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Obsoleted terms + corrected definitions
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@ar-ibrahim
ar-ibrahim committed Sep 14, 2023
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Showing 3 changed files with 35 additions and 17 deletions.
46 changes: 29 additions & 17 deletions src/ontology/efo-edit.owl
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Expand Up @@ -28915,7 +28915,7 @@ AnnotationAssertion(rdfs:label obo:RO_0001025 "located_in")

AnnotationAssertion(rdfs:label obo:RO_0002104 "has_plasma_membrane_part")

# Object Property: obo:RO_0002160 (only in taxon)
# Object Property: obo:RO_0002160 (only_in_taxon)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20973947") obo:IAO_0000115 obo:RO_0002160 "S only_in_taxon T iff: S SubClassOf in_taxon only T")
AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0002160 "RO:0002160")
Expand Down Expand Up @@ -153152,11 +153152,15 @@ AnnotationAssertion(obo:IAO_0000117 efo:EFO_0008169 "Dani Welter")
AnnotationAssertion(rdfs:label efo:EFO_0008169 "interleukin 1 receptor-like 2 measurement")
SubClassOf(efo:EFO_0008169 efo:EFO_0007937)

# Class: efo:EFO_0008170 (interleukin 12 receptor subunit beta-1 measurement)
# Class: efo:EFO_0008170 (obsolete_interleukin 12 receptor subunit beta-1 measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0008170 "quantification of the amount of interleukin 12 receptor subunit beta-1 in a sample")
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0008170 "Dani Welter")
AnnotationAssertion(rdfs:label efo:EFO_0008170 "interleukin 12 receptor subunit beta-1 measurement")
AnnotationAssertion(obo:IAO_0100001 efo:EFO_0008170 "http://www.ebi.ac.uk/efo/EFO_0801715")
AnnotationAssertion(efo:obsoleted_in_version efo:EFO_0008170 "3.58.0")
AnnotationAssertion(efo:reason_for_obsolescence efo:EFO_0008170 "Duplication")
AnnotationAssertion(rdfs:label efo:EFO_0008170 "obsolete_interleukin 12 receptor subunit beta-1 measurement")
AnnotationAssertion(owl:deprecated efo:EFO_0008170 "true"^^xsd:boolean)
SubClassOf(efo:EFO_0008170 efo:EFO_0007937)

# Class: efo:EFO_0008171 (interleukin 13 measurement)
Expand Down Expand Up @@ -165254,13 +165258,13 @@ AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0009411 "monocyte chemotact
AnnotationAssertion(rdfs:label efo:EFO_0009411 "CCL13 measurement")
SubClassOf(efo:EFO_0009411 efo:EFO_0007937)

# Class: efo:EFO_0009412 (interleukin 1 alpha measurement)
# Class: efo:EFO_0009412 (interleukin-1 alpha measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0009412 "Quantification of the amount of interleukin 1-alpha protein in a sample.")
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0009412 "Laura Harris")
AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0009412 "PMID:30134952")
AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0009412 "IL-1A measurement")
AnnotationAssertion(rdfs:label efo:EFO_0009412 "interleukin 1 alpha measurement")
AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0009412 "IL1A measurement")
AnnotationAssertion(rdfs:label efo:EFO_0009412 "interleukin-1 alpha measurement")
SubClassOf(efo:EFO_0009412 efo:EFO_0004873)

# Class: efo:EFO_0009413 (CCL15 measurement)
Expand Down Expand Up @@ -176265,13 +176269,17 @@ AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0010593 "Cystatin B")
AnnotationAssertion(rdfs:label efo:EFO_0010593 "cystatin B measurement"@en)
SubClassOf(efo:EFO_0010593 efo:EFO_0007937)

# Class: efo:EFO_0010594 (Fms-related tyrosine kinase 3 ligand measurement)
# Class: efo:EFO_0010594 (obsolete_Fms-related tyrosine kinase 3 ligand measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010594 "quantification of the amount of Fms-related tyrosine kinase 3 ligand in a sample")
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0010594 "Elizabeth Lewis")
AnnotationAssertion(obo:IAO_0100001 efo:EFO_0010594 "http://www.ebi.ac.uk/efo/EFO_0010785")
AnnotationAssertion(efo:obsoleted_in_version efo:EFO_0010594 "3.58.0")
AnnotationAssertion(efo:reason_for_obsolescence efo:EFO_0010594 "Duplication")
AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0010594 "PMID:28915241")
AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0010594 "Flt3L")
AnnotationAssertion(rdfs:label efo:EFO_0010594 "Fms-related tyrosine kinase 3 ligand measurement"@en)
AnnotationAssertion(rdfs:label efo:EFO_0010594 "obsolete_Fms-related tyrosine kinase 3 ligand measurement"@en)
AnnotationAssertion(owl:deprecated efo:EFO_0010594 "true"^^xsd:boolean)
SubClassOf(efo:EFO_0010594 efo:EFO_0007937)

