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Minor changes after merge conflicts #734

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merged 5 commits into from
Jul 17, 2023
Merged

Minor changes after merge conflicts #734

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058069f
update term-editor-uri-violation query to accept only https url
anitacaron Jul 7, 2023
733ed9a
remove caro import from catalog
anitacaron Jul 7, 2023
7fe93c3
update orcid to use https
anitacaron Jul 7, 2023
291dde2
remove duplicated obi import and reorder edit file
anitacaron Jul 7, 2023
b1580ce
Merge branch 'master' into anitacaron/issue733
Jul 12, 2023
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2 changes: 0 additions & 2 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -10,7 +10,6 @@
<uri name="http://purl.obolibrary.org/obo/ro/imports/envo_import.owl" uri="imports/envo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/orcidio_import.owl" uri="imports/orcidio_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/go_import.owl" uri="imports/go_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/imports/caro_import.owl" uri="imports/caro_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/core.owl" uri="components/core.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/el-constraints.owl" uri="components/el-constraints.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/generated-axioms.owl" uri="components/generated-axioms.owl"/>
Expand All @@ -20,5 +19,4 @@
<uri name="http://purl.obolibrary.org/obo/ro/components/bfo-classes-minimal.owl" uri="components/bfo-classes-minimal.owl"/>
<uri name="http://purl.obolibrary.org/obo/ro/components/bfo-axioms.owl" uri="components/bfo-axioms.owl"/>
</group>
>>>>>>> master
</catalog>
34 changes: 16 additions & 18 deletions src/ontology/ro-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,13 +17,13 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)

Ontology(<http://purl.obolibrary.org/obo/ro.owl>
<http://purl.obolibrary.org/obo/ro-edit.owl>
Import(<http://purl.obolibrary.org/obo/ro/components/bfo-axioms.owl>)
Import(<http://purl.obolibrary.org/obo/ro/components/bfo-classes-minimal.owl>)
Import(<http://purl.obolibrary.org/obo/ro/components/core.owl>)
Import(<http://purl.obolibrary.org/obo/ro/components/el-constraints.owl>)
Import(<http://purl.obolibrary.org/obo/ro/components/generated-axioms.owl>)
Import(<http://purl.obolibrary.org/obo/ro/components/rohom.owl>)
Import(<http://purl.obolibrary.org/obo/ro/components/temporal-intervals.owl>)
Import(<http://purl.obolibrary.org/obo/ro/components/bfo-classes-minimal.owl>)
Import(<http://purl.obolibrary.org/obo/ro/components/bfo-axioms.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/cl_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/envo_import.owl>)
Expand All @@ -34,7 +34,6 @@ Import(<http://purl.obolibrary.org/obo/ro/imports/orcidio_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/other_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/pato_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/uberon_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/obi_import.owl>)
Annotation(dc:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en)
Annotation(dc:license <https://creativecommons.org/publicdomain/zero/1.0/>)
Annotation(dc:title "OBO Relations Ontology"@en)
Expand Down Expand Up @@ -703,7 +702,7 @@ Declaration(AnnotationProperty(skos:exactMatch))

AnnotationAssertion(rdfs:label obo:IAO_0000112 "example of usage")

# Annotation Property: obo:IAO_0000426 (obo:IAO_0000426)
# Annotation Property: obo:IAO_0000426 (first order logic expression)

AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000426 "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.")
SubAnnotationPropertyOf(obo:IAO_0000426 obo:RO_0002422)
Expand Down Expand Up @@ -2311,7 +2310,6 @@ AnnotationAssertion(obo:IAO_0000114 obo:RO_0002207 obo:IAO_0000125)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002207 "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002207 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002207 <https://orcid.org/0000-0002-7073-9172>)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002207 "has developmental precursor")
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002207 "FBbt")
AnnotationAssertion(obo:RO_0002575 obo:RO_0002207 obo:RO_0002202)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002207 "has developmental precursor")
Expand Down Expand Up @@ -6478,7 +6476,7 @@ AnnotationAssertion(rdfs:seeAlso obo:RO_0016001 "https://github.com/oborel/obo-r
# Object Property: obo:RO_0016002 (has disease)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0016002 "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.")
AnnotationAssertion(dc:contributor obo:RO_0016002 <http://orcid.org/0000-0002-7463-6306>)
AnnotationAssertion(dc:contributor obo:RO_0016002 <https://orcid.org/0000-0002-7463-6306>)
AnnotationAssertion(dc:date obo:RO_0016002 "2021-11-05T17:30:44Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0016002 "has disease")
AnnotationAssertion(rdfs:seeAlso obo:RO_0016002 "https://github.com/oborel/obo-relations/issues/478")
Expand All @@ -6501,7 +6499,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0017001 <https://orcid.org/0000-0001-
AnnotationAssertion(obo:IAO_0000117 obo:RO_0017001 <https://orcid.org/0000-0003-2620-0345>)
AnnotationAssertion(obo:IAO_0000232 obo:RO_0017001 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0017001 "See github ticket https://github.com/oborel/obo-relations/issues/497")
AnnotationAssertion(oboInOwl:creation_date obo:RO_0017001 "2021-11-08T12:00:00Z")
AnnotationAssertion(oboInOwl:creation_date obo:RO_0017001 "2021-11-08T12:00:00Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:RO_0017001 "utilizes")
AnnotationAssertion(rdfs:label obo:RO_0017001 "device utilizes material"@en)

Expand Down Expand Up @@ -6608,9 +6606,9 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0018033 "A is a deprotonated form of

This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.")
AnnotationAssertion(dc:creator obo:RO_0018033 <https://orcid.org/0000-0003-4423-4370>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018033 "obo:chebi#is_conjugate_base_of")
AnnotationAssertion(rdfs:label obo:RO_0018033 "is deprotonated form of")
AnnotationAssertion(rdfs:seeAlso obo:RO_0018033 <https://github.com/oborel/obo-relations/issues/643>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018033 "obo:chebi#is_conjugate_base_of")
SubObjectPropertyOf(obo:RO_0018033 obo:RO_0018030)
InverseObjectProperties(obo:RO_0018033 obo:RO_0018034)
TransitiveObjectProperty(obo:RO_0018033)
Expand All @@ -6622,9 +6620,9 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0018034 "A is a protonated form of B

This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.")
AnnotationAssertion(dc:creator obo:RO_0018034 <https://orcid.org/0000-0003-4423-4370>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018034 "obo:chebi#is_conjugate_acid_of")
AnnotationAssertion(rdfs:label obo:RO_0018034 "is protonated form of")
AnnotationAssertion(rdfs:seeAlso obo:RO_0018034 <https://github.com/oborel/obo-relations/issues/643>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018034 "obo:chebi#is_conjugate_acid_of")
SubObjectPropertyOf(obo:RO_0018034 obo:RO_0018030)
TransitiveObjectProperty(obo:RO_0018034)

Expand Down Expand Up @@ -6654,10 +6652,10 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0018036 "Two chemicals are tautomers
This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms.")
AnnotationAssertion(dc:creator obo:RO_0018036 <https://orcid.org/0000-0003-4423-4370>)
AnnotationAssertion(dc:date obo:RO_0018036 "2023-03-18T23:49:31Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018036 "obo:chebi#is_tautomer_of")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0018036 "is desmotrope of")
AnnotationAssertion(rdfs:label obo:RO_0018036 "is tautomer of"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0018036 <https://github.com/oborel/obo-relations/issues/697>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018036 "obo:chebi#is_tautomer_of")
SubObjectPropertyOf(obo:RO_0018036 obo:RO_0018030)
SymmetricObjectProperty(obo:RO_0018036)

Expand All @@ -6667,9 +6665,9 @@ AnnotationAssertion(Annotation(rdfs:seeAlso obo:CHEBI_30795) Annotation(rdfs:see
AnnotationAssertion(obo:IAO_0000115 obo:RO_0018037 "Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization.")
AnnotationAssertion(dc:creator obo:RO_0018037 <https://orcid.org/0000-0003-4423-4370>)
AnnotationAssertion(dc:date obo:RO_0018037 "2023-03-18T23:49:31Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018037 "obo:chebi#is_substituent_group_from")
AnnotationAssertion(rdfs:label obo:RO_0018037 "is substitutent group from"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0018037 <https://github.com/oborel/obo-relations/issues/697>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018037 "obo:chebi#is_substituent_group_from")
SubObjectPropertyOf(obo:RO_0018037 obo:RO_0018030)

