465</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>material anatomical entity</rdfs:label>
     </owl:Class>
@@ -40268,16 +40185,13 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <!-- http://purl.obolibrary.org/obo/UBERON_0000467 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000467">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000480"/>
-        <obo:IAO_0000115>Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia].</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:UBPROP_0000001>Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]</obo:UBPROP_0000001>
-        <obo:UBPROP_0000001>Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]</obo:UBPROP_0000001>
-        <obo:UBPROP_0000001>Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]</obo:UBPROP_0000001>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000061"/>
+        <obo:IAO_0000115>Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.</obo:IAO_0000115>
         <oboInOwl:hasBroadSynonym>system</oboInOwl:hasBroadSynonym>
         <oboInOwl:hasDbXref>AAO:0000007</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000011</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000011</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>BIRNLEX:14</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BSA:0000049</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CALOHA:TS-2088</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CARO:0000011</oboInOwl:hasDbXref>
@@ -40285,16 +40199,13 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>EHDAA:392</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EMAPA:16103</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EV:0100000</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00004856</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:7149</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>HAO:0000011</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MA:0000003</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>NIF_GrossAnatomy:birnlex_14</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>NCIT:C12919</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>SCTID:278195005</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0001439</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001831</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>UMLS:C0460002</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001725</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0005746</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0005763</oboInOwl:hasDbXref>
@@ -40302,16 +40213,51 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>XAO:0003002</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0001439</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>galen:AnatomicalSystem</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>ncithesaurus:Organ_System</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>body system</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>connected anatomical system</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>organ system</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:hasRelatedSynonym>anatomical systems</oboInOwl:hasRelatedSynonym>
         <oboInOwl:id>UBERON:0000467</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#pheno_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#uberon_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>anatomical system</rdfs:label>
-        <rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/EHDAA2_0001330"/>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000011</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
+        <owl:annotatedTarget>system</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>GO:0048731</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget>body system</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>BIRNLEX:14</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget>connected anatomical system</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000011</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
+        <owl:annotatedTarget>anatomical systems</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>ZFA:0001439</oboInOwl:hasDbXref>
+        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/OMO_0003004"/>
+    </owl:Axiom>
     
 
 
@@ -40320,38 +40266,57 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000479">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0010000"/>
         <obo:IAO_0000115>Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
+        <obo:IAO_0000116>changed label and definition to reflect CARO2</obo:IAO_0000116>
         <oboInOwl:hasDbXref>AAO:0000607</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AAO:0010054</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000043</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000043</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>BIRNLEX:19</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CALOHA:TS-2090</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CARO:0000043</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>EHDAA2:0003043</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00007003</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>EMAPA:35868</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:9637</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>HAO:0000043</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MA:0003002</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>MESH:A10</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>NIF_GrossAnatomy:birnlex_19</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>MESH:D014024</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>NCIT:C12801</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0001477</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001844</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>UMLS:C0040300</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001757</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0005729</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0003040</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0001477</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>galen:Tissue</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>ncithesaurus:Tissue</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>portion of tissue</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>tissue portion</oboInOwl:hasExactSynonym>
         <oboInOwl:hasNarrowSynonym>simple tissue</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0000479</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#pheno_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
-        <rdfs:comment>Editor note: changed label and definition to reflect CARO2</rdfs:comment>
         <rdfs:label>tissue</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000479"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000043</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000479"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget>portion of tissue</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000043</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000479"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
+        <owl:annotatedTarget>simple tissue</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>AEO:0000043</oboInOwl:hasDbXref>
+    </owl:Axiom>
     
 
 
@@ -40360,7 +40325,7 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000480">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000061"/>
         <obo:IAO_0000115>Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
+        <obo:IAO_0000116>Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]</obo:IAO_0000116>
         <oboInOwl:hasDbXref>AAO:0010008</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000054</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000054</oboInOwl:hasDbXref>
@@ -40372,21 +40337,34 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>VHOG:0001724</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0003001</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0001512</oboInOwl:hasDbXref>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0000480</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>anatomical group</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000480"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>CARO:0000054</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>http://orcid.org/0000-0001-9114-8737</oboInOwl:hasDbXref>
+    </owl:Axiom>
     
 
 
