Merge pull request #205 from Radiobiology-Informatics-Consortium/berr…

…ios020624 Berrios020624
Radiobiology-Informatics-Consortium · Feb 15, 2024 · c157318 · c157318
2 parents becc1cd + d8e26eb
commit c157318
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Showing 21 changed files with 343,253 additions and 151,032 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -338,7 +338,7 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 # Mirroring upstream ontologies
 # ----------------------------------------
 
-IMP=false # Global parameter to bypass import generation
+IMP=false# Global parameter to bypass import generation
 MIR=false # Global parameter to bypass mirror generation
 IMP_LARGE=false # Global parameter to bypass handling of large imports
 
@@ -362,7 +362,7 @@ mirror-bfo: | $(TMPDIR)
 .PHONY: mirror-chebi
 .PRECIOUS: $(MIRRORDIR)/chebi.owl
 mirror-chebi: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/chebi.owl --create-dirs -o $(MIRRORDIR)/chebi.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/chebi.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L --connect-timeout 500.0 --max-time 36000 $(URIBASE)/chebi.owl --create-dirs -o $(MIRRORDIR)/chebi.owl && $(ROBOT) convert -i $(MIRRORDIR)/chebi.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: pato

diff --git a/src/ontology/components/all_templates.owl b/src/ontology/components/all_templates.owl
diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl
@@ -7,12 +7,13 @@
      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:foaf="http://xmlns.com/foaf/0.1/"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:terms="http://purl.org/dc/terms/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/rbo/imports/bfo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rbo/releases/2022-10-05/imports/bfo_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rbo/releases/2024-02-06/imports/bfo_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-05</owl:versionInfo>
+        <owl:versionInfo>2024-02-06</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -124,12 +125,36 @@
 
 
 
+    <!-- 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/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"/>
 
 
 
+    <!-- http://xmlns.com/foaf/0.1/homepage -->
+
+    <owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
+
+
+
+    <!-- http://xmlns.com/foaf/0.1/mbox -->
+
+    <owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/mbox"/>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -735,5 +760,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl
diff --git a/src/ontology/imports/chmo_import.owl b/src/ontology/imports/chmo_import.owl
@@ -9,11 +9,12 @@
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:chmo="http://purl.obolibrary.org/obo/chmo#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/rbo/imports/chmo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rbo/releases/2022-10-05/imports/chmo_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rbo/releases/2024-02-06/imports/chmo_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/chmo/releases/2022-04-19/chmo.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-05</owl:versionInfo>
+        <owl:versionInfo>2024-02-06</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -109,6 +110,30 @@
 
 
 
+    <!-- http://purl.org/dc/elements/1.1/description -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
+
+
+
+    <!-- http://purl.org/dc/elements/1.1/source -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source"/>
+
+
+
+    <!-- http://purl.org/dc/elements/1.1/title -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>
+
+
+
+    <!-- http://purl.org/dc/terms/license -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
+
+
+
     <!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by"/>
@@ -143,12 +168,24 @@
 
 
 
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion"/>
+
+
+
     <!-- http://www.geneontology.org/formats/oboInOwl#id -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
 
 
 
+    <!-- http://www.geneontology.org/formats/oboInOwl#saved-by -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#saved-by"/>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -324,7 +361,7 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CHMO_0000993"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>An independent material continuant that is self-connected and retains its identity over time.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://orcid.org/0000-0001-5985-7429</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>https://orcid.org/0000-0001-5985-7429</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -341,7 +378,7 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CHMO_0002793"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>A piece of apparatus that is used to measure a physical quantity.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://orcid.org/0000-0001-5985-7429</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>https://orcid.org/0000-0001-5985-7429</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -364,7 +401,7 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CHMO_0002796"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>Measurement of the dose of a substance taken up by an object.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://doi.org/10.1039/9781847559753-00013</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>https://doi.org/10.1039/9781847559753-00013</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -381,7 +418,7 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CHMO_0002797"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>A sensor that is used to measure the dose of a substance taken by up an object.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://doi.org/10.1039/9781847559753-00013</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>https://doi.org/10.1039/9781847559753-00013</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -442,7 +479,7 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obi:pppb</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>obi:pppb</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -479,11 +516,11 @@
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/OBI_0001138"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>A device that is used to generate X-rays.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obi:es</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>obi:es</oboInOwl:hasDbXref>
     </owl:Axiom>
 </rdf:RDF>
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl
@@ -10,8 +10,8 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:terms="http://purl.org/dc/terms/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/rbo/imports/cob_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rbo/releases/2022-10-05/imports/cob_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-05</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rbo/releases/2024-02-06/imports/cob_import.owl"/>
+        <owl:versionInfo>2024-02-06</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -47,6 +47,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
+
+
+
+    <!-- http://purl.org/dc/elements/1.1/date -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date"/>
+
+
+
     <!-- http://purl.org/dc/elements/1.1/description -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
@@ -183,7 +195,7 @@
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000053">
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#InverseFunctionalProperty"/>
-        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <rdfs:label>has characteristic</rdfs:label>
         <rdfs:seeAlso>https://github.com/oborel/obo-relations/pull/284</rdfs:seeAlso>
     </owl:ObjectProperty>
@@ -286,12 +298,43 @@
     <!-- 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/PATO_0000001"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <rdfs:label xml:lang="en">realizable</rdfs:label>
     </owl:Class>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/BFO_0000020 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
+        <rdfs:subClassOf rdf:nodeID="genid2"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+                <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <rdfs:label xml:lang="en">characteristic</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:Restriction rdf:nodeID="genid2">
+        <owl:onProperty>
+            <rdf:Description>
+                <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+            </rdf:Description>
+        </owl:onProperty>
+        <owl:someValuesFrom rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
+    </owl:Restriction>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+        <owl:annotatedTarget rdf:nodeID="genid2"/>
+        <rdfs:comment>We should name the inverse in COB and avoid the confusing inverse(..) construct</rdfs:comment>
+    </owl:Axiom>
+
+
+
     <!-- http://purl.obolibrary.org/obo/BFO_0000023 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023">
@@ -425,7 +468,7 @@
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
             </owl:Restriction>
         </owl:equivalentClass>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <obo:COB_based_on>http://purl.obolibrary.org/obo/IAO_0000015</obo:COB_based_on>
         <rdfs:comment>Pier &apos;representational entity&apos;</rdfs:comment>
         <rdfs:comment>This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc</rdfs:comment>
@@ -562,47 +605,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/PATO_0000001 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000001">
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty>
-                    <rdf:Description>
-                        <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
-                    </rdf:Description>
-                </owl:onProperty>
-                <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/BFO_0000051"/>
-                <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:label xml:lang="en">characteristic</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/PATO_0000001"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
-        <owl:annotatedTarget>
-            <owl:Restriction>
-                <owl:onProperty>
-                    <rdf:Description>
-                        <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
-                    </rdf:Description>
-                </owl:onProperty>
-                <owl:someValuesFrom rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
-            </owl:Restriction>
-        </owl:annotatedTarget>
-        <rdfs:comment>We should name the inverse in COB and avoid the confusing inverse(..) construct</rdfs:comment>
-    </owl:Axiom>
-
-
-
     <!-- http://purl.obolibrary.org/obo/SEPIO_0000048 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000048">
@@ -614,5 +616,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->