# Object Property: obo:RO_0018038 (has functional parent)
Expand All @@ -6680,9 +6678,9 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0018038 "Chemical A has functional pa
For example, the relationship between a salt and a freebased compound is a \"has functional parent\" relationship.")
AnnotationAssertion(dc:creator obo:RO_0018038 <https://orcid.org/0000-0003-4423-4370>)
AnnotationAssertion(dc:date obo:RO_0018038 "2023-03-18T23:49:31Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018038 "obo:chebi#has_functional_parent")
AnnotationAssertion(rdfs:label obo:RO_0018038 "has functional parent"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0018038 <https://github.com/oborel/obo-relations/issues/697>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018038 "obo:chebi#has_functional_parent")
SubObjectPropertyOf(obo:RO_0018038 obo:RO_0018030)

# Object Property: obo:RO_0018039 (is enantiomer of)
Expand All @@ -6693,10 +6691,10 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0018039 "Chemicals A and B are enanti
A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers).")
AnnotationAssertion(dc:creator obo:RO_0018039 <https://orcid.org/0000-0003-4423-4370>)
AnnotationAssertion(dc:date obo:RO_0018039 "2023-03-18T23:49:31Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018039 "obo:chebi#is_enantiomer_of")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0018039 "is optical isomer of")
AnnotationAssertion(rdfs:label obo:RO_0018039 "is enantiomer of"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0018039 <https://github.com/oborel/obo-relations/issues/697>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018039 "obo:chebi#is_enantiomer_of")
SubObjectPropertyOf(obo:RO_0018039 obo:RO_0018030)
SymmetricObjectProperty(obo:RO_0018039)

Expand All @@ -6706,9 +6704,9 @@ AnnotationAssertion(Annotation(rdfs:seeAlso obo:CHEBI_39106) Annotation(rdfs:see
AnnotationAssertion(obo:IAO_0000115 obo:RO_0018040 "Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B.")
AnnotationAssertion(dc:creator obo:RO_0018040 <https://orcid.org/0000-0003-4423-4370>)
AnnotationAssertion(dc:date obo:RO_0018040 "2023-03-18T23:49:31Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018040 "obo:chebi#has_parent_hydride")
AnnotationAssertion(rdfs:label obo:RO_0018040 "has parent hydride"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0018040 <https://github.com/oborel/obo-relations/issues/697>)
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018040 "obo:chebi#has_parent_hydride")
SubObjectPropertyOf(obo:RO_0018040 obo:RO_0018030)

# Object Property: obo:RO_0019000 (regulates characteristic)
Expand Down Expand Up @@ -6791,16 +6789,16 @@ DataPropertyRange(obo:RO_0002029 DatatypeRestriction(xsd:short xsd:minInclusive
# Classes
############################

# Class: obo:BFO_0000002 (obo:BFO_0000002)
# Class: obo:BFO_0000002 (continuant)

SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000002))
SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_HOM0000000 obo:BFO_0000002))

# Class: obo:BFO_0000003 (obo:BFO_0000003)
# Class: obo:BFO_0000003 (occurrent)

SubClassOf(obo:BFO_0000003 ObjectAllValuesFrom(obo:RO_HOM0000000 obo:BFO_0000003))

# Class: obo:BFO_0000015 (obo:BFO_0000015)
# Class: obo:BFO_0000015 (process)

SubClassOf(obo:BFO_0000015 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000015))

Expand Down Expand Up @@ -7102,4 +7100,4 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002086 subsets:ro-eco)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002089 subsets:ro-eco)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002093 subsets:ro-eco)
AnnotationAssertion(Annotation(rdfs:comment "This is an experimental annotation") obo:IAO_0000589 rdfs:isDefinedBy "is defined by")
)
)
2 changes: 1 addition & 1 deletion src/sparql/term-editor-uri-violation.sparql
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Expand Up @@ -8,7 +8,7 @@ WHERE {
VALUES ?predicate { dc:contributor dc:creator term_editor: oio:created_by }
?subject ?predicate ?orcid .
FILTER(!regex(str(?orcid), "^https://github.com/orgs/[a-z-_]+/teams/") &&
!regex(str(?orcid), "^(https?://orcid.org/)[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}(?:[0-9]|X)") &&
!regex(str(?orcid), "^(https://orcid.org/)[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}(?:[0-9]|X)") &&
!regex(str(?orcid), "^(https://www.wikidata.org/wiki/Q)[0-9]+") &&
!regex(str(?orcid), "^(https://ror.org/)[0-9a-z]{9}") )
}