Merge pull request #265 from ApolloDev/issue258

removed obsolated UBERON class life-death temporal boundary. To do so…

Double checked build on second machine.

Author: hoganwr

docs/odk-workflows/RepositoryFileStructure.md

@@ -25,6 +25,7 @@ These are the current imports in APOLLO_SV
 | omrse | http://purl.obolibrary.org/obo/omrse.owl | slme |
 | dron | http://purl.obolibrary.org/obo/dron.owl | filter |
 | ogms | http://purl.obolibrary.org/obo/ogms.owl | filter |
+| uberon | http://purl.obolibrary.org/obo/uberon.owl | filter |
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:
 

src/ontology/Makefile

@@ -16,7 +16,7 @@
 # 3. [Update repo to latest ODK](update_repo)
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                f10687d13b9fb4d82c6a832e60b296d76dadc31432fe22bb1f06ab3cc66d4a02
+CONFIG_HASH=                0625a31aff99dcab0d48bca6e3dddd2614c7f65055668a9ae139332d9e4f5f5f
 
 
 # ----------------------------------------
@@ -193,7 +193,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro geo ido mf go iao omrse dron ogms
+IMPORTS =  ro geo ido mf go iao omrse dron ogms uberon
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -647,6 +647,14 @@ mirror-ogms: | $(TMPDIR)
 	$(ROBOT) remove -i $(TMPDIR)/ogms-download.owl --base-iri http://purl.obolibrary.org/obo/OGMS_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
 
 
+## ONTOLOGY: uberon
+.PHONY: mirror-uberon
+.PRECIOUS: $(MIRRORDIR)/uberon.owl
+mirror-uberon: | $(TMPDIR)
+	curl -L $(OBOBASE)/uberon.owl --create-dirs -o $(TMPDIR)/uberon-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) remove -i $(TMPDIR)/uberon-download.owl --base-iri http://purl.obolibrary.org/obo/UBERON_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi

src/ontology/apollo-sv.owl

@@ -50,6 +50,11 @@ import_group:
       make_base: true
       base_iris:
         - http://purl.obolibrary.org/obo/OGMS_
+    - id: uberon
+      module_type: filter
+      make_base: true
+      base_iris:
+        - http://purl.obolibrary.org/obo/UBERON_
 use_custom_import_module: TRUE
 robot_java_args: '-Xmx16G'
 custom_makefile_header: |

src/ontology/apollo_sv-edit.owl

@@ -10,6 +10,7 @@
     <uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/omrse_import.owl" uri="imports/omrse_import.owl" />
     <uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/dron_import.owl" uri="imports/dron_import.owl" />
     <uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/ogms_import.owl" uri="imports/ogms_import.owl" />
+    <uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/uberon_import.owl" uri="imports/uberon_import.owl" />
   </group>
   <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public">
     <uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/ro_import.obo" uri="imports/ro_import.obo" />

src/ontology/apollo_sv-odk.yaml

@@ -96,7 +96,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000045>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000063>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000087>))
 Declaration(Class(<http://purl.obolibrary.org/obo/TRANS_0000000>))
-Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0035944>))
 Declaration(Class(<http://www.geneontology.org/formats/oboInOwl#ObsoleteClass>))
 Declaration(Class(<http://www.geneontology.org/formats/oboInOwl#Subset>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
@@ -1635,13 +1634,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000412> <http://purl.ob
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/TRANS_0000000> "transmission process")
 SubClassOf(<http://purl.obolibrary.org/obo/TRANS_0000000> <http://purl.obolibrary.org/obo/BFO_0000015>)
 
-# Class: <http://purl.obolibrary.org/obo/UBERON_0035944> (life-death temporal boundary)
-
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0035944> "A life cycle temporal boundary that marks the end of the life cycle of the organism.")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000412> <http://purl.obolibrary.org/obo/UBERON_0035944> <http://purl.obolibrary.org/obo/uberon.owl>)
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0035944> "life-death temporal boundary")
-SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0035944> <http://purl.obolibrary.org/obo/BFO_0000015>)
-
 # Class: <http://www.geneontology.org/formats/oboInOwl#ObsoleteClass> (Obsolete Class)
 
 AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#ObsoleteClass> "Obsolete Class")

src/ontology/catalog-v001.xml

@@ -64,7 +64,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9443>))
 Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9606>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000245>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0200000>))
-Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000045>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000096>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000097>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000100>))
@@ -2555,15 +2554,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.ob
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0200000> "data transformation"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0200000> <http://purl.obolibrary.org/obo/COB_0000035>)
 
-# Class: <http://purl.obolibrary.org/obo/OGMS_0000045> (disorder)
-
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OGMS_0000045> "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease."@en)
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OGMS_0000045> "Albert Goldfain")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/OGMS_0000045> "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/OGMS_0000045> "creation date: 2009-06-23T11:39:44Z")
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OGMS_0000045> "disorder")
-SubClassOf(<http://purl.obolibrary.org/obo/OGMS_0000045> <http://purl.obolibrary.org/obo/BFO_0000040>)
-
 # Class: <http://purl.obolibrary.org/obo/OGMS_0000096> (health care process)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OGMS_0000096> "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"@en)

src/ontology/imports/ido_import.owl

@@ -36,7 +36,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000061>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000465>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001062>))
-Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0010000>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000054>))
@@ -211,9 +210,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#commo
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#human_subset>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#mouse_subset>))
-Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#uberon_slim>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#upper_level>))
-Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#vertebrate_core>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
@@ -450,7 +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> (database_cross_reference)
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (has 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.")
@@ -2249,19 +2246,6 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001062> "
 EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0001062> ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0020105>))
 SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001062> <http://purl.obolibrary.org/obo/BFO_0000004>)
 
-# Class: <http://purl.obolibrary.org/obo/UBERON_0010000> (multicellular anatomical structure)
-
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "CARO:0010000") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0010000> "An anatomical structure that has more than one cell as a part.")
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0010000> "CARO:0010000")
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBbt:00100313") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_0010000> "multicellular structure")
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0010000> "UBERON:0010000")
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/uberon/core#common_anatomy>)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/uberon/core#human_subset>)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/uberon/core#mouse_subset>)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/uberon/core#upper_level>)
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010000> "multicellular anatomical structure")
-SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/UBERON_0000061>)
-
 
 ############################
 #   Named Individuals