     <!-- http://purl.obolibrary.org/obo/UBERON_0001062 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001062">
+        <owl:equivalentClass>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0020105"/>
+                <owl:hasSelf rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:hasSelf>
+            </owl:Restriction>
+        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
         <obo:IAO_0000115>Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.</obo:IAO_0000115>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_4751"/>
         <oboInOwl:hasDbXref>AAO:0010841</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>AEO:0000000</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BFO:0000004</oboInOwl:hasDbXref>
@@ -40400,12 +40378,13 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>NCIT:C12219</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0100000</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TGMA:0001822</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>UMLS:C1515976</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0000100</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0000000</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0100000</oboInOwl:hasDbXref>
         <oboInOwl:id>UBERON:0001062</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>anatomical entity</rdfs:label>
     </owl:Class>
@@ -40416,44 +40395,43 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <oboInOwl:hasDbXref>FMA:62955</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>http://orcid.org/0000-0001-9114-8737</oboInOwl:hasDbXref>
     </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001062"/>
-        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
-        <owl:annotatedTarget>UMLS:C1515976</owl:annotatedTarget>
-        <oboInOwl:source>ncithesaurus:Anatomic_Structure_System_or_Substance</oboInOwl:source>
-    </owl:Axiom>
     
 
 
     <!-- http://purl.obolibrary.org/obo/UBERON_0002405 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002405">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
         <obo:IAO_0000115>Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:UBPROP_0000003>The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]</obo:UBPROP_0000003>
         <oboInOwl:hasDbXref>AAO:0011003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>BILA:0000104</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>BTO:0005810</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:9825</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GAID:328</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MA:0002711</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>MESH:A15.382</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>MESH:D007107</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>NCIT:C12735</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>SCTID:362590003</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>TAO:0001159</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>UMLS:C0020962</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001247</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>Wikipedia:Immune_system</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>XAO:0003152</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>ZFA:0001159</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>ncithesaurus:Immune_System</oboInOwl:hasDbXref>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0002405</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#pheno_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#uberon_slim"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#vertebrate_core"/>
-        <rdfs:comment>This class was created automatically from a combination of ontologies</rdfs:comment>
         <rdfs:label>immune system</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002405"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>Wikipedia:Immune_system</oboInOwl:hasDbXref>
+    </owl:Axiom>
     
 
 
@@ -40462,15 +40440,12 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0010000">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000061"/>
         <obo:IAO_0000115>An anatomical structure that has more than one cell as a part.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
-        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_4751"/>
         <oboInOwl:hasDbXref>CARO:0010000</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FBbt:00100313</oboInOwl:hasDbXref>
         <oboInOwl:hasExactSynonym>multicellular structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0010000</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>multicellular anatomical structure</rdfs:label>
     </owl:Class>
@@ -40492,33 +40467,21 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <!-- http://purl.obolibrary.org/obo/UBERON_0035943 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0035943">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000035"/>
         <obo:IAO_0000115>A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.</obo:IAO_0000115>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>UBERON:0035943</oboInOwl:id>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#common_anatomy"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_subset"/>
+        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#mouse_subset"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#upper_level"/>
         <rdfs:label>life cycle temporal boundary</rdfs:label>
     </owl:Class>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/UBERON_0035944 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0035944">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035943"/>
-        <obo:IAO_0000115>A life cycle temporal boundary that marks the end of the life cycle of the organism.</obo:IAO_0000115>
-        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
-        <obo:IAO_0000412>http://purl.obolibrary.org/obo/uberon.owl</obo:IAO_0000412>
-        <oboInOwl:hasExactSynonym>end of life cycle</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>moment of death</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>time of death</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
-        <oboInOwl:hasRelatedSynonym>death</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasRelatedSynonym>end of life</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:id>UBERON:0035944</oboInOwl:id>
-        <rdfs:label>life-death temporal boundary</rdfs:label>
-    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0035943"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>https://orcid.org/0000-0002-6601-2165</oboInOwl:hasDbXref>
+    </owl:Axiom>
     
 
 
@@ -40950,9 +40913,13 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">failed exploratory term</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">Terms created as placeholders with the expectation of being permanent should instead be deprecated using the &quot;placeholder removed&quot; (obo:IAO_0000226) justification.</obo:IAO_0000116>
         <obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">failed exploratory term</rdfs:label>
     </owl:Thing>
     
