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4 restructure calibration compound #45

Merged
merged 22 commits into from
Sep 19, 2024
Merged

4 restructure calibration compound #45

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b0cd125
fix the hierarchy of the calibration compound branch
NRayya Aug 22, 2024
49bf465
enhance definitions of the entities within the calibration compound b…
NRayya Aug 22, 2024
1f84765
enhance the labels of the entities within calibration compound branch
NRayya Aug 22, 2024
baf5eab
create the corresponding roles of the calibration compound branch
NRayya Aug 22, 2024
28a058d
assign the roles for the calibration compound branch
NRayya Aug 22, 2024
201a8aa
Add nucleus-based grouping classes from 2001 IUPAC recommendations
NRayya Aug 22, 2024
1d2c0f8
Add additional definition source to reference compounds
NRayya Aug 26, 2024
2d5c247
Add nucleus-based grouping classes from 2008 IUPAC recommendations.
NRayya Aug 26, 2024
1570278
adhere definitions to agreed upon conventions
NRayya Aug 26, 2024
42310dc
deprecate children of concentration calibration compound
NRayya Aug 26, 2024
7234e8e
minor fixes
NRayya Aug 26, 2024
be3c4b6
Import IAO:0000140 setting datum
NRayya Sep 6, 2024
351fe25
Merge branch 'main' of https://github.com/nmrML/nmrCV into 4-restruct…
NRayya Sep 10, 2024
2016efc
Merge branch '43-import-setting-datum' of https://github.com/nmrML/nm…
NRayya Sep 10, 2024
4494a2c
Save as in Protégé to let OWL API autosort fix order
StroemPhi Sep 19, 2024
91fd23c
Enhance wording
NRayya Sep 19, 2024
6d4ca51
Enhance wording
NRayya Sep 19, 2024
92365cf
Enhance wording
NRayya Sep 19, 2024
544d238
Adding NMR prefix to make the context of this role more clear.
NRayya Sep 19, 2024
93cddea
Adding NMR prefix to make the context of this role more clear
NRayya Sep 19, 2024
af582c3
Adding NMR prefix to make the context of this role more clear
NRayya Sep 19, 2024
6807abc
Add an annotation to the subclassOf axiom
NRayya Sep 19, 2024
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33 changes: 31 additions & 2 deletions src/ontology/imports/iao_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://nmrML.org/nmrCV/imports/iao_import.owl>
<http://nmrML.org/nmrCV/releases/2024-08-21/imports/iao_import.owl>
<http://nmrML.org/nmrCV/releases/2024-09-06/imports/iao_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl>)
Annotation(owl:versionInfo "2024-08-21")
Annotation(owl:versionInfo "2024-09-06")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
Expand All @@ -26,11 +26,14 @@ Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000033>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000078>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000102>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000104>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000140>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000225>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000409>))
Declaration(Class(<http://www.geneontology.org/formats/oboInOwl#ObsoleteClass>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IAO_0000136>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/OBI_0000299>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000002>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000103>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000120>))
Expand Down Expand Up @@ -59,6 +62,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000117>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000118>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000231>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000233>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
Expand Down Expand Up @@ -139,6 +143,17 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.ob
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/IAO_0000231> "PERSON:Melanie Courtot"@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000231> "has obsolescence reason"@en)

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000233> (term tracker item)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000233> "term tracker item"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/IAO_0000233> "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/IAO_0000233> <http://purl.obolibrary.org/obo/IAO_0000125>)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000233> "An IRI or similar locator for a request or discussion of an ontology term."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/IAO_0000233> "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0000233> "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IAO_0000233> "The 'tracker item' can associate a tracker with a specific ontology term."@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000233> "term tracker item"@en)

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0100001> (term replaced by)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0100001> "term replaced by"@en)
Expand Down Expand Up @@ -306,6 +321,20 @@ SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000104> <http://purl.obolibrary.
SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000104> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/IAO_0000005>))
SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000104> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/IAO_0000007>))

# Class: <http://purl.obolibrary.org/obo/IAO_0000140> (setting datum)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/IAO_0000140> <http://purl.obolibrary.org/obo/IAO_0000123>)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000140> "A settings datum is a datum that denotes some configuration of an instrument."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/IAO_0000140> "2/3/2009 Feedback from OBI

This should be a \"setting specification\". There is a question of whether it is information about a realizable or not.

Pro other specification are about realizables.
Cons sometimes specifies a quality which is not a realizable."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/IAO_0000140> "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum."@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000140> "setting datum"@en)
SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000140> <http://purl.obolibrary.org/obo/IAO_0000027>)

# Class: <http://purl.obolibrary.org/obo/IAO_0000225> (obsolescence reason specification)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000225> "obsolescence reason specification"@en)
Expand Down
3 changes: 2 additions & 1 deletion src/ontology/imports/iao_terms.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
IAO:0000033 # 'directive information entity'
IAO:0000005 # 'objective specification'
IAO:0000104 # 'plan specification'
IAO:0000104 # 'plan specification'
IAO:0000140 # 'setting datum'
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