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MSIO-edit.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/MSIO.owl#"
xml:base="http://purl.obolibrary.org/obo/MSIO.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:msio="http://purl.obolibrary.org/obo/MSIO.owl#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:chebi="http://purl.obolibrary.org/obo/chebi/"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/msio.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/msio/2020-02-20/msio.owl"/>
<owl:imports rdf:resource="http://nmrML.org/nmrCV"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_CHMO_import.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_ChEBI_import.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_OBI_import.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_PSIMS_import.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_UO_import.owl"/>
<dc:contributor xml:lang="en">Alejandra Gonzalez-Beltran</dc:contributor>
<dc:contributor xml:lang="en">Andrew Lane</dc:contributor>
<dc:contributor xml:lang="en">Hunter Moseley</dc:contributor>
<dc:contributor xml:lang="en">Marta Cascante</dc:contributor>
<dc:contributor xml:lang="en">Pedro Ramon de Atauri Carulla</dc:contributor>
<dc:contributor xml:lang="en">Silvia Marin</dc:contributor>
<dc:contributor>Teresa Fan</dc:contributor>
<dc:contributor>Vitaly Selivanov</dc:contributor>
<dc:creator>Philippe Rocca-Serra</dc:creator>
<dc:description xml:lang="en">an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.</dc:description>
<dc:format>OWL</dc:format>
<dc:license>http://creativecommons.org/licenses/by/3.0/</dc:license>
<dc:title xml:lang="en">Metabolomics Standards Initiative Ontology (MSIO)</dc:title>
<doap:bug-database>https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues</doap:bug-database>
<doap:homepage>https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO</doap:homepage>
<owl:versionInfo>1.0.1</owl:versionInfo>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000179 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000179"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000180 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000180"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000600 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000600"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000601 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000601"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000602 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000602"/>
<!-- http://purl.obolibrary.org/obo/IAO_0010000 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0010000"/>
<!-- http://purl.org/dc/elements/1.1/contributor -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
<!-- http://purl.org/dc/elements/1.1/identifier -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/identifier"/>
<!-- http://purl.org/dc/elements/1.1/language -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/language"/>
<!-- http://purl.org/dc/elements/1.1/publisher -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/publisher"/>
<!-- http://purl.org/dc/elements/1.1/relation -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/relation"/>
<!-- http://purl.org/dc/elements/1.1/rights -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/rights"/>
<!-- http://purl.org/dc/elements/1.1/type -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/type"/>
<!-- http://usefulinc.com/ns/doap#revision -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#revision"/>
<!-- http://www.geneontology.org/formats/oboInOwl#id -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
<!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand"/>
<!-- http://www.w3.org/2004/02/skos/core#note -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#note"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<rdfs:label>has part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000063 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000063"/>
<!-- http://purl.obolibrary.org/obo/DUO_0000010 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/DUO_0000010">
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An object property linking a consent code to a specific restriction which further constrains it, such as research should be restricted to a specific disease or geographical location.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000010</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is restricted to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000136 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000136">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000112 xml:lang="en">This document is about information artifacts and their representations</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">is_about is a (currently) primitive relation that relates an information artifact to an entity.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some 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.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Smith, Ceusters, Ruttenberg, 2000 years of philosophy</obo:IAO_0000119>
<rdfs:label xml:lang="en">is about</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000219 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000219"/>
<!-- http://purl.obolibrary.org/obo/MSIO_0000179 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/MSIO_0000179">
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a chemical entity is said to be an isotopomer of another one if it has the same number of each isotopic atom but differs in their positions. isotopomer is a contraction of isotopic isomer</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">CH2DCH=0 is isotopomer of CH3CD=0</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">IUPAC compendium of chemical terminology (2nd edition, 1997)</obo:IAO_0000119>
<rdfs:label xml:lang="en">is isotopomer of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/MSIO_0000180 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/MSIO_0000180">
<obo:IAO_0000112 xml:lang="en">CH4 is isotopologue of CH3D which is isotopologue of CH2D2</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a molecular entity which differs only in isotopic composition (i.e the number of isotopic substitution differs but the overall chemical structure is unchanged) is said to be an isotologue</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">IUPAC compendium of chemical terminology (2nd edition, 1997)</obo:IAO_0000119>
<rdfs:label>is isotopologue of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/MSIO_0000183 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/MSIO_0000183">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000115 xml:lang="en">A relation associating a product to its manufacturer.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">manufactured by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000293 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000293">
<rdfs:label xml:lang="en">has_specified_input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000295 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000295">
<rdfs:label xml:lang="en">is_specified_input_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000299 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
<rdfs:label xml:lang="en">has_specified_output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000312 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312"/>