@@ -40975,6 +40942,7 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
         <obo:IAO_0000111 xml:lang="en">organizational term</obo:IAO_0000111>
         <obo:IAO_0000115 xml:lang="en">Term created to ease viewing/sort terms for development purpose, and will not be included in a release</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">term created to ease viewing/sort terms for development purpose, and will not be included in a release</obo:IAO_0000115>
         <rdfs:label xml:lang="en">organizational term</rdfs:label>
     </owl:NamedIndividual>
@@ -41047,6 +41015,10 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">placeholder removed</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined.</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider.</obo:IAO_0000116>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">placeholder removed</rdfs:label>
     </owl:Thing>
     
@@ -41057,7 +41029,11 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000227">
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">terms merged</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term has been combined with one or more other terms to create a more encompassing (merged) term.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">An editor note should explain what were the merged terms and the reason for the merge.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge.</obo:IAO_0000116>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">terms merged</rdfs:label>
     </owl:NamedIndividual>
     
@@ -41068,7 +41044,11 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000228">
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">term imported</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term has been replaced by a term imported from another ontology.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001.</obo:IAO_0000116>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">term imported</rdfs:label>
     </owl:NamedIndividual>
     
@@ -41079,7 +41059,11 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000229">
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000111 xml:lang="en">term split</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">The term has been split into two or more new terms.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001.</obo:IAO_0000116>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label xml:lang="en">term split</rdfs:label>
     </owl:NamedIndividual>
     
@@ -41180,9 +41164,12 @@ np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
         <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
         <obo:IAO_0000115 xml:lang="en">The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype.</obo:IAO_0000116>
         <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
         <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/77</obo:IAO_0000233>
         <obo:IAO_0000234>https://orcid.org/0000-0001-5208-3432</obo:IAO_0000234>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0001-6875-5360"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
         <rdfs:label>out of scope</rdfs:label>
     </owl:NamedIndividual>
     