# Class: efo:EFO_0010595 (heat shock protein beta-1 measurement)
Expand Down Expand Up @@ -177999,7 +178007,7 @@ SubClassOf(efo:EFO_0010781 ObjectSomeValuesFrom(obo:IAO_0000136 obo:UBERON_00001

# Class: efo:EFO_0010782 (fibroblast growth factor 19 measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010782 "Quantification of the amount of fms related receptor tyrosine kinase 3 ligand in a sample")
AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010782 "Quantification of the amount of fibroblast growth factor 19 in a sample")
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0010782 "Annalisa Buniello")
AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0010782 "PMID:32641083")
AnnotationAssertion(rdfs:label efo:EFO_0010782 "fibroblast growth factor 19 measurement")
Expand All @@ -178008,7 +178016,7 @@ SubClassOf(efo:EFO_0010782 ObjectSomeValuesFrom(obo:IAO_0000136 obo:UBERON_00001

# Class: efo:EFO_0010783 (fibroblast growth factor 21 measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010783 "Quantification of the amount of fibroblast growth factor 5 in a sample")
AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010783 "Quantification of the amount of fibroblast growth factor 21 in a sample")
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0010783 "Annalisa Buniello")
AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0010783 "PMID:32641083")
AnnotationAssertion(rdfs:label efo:EFO_0010783 "fibroblast growth factor 21 measurement")
Expand All @@ -178017,20 +178025,20 @@ SubClassOf(efo:EFO_0010783 ObjectSomeValuesFrom(obo:IAO_0000136 obo:UBERON_00001

# Class: efo:EFO_0010784 (fibroblast growth factor 5 measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010784 "Quantification of the amount of fibroblast growth factor 21 in a sample")
AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010784 "Quantification of the amount of fibroblast growth factor 5 in a sample")
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0010784 "Annalisa Buniello")
AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0010784 "PMID:32641083")
AnnotationAssertion(rdfs:label efo:EFO_0010784 "fibroblast growth factor 5 measurement")
SubClassOf(efo:EFO_0010784 efo:EFO_0007937)
SubClassOf(efo:EFO_0010784 ObjectSomeValuesFrom(obo:IAO_0000136 obo:UBERON_0000178))

# Class: efo:EFO_0010785 (fms related receptor tyrosine kinase-3 ligand measurement)
# Class: efo:EFO_0010785 (fms-related tyrosine kinase 3 ligand measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010785 "Quantification of the amount of fibroblast growth factor 19 in a sample")
AnnotationAssertion(obo:IAO_0000115 efo:EFO_0010785 "Quantification of the amount of fms-related tyrosine kinase 3 ligand in a sample.")
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0010785 "Annalisa Buniello")
AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0010785 "PMID:32641083")
AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0010785 "FLT3L")
AnnotationAssertion(rdfs:label efo:EFO_0010785 "fms related receptor tyrosine kinase-3 ligand measurement")
AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0010785 "Flt3L")
AnnotationAssertion(rdfs:label efo:EFO_0010785 "fms-related tyrosine kinase 3 ligand measurement")
SubClassOf(efo:EFO_0010785 efo:EFO_0007937)
SubClassOf(efo:EFO_0010785 ObjectSomeValuesFrom(obo:IAO_0000136 obo:UBERON_0000178))

Expand Down Expand Up @@ -223045,12 +223053,16 @@ AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0802652 "PMID:29875488")
AnnotationAssertion(rdfs:label efo:EFO_0802652 "interleukin enhancer-binding factor 3 measurement")
SubClassOf(efo:EFO_0802652 efo:EFO_0004747)

# Class: efo:EFO_0802653 (interleukin-1 alpha measurement)
# Class: efo:EFO_0802653 (obsolete_interleukin-1 alpha measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0802653 "Quantification of interleukin-1 alpha in a sample.")
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0802653 "Elizabeth Lewis")
AnnotationAssertion(obo:IAO_0100001 efo:EFO_0802653 "http://www.ebi.ac.uk/efo/EFO_0009412")
AnnotationAssertion(efo:obsoleted_in_version efo:EFO_0802653 "3.58.0")
AnnotationAssertion(efo:reason_for_obsolescence efo:EFO_0802653 "Duplication")
AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0802653 "PMID:29875488")
AnnotationAssertion(rdfs:label efo:EFO_0802653 "interleukin-1 alpha measurement")
AnnotationAssertion(rdfs:label efo:EFO_0802653 "obsolete_interleukin-1 alpha measurement")
AnnotationAssertion(owl:deprecated efo:EFO_0802653 "true"^^xsd:boolean)
SubClassOf(efo:EFO_0802653 efo:EFO_0004747)