<!-- http://purl.obolibrary.org/obo/RO_0000053 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000053"/>
<!-- http://purl.obolibrary.org/obo/RO_0000057 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000057"/>
<!-- http://purl.obolibrary.org/obo/RO_0000086 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000086"/>
<!-- http://purl.obolibrary.org/obo/RO_0000087 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000087">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<rdfs:label xml:lang="en">has_role</rdfs:label>
</owl:ObjectProperty>
<!-- http://usefulinc.com/ns/doap#file-release -->
<owl:ObjectProperty rdf:about="http://usefulinc.com/ns/doap#file-release">
<rdfs:isDefinedBy rdf:resource="http://usefulinc.com/ns/doap"/>
</owl:ObjectProperty>
<!-- http://usefulinc.com/ns/doap#homepage -->
<owl:ObjectProperty rdf:about="http://usefulinc.com/ns/doap#homepage"/>
<!-- http://usefulinc.com/ns/doap#mailing-list -->
<owl:ObjectProperty rdf:about="http://usefulinc.com/ns/doap#mailing-list">
<rdfs:isDefinedBy rdf:resource="http://usefulinc.com/ns/doap"/>
</owl:ObjectProperty>
<!-- http://usefulinc.com/ns/doap#release -->
<owl:ObjectProperty rdf:about="http://usefulinc.com/ns/doap#release">
<rdfs:isDefinedBy rdf:resource="http://usefulinc.com/ns/doap"/>
</owl:ObjectProperty>
<!-- http://usefulinc.com/ns/doap#repository -->
<owl:ObjectProperty rdf:about="http://usefulinc.com/ns/doap#repository">
<rdfs:isDefinedBy rdf:resource="http://usefulinc.com/ns/doap"/>
</owl:ObjectProperty>
<!-- http://usefulinc.com/ns/doap#wiki -->
<owl:ObjectProperty rdf:about="http://usefulinc.com/ns/doap#wiki">
<rdfs:isDefinedBy rdf:resource="http://usefulinc.com/ns/doap"/>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
<obo:BFO_0000179>entity</obo:BFO_0000179>
<obo:BFO_0000180>Entity</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">Julius Caesar</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">Verdi’s Requiem</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the Second World War</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">your body mass index</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">entity</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
<owl:annotatedTarget xml:lang="en">Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000004"/>
<rdfs:comment>per discussion with Barry Smith</rdfs:comment>
<rdfs:seeAlso rdf:resource="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/001-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<obo:BFO_0000179>continuant</obo:BFO_0000179>
<obo:BFO_0000180>Continuant</obo:BFO_0000180>
<obo:IAO_0000115 xml:lang="en">An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">continuant</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/008-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/011-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
<owl:annotatedTarget xml:lang="en">Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000007"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/008-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/126-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/009-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/011-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/009-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/126-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:BFO_0000179>ic</obo:BFO_0000179>
<obo:BFO_0000180>IndependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">a chair</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a heart</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a leg</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a molecule</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a spatial region</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an atom</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an orchestra.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an organism</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the bottom right portion of a human torso</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of your mouth</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">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])</obo:IAO_0000115>
<obo:IAO_0000601 xml:lang="en">For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] </obo:IAO_0000602>
<obo:IAO_0000602>(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">independent continuant</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">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])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/017-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/134-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/018-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/134-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/018-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/017-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:BFO_0000179>disposition</obo:BFO_0000179>
<obo:BFO_0000180>Disposition</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">an atom of element X has the disposition to decay to an atom of element Y</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">certain people have a predisposition to colon cancer</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">children are innately disposed to categorize objects in certain ways.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the cell wall is disposed to filter chemicals in endocytosis and exocytosis</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">disposition</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/062-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/063-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/063-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/062-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:BFO_0000179>realizable</obo:BFO_0000179>
<obo:BFO_0000180>RealizableEntity</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">the disposition of this piece of metal to conduct electricity.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the disposition of your blood to coagulate</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of your reproductive organs</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of being a doctor</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of this boundary to delineate where Utah and Colorado meet</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
<obo:IAO_0000600 xml:lang="en">To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])</obo:IAO_0000601>
<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 entity</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/058-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/060-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(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] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/060-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(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] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/058-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:BFO_0000179>sdc</obo:BFO_0000179>