@@ -41423,13 +41410,10 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
     <rdf:Description rdf:about="urn:swrl#e">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
-    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ro.owl#z">
-        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
-    </rdf:Description>
-    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ro.owl#y">
+    <rdf:Description rdf:about="urn:swrl:var#e">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
-    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ro.owl#x">
+    <rdf:Description rdf:about="urn:swrl:var#d">
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
     </rdf:Description>
     <rdf:Description rdf:about="urn:swrl:var#y">
@@ -41490,10 +41474,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                 <rdf:first>
                     <rdf:Description>
-                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002180"/>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
                         <swrl:argument1 rdf:resource="urn:swrl:var#w"/>
-                        <swrl:argument2 rdf:resource="urn:swrl:var#p"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41501,9 +41484,10 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                         <rdf:first>
                             <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002180"/>
                                 <swrl:argument1 rdf:resource="urn:swrl:var#w"/>
+                                <swrl:argument2 rdf:resource="urn:swrl:var#p"/>
                             </rdf:Description>
                         </rdf:first>
                         <rdf:rest>
@@ -41581,6 +41565,49 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
             </rdf:Description>
         </swrl:head>
     </rdf:Description>
+    <rdf:Description>
+        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
+        <swrl:body>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                        <rdf:first>
+                            <rdf:Description>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#d"/>
+                            </rdf:Description>
+                        </rdf:first>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+                    </rdf:Description>
+                </rdf:rest>
+            </rdf:Description>
+        </swrl:body>
+        <swrl:head>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000091"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+            </rdf:Description>
+        </swrl:head>
+    </rdf:Description>
     <rdf:Description>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>
@@ -41631,9 +41658,10 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                 <rdf:first>
                     <rdf:Description>
-                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
-                        <swrl:argument1 rdf:resource="urn:swrl#d"/>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41641,10 +41669,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                         <rdf:first>
                             <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
-                                <swrl:argument1 rdf:resource="urn:swrl#e"/>
-                                <swrl:argument2 rdf:resource="urn:swrl#d"/>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#d"/>
                             </rdf:Description>
                         </rdf:first>
                         <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41658,9 +41685,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
-                        <swrl:argument1 rdf:resource="urn:swrl#e"/>
-                        <swrl:argument2 rdf:resource="urn:swrl#d"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41675,7 +41702,7 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
+                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
                         <swrl:argument1 rdf:resource="urn:swrl#d"/>
                     </rdf:Description>
                 </rdf:first>
@@ -41701,7 +41728,7 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
                         <swrl:argument1 rdf:resource="urn:swrl#e"/>
                         <swrl:argument2 rdf:resource="urn:swrl#d"/>
                     </rdf:Description>
@@ -41711,9 +41738,6 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
         </swrl:head>
     </rdf:Description>
     <rdf:Description>
-        <swrla:isRuleEnabled rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</swrla:isRuleEnabled>
-        <rdfs:comment>MF(X)-directly_regulates-&gt;MF(Y)-enabled_by-&gt;GP(Z) =&gt; MF(Y)-has_input-&gt;GP(Y) e.g. if &apos;protein kinase activity&apos;(X) directly_regulates &apos;protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z</rdfs:comment>
-        <rdfs:label>infer input from direct reg</rdfs:label>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>
             <rdf:Description>
@@ -41721,9 +41745,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
-                        <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#z"/>
-                        <swrl:argument2 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#y"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41731,37 +41755,12 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                         <rdf:first>
                             <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
-                                <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#x"/>
-                                <swrl:argument2 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#y"/>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#d"/>
                             </rdf:Description>
                         </rdf:first>
-                        <rdf:rest>
-                            <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
-                                <rdf:first>
-                                    <rdf:Description>
-                                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
-                                        <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#x"/>
-                                    </rdf:Description>
-                                </rdf:first>
-                                <rdf:rest>
-                                    <rdf:Description>
-                                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
-                                        <rdf:first>
-                                            <rdf:Description>
-                                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
-                                                <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#y"/>
-                                            </rdf:Description>
-                                        </rdf:first>
-                                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
-                                    </rdf:Description>
-                                </rdf:rest>
-                            </rdf:Description>
-                        </rdf:rest>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
                     </rdf:Description>
                 </rdf:rest>
             </rdf:Description>
@@ -41772,9 +41771,9 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002233"/>
-                        <swrl:argument1 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#x"/>
-                        <swrl:argument2 rdf:resource="http://purl.obolibrary.org/obo/ro.owl#z"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41782,9 +41781,6 @@ This interpretation is *not* the same as an at-all-times relation</obo:IAO_00001
         </swrl:head>
     </rdf:Description>
     <rdf:Description>
-        <rdfs:comment>GP(X)-enables-&gt;MF(Y)-has_part-&gt;MF(Z) =&gt; GP(X) enables MF(Z),
-e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase coupled transporter activity&apos; has_part &apos;ATPase activity&apos; then GP(X) enables &apos;ATPase activity&apos;</rdfs:comment>
-        <rdfs:label>enabling an MF enables its parts</rdfs:label>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>
             <rdf:Description>
@@ -41792,8 +41788,8 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
-                        <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
+                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
+                        <swrl:argument1 rdf:resource="urn:swrl#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41802,25 +41798,55 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                         <rdf:first>
                             <rdf:Description>
                                 <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
-                                <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
-                                <swrl:argument2 rdf:resource="urn:swrl:var#y"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                                <swrl:argument1 rdf:resource="urn:swrl#e"/>
+                                <swrl:argument2 rdf:resource="urn:swrl#d"/>
                             </rdf:Description>
                         </rdf:first>
-                        <rdf:rest>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+                    </rdf:Description>
+                </rdf:rest>
+            </rdf:Description>
+        </swrl:body>
+        <swrl:head>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
+                        <swrl:argument1 rdf:resource="urn:swrl#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl#d"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+            </rdf:Description>
+        </swrl:head>
+    </rdf:Description>
+    <rdf:Description>
+        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
+        <swrl:body>
