Merge pull request #213 from ufbmi/issue211socialcategories

Closes issue #205, issue #210, issue #211, and issue #212: Added 'U.S…
mcwdsi · Sep 18, 2023 · 20ae337 · 20ae337
2 parents d6fff9e + 85cd77d
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -30,6 +30,7 @@ These are the current imports in OMRSE
 | pno | http://purl.obolibrary.org/obo/iao/pno.owl | mirror |
 | d-acts | http://purl.obolibrary.org/obo/iao/d-acts.owl | mirror |
 | geo | http://purl.obolibrary.org/obo/geo.owl | None |
+| mf | http://purl.obolibrary.org/obo/mf.owl | None |
 
 ## 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:

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for omrse
 # Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.4.1
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use omrse.Makefile instead
 
@@ -49,7 +49,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.4
+ODK_VERSION_MAKEFILE =      v1.4.1
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -114,7 +114,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro ogms obi apollo_sv obib go oae pco bfo oostt omo pno d-acts geo
+IMPORTS =  ro ogms obi apollo_sv obib go oae pco bfo oostt omo pno d-acts geo mf
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -539,6 +539,15 @@ mirror-geo: | $(TMPDIR)
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
+## ONTOLOGY: mf
+.PHONY: mirror-mf
+.PRECIOUS: $(MIRRORDIR)/mf.owl
+mirror-mf: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/mf.owl --create-dirs -o $(MIRRORDIR)/mf.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/mf.owl -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -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

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/omrse/releases/2023-09-08/imports/mf_import.owl" uri="imports/mf_import.owl"/>
     <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/omrse/external_import.owl" uri="imports/external_import.owl"/>
     <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
         <uri name="http://purl.obolibrary.org/obo/omrse/imports/ro_import.owl" uri="imports/ro_import.owl"/>
@@ -31,6 +32,8 @@
         <uri name="http://purl.obolibrary.org/obo/omrse/imports/d-acts_import.owl" uri="imports/d-acts_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/omrse/imports/geo_import.owl" uri="imports/geo_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/omrse/imports/geo_import.obo" uri="imports/geo_import.obo"/>
+        <uri name="http://purl.obolibrary.org/obo/omrse/imports/mf_import.owl" uri="imports/mf_import.owl"/>
+        <uri name="http://purl.obolibrary.org/obo/omrse/imports/mf_import.obo" uri="imports/mf_import.obo"/>
         <uri name="http://purl.obolibrary.org/obo/omrse/components/pno.owl" uri="components/pno.owl"/>
         <uri name="http://purl.obolibrary.org/obo/omrse/components/d-acts.owl" uri="components/d-acts.owl"/>
         <uri name="http://purl.obolibrary.org/obo/omrse/components/import_terms.owl" uri="components/import_terms.owl"/>

diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl
@@ -154,6 +154,12 @@
 
 
 
+    <!-- http://purl.org/dc/elements/1.1/source -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source"/>
+
+
+
     <!-- http://purl.org/dc/terms/license -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
@@ -1112,5 +1118,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/imports/d-acts_import.owl b/src/ontology/imports/d-acts_import.owl
@@ -18,7 +18,7 @@
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/omrse/imports/d-acts_import.owl">
         <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/omrse/releases/2023-05-02/imports/d-acts_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/iao/d-acts/release/2022-07-05/d-acts.owl"/>
-        <owl:versionInfo>2023-05-02</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2023-05-02</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -2597,12 +2597,6 @@ It is important to note that this going out of existence of s is complete and un
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
         <rdfs:label xml:lang="en">spatiotemporal region</rdfs:label>
     </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
-        <owl:annotatedTarget>(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/107-002"/>
-    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
@@ -2657,6 +2651,12 @@ It is important to note that this going out of existence of s is complete and un
         <owl:annotatedTarget xml:lang="en">Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])</owl:annotatedTarget>
         <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/107-002"/>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+        <owl:annotatedTarget>(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] </owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/107-002"/>
+    </owl:Axiom>
 
 
 
@@ -9463,5 +9463,5 @@ Amanda Hicks</obo:IAO_0000117>
 
 
 