<obo:BFO_0000180>SpecificallyDependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">of one-sided specifically dependent continuants: the mass of this tomato</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the disposition of this fish to decay</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of this heart: to pump blood</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mutual dependence of proton donors and acceptors in chemical reactions [79</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the pink color of a medium rare piece of grilled filet mignon at its center</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of being a doctor</obo:IAO_0000112>
<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 &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])</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">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])</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">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.</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:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
</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 &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])</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"/>
<owl:annotatedTarget xml:lang="en">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])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/050-003"/>
</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_0000116"/>
<owl:annotatedTarget xml:lang="en">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.</owl:annotatedTarget>
<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"/>
<owl:annotatedTarget>(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] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/050-003"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000029">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<obo:BFO_0000179>site</obo:BFO_0000179>
<obo:BFO_0000180>Site</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">Manhattan Canyon)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a hole in the interior of a portion of cheese</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a rabbit hole</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an air traffic control region defined in the airspace above an airport</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the Grand Canyon</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the Piazza San Marco</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the cockpit of an aircraft</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the hold of a ship</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of a kangaroo pouch</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of the trunk of your car</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of your bedroom</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of your office</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of your refrigerator</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the lumen of your gut</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">your left nostril (a fiat part – the opening – of your left nasal cavity)</obo:IAO_0000112>
<obo:IAO_0000600 xml:lang="en">b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">site</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000029"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/034-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000029"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/034-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:BFO_0000179>gdc</obo:BFO_0000179>
<obo:BFO_0000180>GenericallyDependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the pdf file on your laptop, the pdf file that is a copy thereof on my laptop</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">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])</obo:IAO_0000115>
<obo:IAO_0000602>(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">generically dependent continuant</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">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])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/074-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/074-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000141 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:BFO_0000179>immaterial</obo:BFO_0000179>
<obo:BFO_0000180>ImmaterialEntity</obo:BFO_0000180>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10</obo:IAO_0000116>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">immaterial entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_18059 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_18059"/>
<!-- http://purl.obolibrary.org/obo/CHEBI_23367 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_23367"/>
<!-- http://purl.obolibrary.org/obo/CHEBI_24431 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_24431">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_25212 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_25212"/>
<!-- http://purl.obolibrary.org/obo/CHEBI_33839 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33839"/>
<!-- http://purl.obolibrary.org/obo/CHEBI_85060 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_85060">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MSIO_0000115"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MSIO_0000117"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MSIO_0000003"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000010"/>
<!-- http://purl.obolibrary.org/obo/DOID_4 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_4">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. [url:http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf ]</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:4</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/DUO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000001</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">consent code</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/DUO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000001"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000002</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">consent code primary category</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/DUO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000001"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000003</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">consent code secondary category</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/DUO_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000002"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This consent code primary category indicates there is no restriction on use.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000004</oboInOwl:id>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">no restriction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/DUO_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000005">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000002"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This primary category consent code indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000005</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">general research use and clinical care</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/DUO_0000006 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000006">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000002"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000006</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">health/medical/biomedical research and clinical care</rdfs:label>
</owl:Class>