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Berrios020624 #205

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merged 8 commits into from
Feb 15, 2024
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Berrios020624 #205

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168cfd0
Debugging unsatisfiability
DanBerrios Feb 6, 2024
1a93519
Switch ENVO import to envo-basic subset to eval
DanBerrios Feb 7, 2024
2488b0e
Continue debug
DanBerrios Feb 7, 2024
1eb0564
Further debugging
DanBerrios Feb 8, 2024
2bfd8bd
Remove debug code and output
DanBerrios Feb 8, 2024
41f629d
Fix typo in Makefile
DanBerrios Feb 8, 2024
cbe6111
Turn off imports
DanBerrios Feb 15, 2024
d8e26eb
turn off iimports in makefile
reality Feb 15, 2024
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4 changes: 2 additions & 2 deletions src/ontology/Makefile
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Expand Up @@ -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

Expand All @@ -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 [email protected] && mv [email protected] $(TMPDIR)/[email protected]; 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 [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: pato
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2,466 changes: 1,233 additions & 1,233 deletions src/ontology/components/all_templates.owl
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31 changes: 28 additions & 3 deletions src/ontology/imports/bfo_import.owl
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Expand Up @@ -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>


Expand Down Expand Up @@ -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"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand Down Expand Up @@ -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 -->

6,962 changes: 3,932 additions & 3,030 deletions src/ontology/imports/chebi_import.owl
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55 changes: 46 additions & 9 deletions src/ontology/imports/chmo_import.owl
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Expand Up @@ -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>


Expand Down Expand Up @@ -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"/>
Expand Down Expand Up @@ -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"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand Down Expand Up @@ -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>


Expand All @@ -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>


Expand All @@ -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>


Expand All @@ -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>


Expand Down Expand Up @@ -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>


Expand Down Expand Up @@ -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 -->

96 changes: 49 additions & 47 deletions src/ontology/imports/cob_import.owl
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Expand Up @@ -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>


Expand Down Expand Up @@ -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"/>
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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">
Expand All @@ -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 -->

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