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Ready to merge: Domain and range constraints #261

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merged 13 commits into from
Oct 20, 2018
Merged

Ready to merge: Domain and range constraints #261

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dbf86d2
imports
cmungall Sep 25, 2018
e8ad2e9
for-SLME
cmungall Sep 25, 2018
ddbe35e
Separating out chemical relations into separate module
cmungall Sep 25, 2018
5f61d08
domain and range constraints
cmungall Sep 26, 2018
c68f0a1
domain/range
cmungall Sep 26, 2018
e8c15a3
Adding organism from CARO - may change label, see https://github.com/…
cmungall Sep 26, 2018
c677fb5
domain-range constrs
cmungall Sep 26, 2018
98157a6
domain-range constrs
cmungall Sep 26, 2018
a8554e8
Adding SWRL for phosphorylates, see #259
cmungall Sep 26, 2018
ae9eae1
mireot spatial region
cmungall Sep 28, 2018
77d7387
Further constraining located_in, see comments from Alan: https://gith…
cmungall Sep 28, 2018
d852a55
Including additional CARO classes in import, in particular the more g…
cmungall Oct 19, 2018
b986d61
prepared new release
cmungall Oct 20, 2018
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22 changes: 13 additions & 9 deletions src/ontology/Makefile
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@@ -1,6 +1,8 @@
OBO=http://purl.obolibrary.org/obo
SRC=ro-edit.owl
ROBOT=robot

ONTS= ro.obo ro.owl ro.json ro-base.owl ro-base.obo ro-base.json annotations.owl core.owl go-biotic.owl pato_import.owl temporal-intervals.owl bfo-axioms.owl bfo-classes-minimal.owl el-constraints.owl go_mf_import.owl go_cc_import.owl rohom.owl
ONTS= ro.obo ro.owl ro.json ro-base.owl ro-base.obo ro-base.json chemical.owl annotations.owl core.owl go-biotic.owl pato_import.owl temporal-intervals.owl bfo-axioms.owl bfo-classes-minimal.owl el-constraints.owl go_mf_import.owl go_cc_import.owl rohom.owl

# ========================================
# PRODUCTION
Expand Down Expand Up @@ -61,16 +63,18 @@ ro-diff.html: ro-diff.md
# ========================================
# IMPORTS
# ========================================
seed.owl: ro-edit.owl
owltools --use-catalog $< --merge-imports-closure --remove-imports-declarations -o $@
seed.txt: $(SRC)
$(ROBOT) query -f csv -i $< --query sparql/terms.sparql $@

# TODO - have to manually remove OPs for now...
#pato_mirror.owl: ro-edit.owl
# owltools $(OBO)/pato.owl --extract-mingraph --make-subset-by-properties // --remove-dangling-annotations --set-ontology-id $(OBO)/pato.owl -o $@
#pato_import.owl: seed.owl pato_mirror.owl
# owltools --use-catalog $< pato_mirror.owl --add-imports-from-supports --extract-module -c -s $(OBO)/pato.owl --set-ontology-id $(OBO)/ro/$@ -o $@
## owltools --use-catalog --map-ontology-iri $(OBO)/ro/pato_import.owl pato_mirror.owl ro-edit.owl --extract-module -s $(OBO)/pato.owl --set-ontology-id $(OBO)/ro/$@ -o $@
imports/%_terms_combined.txt: seed.txt
cat $< imports/$*_terms.txt | sort | uniq > $@

%_import.owl: mirror/%.owl imports/%_terms.txt
$(ROBOT) extract -i $< -T imports/$*_terms.txt --method BOT -O $(BASE)/$@ -o $@
.PRECIOUS: imports/%_import.owl

mirror/%.owl:
wget --no-check-certificate $(OBO)/$*.owl -O $@

# ========================================
# MIREOT
Expand Down
1 change: 1 addition & 0 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -3,6 +3,7 @@
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ro.owl" uri="ro-edit.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ro/annotations.owl" uri="annotations.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ro/temporal-intervals.owl" uri="temporal-intervals.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ro/chemical.owl" uri="chemical.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ro/core.owl" uri="core.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ro/el-constraints.owl" uri="el-constraints.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ro/rohom.owl" uri="rohom.owl"/>
Expand Down
39 changes: 39 additions & 0 deletions src/ontology/chemical.owl
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@@ -0,0 +1,39 @@
Prefix(:=<http://purl.obolibrary.org/obo/ro.owl/>)
Prefix(dc:=<http://purl.org/dc/elements/1.1/>)
Prefix(obo:=<http://purl.obolibrary.org/obo/>)
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(cito:=<http://purl.org/spar/cito/>)
Prefix(foaf:=<http://xmlns.com/foaf/0.1/>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Prefix(swrl:=<http://www.w3.org/2003/11/swrl#>)
Prefix(swrla:=<http://swrl.stanford.edu/ontologies/3.3/swrla.owl#>)
Prefix(swrlb:=<http://www.w3.org/2003/11/swrlb#>)
Prefix(subsets:=<http://purl.obolibrary.org/obo/ro/subsets#>)
Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)


Ontology(<http://purl.obolibrary.org/obo/ro/chemical.owl>
Annotation(dc:description "RO chemical module."@en)

# Object Property: obo:RO_0002260 (has biological role)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002260 "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)")
AnnotationAssertion(rdfs:label obo:RO_0002260 "has biological role")
SubObjectPropertyOf(obo:RO_0002260 obo:RO_0000087)

# Object Property: obo:RO_0002261 (has application role)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002261 "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)")
AnnotationAssertion(rdfs:label obo:RO_0002261 "has application role")
SubObjectPropertyOf(obo:RO_0002261 obo:RO_0000087)

# Object Property: obo:RO_0002262 (has chemical role)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002262 "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)")
AnnotationAssertion(rdfs:label obo:RO_0002262 "has chemical role")
SubObjectPropertyOf(obo:RO_0002262 obo:RO_0000087)

)
56 changes: 53 additions & 3 deletions src/ontology/other_import.owl
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Expand Up @@ -6,8 +6,12 @@
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro/other_import.owl"/>
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro/other_import.owl">
<rdfs:comment>This should be split into sub-modules</rdfs:comment>
<dc:title>ad-hoc additional imports</dc:title>
</owl:Ontology>



Expand All @@ -28,6 +32,18 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000136 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000136"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412"/>
Expand Down Expand Up @@ -77,6 +93,12 @@



<!-- http://purl.obolibrary.org/obo/BFO_0000016 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016"/>



<!-- http://purl.obolibrary.org/obo/BFO_0000019 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019"/>
Expand Down Expand Up @@ -171,6 +193,15 @@



<!-- http://purl.obolibrary.org/obo/CARO_0001010 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0001010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">organism or virus or viroid</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CARO_0010000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0010000">
Expand Down Expand Up @@ -240,6 +271,16 @@



<!-- http://purl.obolibrary.org/obo/OGMS_0000031 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<obo:IAO_0000115 xml:lang="en">A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.</obo:IAO_0000115>
<rdfs:label>disease</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PATO_0000001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000001">
Expand Down Expand Up @@ -290,6 +331,15 @@



<!-- http://purl.obolibrary.org/obo/UPHENO_0001001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UPHENO_0001001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
<rdfs:label xml:lang="en">phenotype</rdfs:label>
</owl:Class>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand Down Expand Up @@ -326,5 +376,5 @@



<!-- Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->

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