+            <rdf:Description>
+                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                <rdf:first>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
+                    </rdf:Description>
+                </rdf:first>
+                <rdf:rest>
+                    <rdf:Description>
+                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+                        <rdf:first>
                             <rdf:Description>
-                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
-                                <rdf:first>
-                                    <rdf:Description>
-                                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
-                                        <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
-                                        <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
-                                    </rdf:Description>
-                                </rdf:first>
-                                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
+                                <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#d"/>
                             </rdf:Description>
-                        </rdf:rest>
+                        </rdf:first>
+                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
                     </rdf:Description>
                 </rdf:rest>
             </rdf:Description>
@@ -41831,9 +41857,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
-                        <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
-                        <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#e"/>
+                        <swrl:argument2 rdf:resource="urn:swrl:var#d"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41841,9 +41867,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
         </swrl:head>
     </rdf:Description>
     <rdf:Description>
-        <swrla:isRuleEnabled rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</swrla:isRuleEnabled>
-        <rdfs:comment>GP(X)-enables-&gt;MF(Y)-part_of-&gt;BP(Z) =&gt; GP(X) involved_in BP(Z) e.g. if X enables &apos;protein kinase activity&apos; and Y &apos;part of&apos; &apos;signal tranduction&apos; then X involved in &apos;signal transduction&apos;</rdfs:comment>
-        <rdfs:label>involved in BP</rdfs:label>
+        <rdfs:comment>GP(X)-enables-&gt;MF(Y)-has_part-&gt;MF(Z) =&gt; GP(X) enables MF(Z),
+e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase coupled transporter activity&apos; has_part &apos;ATPase activity&apos; then GP(X) enables &apos;ATPase activity&apos;</rdfs:comment>
+        <rdfs:label>enabling an MF enables its parts</rdfs:label>
         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
         <swrl:body>
             <rdf:Description>
@@ -41851,8 +41877,8 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
-                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
-                        <swrl:argument1 rdf:resource="urn:swrl:var#z"/>
+                        <swrl:classPredicate rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
+                        <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -41861,9 +41887,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                         <rdf:first>
                             <rdf:Description>
                                 <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
-                                <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
-                                <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
+                                <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
+                                <swrl:argument2 rdf:resource="urn:swrl:var#y"/>
                             </rdf:Description>
                         </rdf:first>
                         <rdf:rest>
@@ -41872,9 +41898,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                                 <rdf:first>
                                     <rdf:Description>
                                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
-                                        <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
-                                        <swrl:argument2 rdf:resource="urn:swrl:var#y"/>
+                                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                                        <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
+                                        <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
                                     </rdf:Description>
                                 </rdf:first>
                                 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
@@ -41890,7 +41916,7 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <rdf:first>
                     <rdf:Description>
                         <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
-                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002331"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
                         <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
                         <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
                     </rdf:Description>
diff --git a/src/ontology/imports/dron_import.owl b/src/ontology/imports/dron_import.owl
index fbe2401..b0d966b 100644
--- a/src/ontology/imports/dron_import.owl
+++ b/src/ontology/imports/dron_import.owl
@@ -6,6 +6,7 @@ Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
 Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
 Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
 Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(core:=<http://purl.obolibrary.org/obo/uberon/core#>)
 Prefix(pato:=<http://purl.obolibrary.org/obo/pato#>)
 Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 Prefix(swrl:=<http://www.w3.org/2003/11/swrl#>)
@@ -20,9 +21,9 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/dron_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/dron_import.owl>
-Annotation(dc:source <http://purl.obolibrary.org/obo/dron/releases/2025-12-19/dron.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/dron_import.owl>
+Annotation(dc:source <http://purl.obolibrary.org/obo/dron/releases/2026-03-04/dron.owl>)
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(obo:BFO_0000040))
 Declaration(Class(obo:DRON_00000005))
diff --git a/src/ontology/imports/geo_import.owl b/src/ontology/imports/geo_import.owl
index 3b2b35b..c39dfce 100644
--- a/src/ontology/imports/geo_import.owl
+++ b/src/ontology/imports/geo_import.owl
@@ -13,10 +13,10 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/geo_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/geo_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/geo_import.owl>
 Import(<http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl>)
 Import(<http://purl.obolibrary.org/obo/ro/core.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(obo:BFO_0000004))
 Declaration(Class(obo:BFO_0000027))
diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl
index f5bdfba..1997ccb 100644
--- a/src/ontology/imports/go_import.owl
+++ b/src/ontology/imports/go_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/go_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/go_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/go_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/go/releases/2026-01-23/go.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0007610>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0008150>))
diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl
index edbe7d2..0096e00 100644
--- a/src/ontology/imports/iao_import.owl
+++ b/src/ontology/imports/iao_import.owl
@@ -15,9 +15,9 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/iao_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/iao_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/iao_import.owl>
 Annotation(dc:source <http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(obo:APOLLO_SV_00000008))
 Declaration(Class(obo:APOLLO_SV_00000032))
diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl
index 1dedaf0..5bc462f 100644
--- a/src/ontology/imports/ido_import.owl
+++ b/src/ontology/imports/ido_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/ido_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/ido_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/ido_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
diff --git a/src/ontology/imports/mf_import.owl b/src/ontology/imports/mf_import.owl
index 0bcb720..2b7eca0 100644
--- a/src/ontology/imports/mf_import.owl
+++ b/src/ontology/imports/mf_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/mf_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/mf_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/mf_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/MF/2025-07-08/MF.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
@@ -29,6 +29,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000029>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000030>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000031>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000034>))
+Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000035>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000038>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000141>))
@@ -456,6 +457,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/BFO_0000180> <http://purl.ob
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000008> "temporal region"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000008> <http://purl.obolibrary.org/obo/BFO_0000003>)
 DisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000008> <http://purl.obolibrary.org/obo/BFO_0000015>)
+DisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000008> <http://purl.obolibrary.org/obo/BFO_0000035>)
 