-<!-- Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/imports/external_import.owl b/src/ontology/imports/external_import.owl
@@ -22,6 +22,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0020023>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0020024>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0021003>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0021009>))
+Declaration(Class(<http://purl.obolibrary.org/obo/MF_0000030>))
+Declaration(Class(<http://purl.obolibrary.org/obo/MF_0000031>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OAE_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OAE_0000067>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OAE_0002807>))

diff --git a/src/ontology/imports/mf_import.owl b/src/ontology/imports/mf_import.owl
@@ -0,0 +1,44 @@
+Prefix(:=<http://purl.obolibrary.org/obo/omrse/imports/mf_import.owl#>)
+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(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/omrse/imports/mf_import.owl>
+<http://purl.obolibrary.org/obo/omrse/releases/2023-09-08/imports/mf_import.owl>
+Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/MF/2022-07-19/MF.owl>)
+Annotation(owl:versionInfo "2023-09-08")
+
+Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000020>))
+Declaration(Class(<http://purl.obolibrary.org/obo/MF_0000030>))
+Declaration(Class(<http://purl.obolibrary.org/obo/MF_0000031>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/license>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/title>))
+
+
+############################
+#   Classes
+############################
+
+# Class: <http://purl.obolibrary.org/obo/MF_0000030> (representation)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MF_0000030> "A dependent continuant which is about a portion of reality.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/MF_0000030> "http://www.jbiomedsem.com/content/1/1/10")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MF_0000030> "representation")
+SubClassOf(<http://purl.obolibrary.org/obo/MF_0000030> <http://purl.obolibrary.org/obo/BFO_0000020>)
+
+# Class: <http://purl.obolibrary.org/obo/MF_0000031> (cognitive representation)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MF_0000031> "A representation which specifically depends on an anatomical structure in the cognitive system of an organism.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/MF_0000031> "http://www.jbiomedsem.com/content/1/1/10")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MF_0000031> "cognitive representation")
+SubClassOf(<http://purl.obolibrary.org/obo/MF_0000031> <http://purl.obolibrary.org/obo/MF_0000030>)
+
+
+)
diff --git a/src/ontology/imports/mf_terms.txt b/src/ontology/imports/mf_terms.txt
@@ -0,0 +1,2 @@
+
+
diff --git a/src/ontology/imports/obib_import.owl b/src/ontology/imports/obib_import.owl
@@ -76,6 +76,12 @@
 
 
 
+    <!-- http://purl.org/dc/elements/1.1/source -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source"/>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -246,7 +252,6 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
     <!-- 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_0000020"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
         <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>
@@ -500,5 +505,5 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/imports/ogms_import.owl b/src/ontology/imports/ogms_import.owl
@@ -75,6 +75,12 @@
 
 
 
+    <!-- http://purl.org/dc/elements/1.1/source -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source"/>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -105,7 +111,6 @@
     <!-- 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_0000020"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
         <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>
@@ -376,5 +381,5 @@ edited date: 30 SEPT 2015</obo:IAO_0000232>
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/imports/pno_import.owl b/src/ontology/imports/pno_import.owl
@@ -2505,24 +2505,6 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
         <rdfs:label xml:lang="en">spatiotemporal region</rdfs:label>
     </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
-        <owl:annotatedTarget xml:lang="en">Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/099-001"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
-        <owl:annotatedTarget xml:lang="en">Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/098-001"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
-        <owl:annotatedTarget xml:lang="en">Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/107-002"/>
-    </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
@@ -2565,6 +2547,24 @@ Werner suggests a solution based on &quot;Magnitudes&quot; a proposal for which
         <owl:annotatedTarget xml:lang="en">All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])</owl:annotatedTarget>
         <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/096-001"/>
     </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+        <owl:annotatedTarget xml:lang="en">Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])</owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/099-001"/>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+        <owl:annotatedTarget xml:lang="en">Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])</owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/098-001"/>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+        <owl:annotatedTarget xml:lang="en">Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])</owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/107-002"/>
+    </owl:Axiom>
 
 
 
@@ -8557,5 +8557,5 @@ This issue is outside the scope of OBI.</obo:IAO_0000116>
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
@@ -4452,5 +4452,5 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
Original file line number	Diff line number	Diff line change
Expand Up		@@ -4452,5 +4452,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase



		<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
		<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->