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Add terms for #1404
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@paolaroncaglia
paolaroncaglia committed Jan 14, 2022
1 parent 6430ec2 commit b9d178b
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97 changes: 97 additions & 0 deletions src/ontology/efo-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -15542,6 +15542,17 @@ Declaration(Class(efo:EFO_0030059))
Declaration(Class(efo:EFO_0030060))
Declaration(Class(efo:EFO_0030061))
Declaration(Class(efo:EFO_0030062))
Declaration(Class(efo:EFO_0030063))
Declaration(Class(efo:EFO_0030064))
Declaration(Class(efo:EFO_0030065))
Declaration(Class(efo:EFO_0030066))
Declaration(Class(efo:EFO_0030067))
Declaration(Class(efo:EFO_0030068))
Declaration(Class(efo:EFO_0030069))
Declaration(Class(efo:EFO_0030070))
Declaration(Class(efo:EFO_0030071))
Declaration(Class(efo:EFO_0030072))
Declaration(Class(efo:EFO_0030073))
Declaration(Class(efo:EFO_0600000))
Declaration(Class(efo:EFO_0600001))
Declaration(Class(efo:EFO_0600002))
Expand Down Expand Up @@ -207526,6 +207537,92 @@ AnnotationAssertion(rdfs:label efo:EFO_0030062 "Slide-seqV2")
SubClassOf(efo:EFO_0030062 efo:EFO_0010183)
SubClassOf(efo:EFO_0030062 efo:EFO_0030005)

# Class: efo:EFO_0030063 (copy number assessment)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0002-9903-4248") obo:IAO_0000115 efo:EFO_0030063 "Result of genomic copy number assessment of a genomic element or region.")
AnnotationAssertion(dc:creator efo:EFO_0030063 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030063 "2022-01-14T11:04:56Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0030063 "copy number variation analysis")
AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0030063 "genomic copy number assessment")
AnnotationAssertion(rdfs:comment efo:EFO_0030063 "Assessment of the copy number of a genomic feature or region, referenced to the expected allele count in a given sample. Examples of an expected count would be: a) autosomal chromosome in human germline: 2; b) X-chromosome in human male: 1; c) triploid cancer cell line: 3, i.e. a region with 2 alleles in a triploid cell line would correspond to a low-level copy number loss.")
AnnotationAssertion(rdfs:label efo:EFO_0030063 "copy number assessment")
SubClassOf(efo:EFO_0030063 obo:IAO_0000030)

# Class: efo:EFO_0030064 (regional base ploidy)

AnnotationAssertion(dc:creator efo:EFO_0030064 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030064 "2022-01-14T11:10:12Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label efo:EFO_0030064 "regional base ploidy")
SubClassOf(efo:EFO_0030064 efo:EFO_0030063)

# Class: efo:EFO_0030065 (copy-neutral loss of heterozygosity)

AnnotationAssertion(dc:creator efo:EFO_0030065 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030065 "2022-01-14T11:10:59Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label efo:EFO_0030065 "copy-neutral loss of heterozygosity")
SubClassOf(efo:EFO_0030065 efo:EFO_0030064)

# Class: efo:EFO_0030066 (relative copy number variation)

AnnotationAssertion(dc:creator efo:EFO_0030066 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030066 "2022-01-14T11:24:49Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym efo:EFO_0030066 "observed copy number variation")
AnnotationAssertion(oboInOwl:hasRelatedSynonym efo:EFO_0030066 "copy number variation")
AnnotationAssertion(oboInOwl:hasRelatedSynonym efo:EFO_0030066 "genomic copy number variation")
AnnotationAssertion(rdfs:label efo:EFO_0030066 "relative copy number variation")
SubClassOf(efo:EFO_0030066 efo:EFO_0030063)

# Class: efo:EFO_0030067 (copy number loss)

AnnotationAssertion(dc:creator efo:EFO_0030067 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030067 "2022-01-14T11:25:28Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label efo:EFO_0030067 "copy number loss")
SubClassOf(efo:EFO_0030067 efo:EFO_0030066)

# Class: efo:EFO_0030068 (low-level copy number loss)

AnnotationAssertion(dc:creator efo:EFO_0030068 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030068 "2022-01-14T11:25:45Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label efo:EFO_0030068 "low-level copy number loss")
SubClassOf(efo:EFO_0030068 efo:EFO_0030067)

# Class: efo:EFO_0030069 (complete genomic deletion)

AnnotationAssertion(dc:creator efo:EFO_0030069 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030069 "2022-01-14T11:26:00Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label efo:EFO_0030069 "complete genomic deletion")
SubClassOf(efo:EFO_0030069 efo:EFO_0030067)

# Class: efo:EFO_0030070 (copy number gain)

AnnotationAssertion(dc:creator efo:EFO_0030070 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030070 "2022-01-14T11:26:27Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label efo:EFO_0030070 "copy number gain")
SubClassOf(efo:EFO_0030070 efo:EFO_0030066)

# Class: efo:EFO_0030071 (low-level copy number gain)

AnnotationAssertion(dc:creator efo:EFO_0030071 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030071 "2022-01-14T11:26:45Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label efo:EFO_0030071 "low-level copy number gain")
SubClassOf(efo:EFO_0030071 efo:EFO_0030070)

# Class: efo:EFO_0030072 (high-level copy number gain)

AnnotationAssertion(dc:creator efo:EFO_0030072 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030072 "2022-01-14T11:27:07Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:comment efo:EFO_0030072 "Commonly but not consistently used for >=5 copies on a bi-allelic genome region.")
AnnotationAssertion(rdfs:label efo:EFO_0030072 "high-level copy number gain")
SubClassOf(efo:EFO_0030072 efo:EFO_0030070)

# Class: efo:EFO_0030073 (focal genome amplification)

AnnotationAssertion(dc:creator efo:EFO_0030073 "paola"^^xsd:string)
AnnotationAssertion(dc:date efo:EFO_0030073 "2022-01-14T11:28:10Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:comment efo:EFO_0030073 "Commonly used for localized multi-copy genome amplification events where the region does not extend >3Mb (varying 1-5Mb) and may exist in a large number of copies.")
AnnotationAssertion(rdfs:label efo:EFO_0030073 "focal genome amplification")
SubClassOf(efo:EFO_0030073 efo:EFO_0030072)

# Class: efo:EFO_0600000 (sortilin measurement)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0600000 "Quantification of the amount of sortilin in a sample.")
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5 changes: 5 additions & 0 deletions src/ontology/efo-edit.properties
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#Fri Jan 14 12:42:00 CET 2022
jdbc.url=
jdbc.driver=
jdbc.user=
jdbc.password=

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