 # Class: <http://purl.obolibrary.org/obo/BFO_0000015> (process)
 
@@ -647,6 +649,14 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.ob
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000034> "function"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000034> <http://purl.obolibrary.org/obo/BFO_0000016>)
 
+# Class: <http://purl.obolibrary.org/obo/BFO_0000035> (process boundary)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/BFO_0000179> <http://purl.obolibrary.org/obo/BFO_0000035> "p-boundary")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/BFO_0000180> <http://purl.obolibrary.org/obo/BFO_0000035> "ProcessBoundary")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000035> "the boundary between the 2nd and 3rd year of your life."@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000035> "process boundary"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000035> <http://purl.obolibrary.org/obo/BFO_0000003>)
+
 # Class: <http://purl.obolibrary.org/obo/BFO_0000038> (one-dimensional temporal region)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/BFO_0000179> <http://purl.obolibrary.org/obo/BFO_0000038> "1d-t-region")
diff --git a/src/ontology/imports/ogms_import.owl b/src/ontology/imports/ogms_import.owl
index d09fd52..6eb1c4d 100644
--- a/src/ontology/imports/ogms_import.owl
+++ b/src/ontology/imports/ogms_import.owl
@@ -13,9 +13,9 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/ogms_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/ogms_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/ogms_import.owl>
 Annotation(dc:source <http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(obo:BFO_0000015))
 Declaration(Class(obo:BFO_0000016))
diff --git a/src/ontology/imports/omrse_import.owl b/src/ontology/imports/omrse_import.owl
index 24c6258..5627f57 100644
--- a/src/ontology/imports/omrse_import.owl
+++ b/src/ontology/imports/omrse_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/omrse_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/omrse_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/omrse_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/omrse/releases/2026-03-05/omrse.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/APOLLO_SV_00000032>))
 Declaration(Class(<http://purl.obolibrary.org/obo/APOLLO_SV_00000480>))
diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
index 1806e36..d172b70 100644
--- a/src/ontology/imports/ro_import.owl
+++ b/src/ontology/imports/ro_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/ro_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/ro_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/ro_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2025-12-17/ro.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
@@ -447,7 +447,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://www.gen
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> "has broad synonym"@en)
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> "has_broad_synonym")
 
-# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (has cross-reference)
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (database_cross_reference)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.")
diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl
index 0e4ff9d..54790e7 100644
--- a/src/ontology/imports/uberon_import.owl
+++ b/src/ontology/imports/uberon_import.owl
@@ -30,9 +30,9 @@ Prefix(ncbitaxon:=<http://purl.obolibrary.org/obo/ncbitaxon#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/uberon_import.owl>
-<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-06/imports/uberon_import.owl>
+<http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/imports/uberon_import.owl>
 Annotation(dc:source <http://purl.obolibrary.org/obo/uberon/releases/2025-12-04/uberon.owl>)
-Annotation(owl:versionInfo "2026-03-06")
+Annotation(owl:versionInfo "2026-03-13")
 
 Declaration(Class(obo:BFO_0000040))
 Declaration(Class(obo:UBERON_0000061))