# Class: efo:EFO_0802654 (interleukin-12 measurement)
Expand Down
3 changes: 3 additions & 0 deletions src/ontology/reports/obsolete_gwas.tsv
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Expand Up @@ -8,6 +8,9 @@
<http://www.ebi.ac.uk/efo/EFO_0004215> "http://purl.obolibrary.org/obo/MONDO_0005351"
<http://www.ebi.ac.uk/efo/EFO_0005192> "http://www.ebi.ac.uk/efo/EFO_0009188"
<http://www.ebi.ac.uk/efo/EFO_0005842> "http://purl.obolibrary.org/obo/MONDO_0005575"
<http://www.ebi.ac.uk/efo/EFO_0008170> "http://www.ebi.ac.uk/efo/EFO_0801715"
<http://www.ebi.ac.uk/efo/EFO_0010594> "http://www.ebi.ac.uk/efo/EFO_0010785"
<http://www.ebi.ac.uk/efo/EFO_0802653> "http://www.ebi.ac.uk/efo/EFO_0009412"
<http://www.ebi.ac.uk/efo/EFO_1000882> "http://purl.obolibrary.org/obo/MONDO_0006715"
<http://www.ebi.ac.uk/efo/EFO_1001457> "http://purl.obolibrary.org/obo/MONDO_0002039"
<http://www.orpha.net/ORDO/Orphanet_139039> "http://purl.obolibrary.org/obo/MONDO_0015335"
Expand Down
3 changes: 3 additions & 0 deletions src/ontology/reports/obsoletes.tsv
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Expand Up @@ -1707,6 +1707,7 @@
<http://www.ebi.ac.uk/efo/EFO_0007483> "http://www.ebi.ac.uk/efo/EFO_1000052"
<http://www.ebi.ac.uk/efo/EFO_0008143> "http://www.ebi.ac.uk/efo/EFO_0008142"
<http://www.ebi.ac.uk/efo/EFO_0008166> "http://www.ebi.ac.uk/efo/EFO_0004812"
<http://www.ebi.ac.uk/efo/EFO_0008170> "http://www.ebi.ac.uk/efo/EFO_0801715"
<http://www.ebi.ac.uk/efo/EFO_0008575> "http://purl.obolibrary.org/obo/HP_0040188"
<http://www.ebi.ac.uk/efo/EFO_0008716> "http://www.ebi.ac.uk/efo/EFO_0003752"
<http://www.ebi.ac.uk/efo/EFO_0008717> "http://www.ebi.ac.uk/efo/EFO_0003752"
Expand All @@ -1723,6 +1724,7 @@
<http://www.ebi.ac.uk/efo/EFO_0009921> "http://www.ebi.ac.uk/efo/EFO_0011025"
<http://www.ebi.ac.uk/efo/EFO_0010254>
<http://www.ebi.ac.uk/efo/EFO_0010338> "http://purl.obolibrary.org/obo/MONDO_0018906"
<http://www.ebi.ac.uk/efo/EFO_0010594> "http://www.ebi.ac.uk/efo/EFO_0010785"
<http://www.ebi.ac.uk/efo/EFO_0010894> "http://purl.obolibrary.org/obo/CL_0009021"
<http://www.ebi.ac.uk/efo/EFO_0010895> "http://purl.obolibrary.org/obo/CL_0009022"
<http://www.ebi.ac.uk/efo/EFO_0010897> "http://purl.obolibrary.org/obo/CL_0009024"
Expand All @@ -1733,6 +1735,7 @@
<http://www.ebi.ac.uk/efo/EFO_0021579> "http://www.ebi.ac.uk/efo/EFO_0010472"
<http://www.ebi.ac.uk/efo/EFO_0021606> "http://www.ebi.ac.uk/efo/EFO_0010504"
<http://www.ebi.ac.uk/efo/EFO_0021673> "http://www.ebi.ac.uk/efo/EFO_0021179"
<http://www.ebi.ac.uk/efo/EFO_0802653> "http://www.ebi.ac.uk/efo/EFO_0009412"
<http://www.ebi.ac.uk/efo/EFO_1000022> "http://www.ebi.ac.uk/efo/EFO_1000172"
<http://www.ebi.ac.uk/efo/EFO_1000031> "http://www.ebi.ac.uk/efo/EFO_0000508"
<http://www.ebi.ac.uk/efo/EFO_1000033> "http://www.orpha.net/ORDO/Orphanet_2189"
Expand Down

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