From b9d178be35a4d6f5d99c6f4ca9a0067c9353438e Mon Sep 17 00:00:00 2001 From: paolaroncaglia Date: Fri, 14 Jan 2022 12:46:15 +0100 Subject: [PATCH] Add terms for #1404 --- src/ontology/efo-edit.owl | 97 ++++++++++++++++++++++++++++++++ src/ontology/efo-edit.properties | 5 ++ 2 files changed, 102 insertions(+) create mode 100644 src/ontology/efo-edit.properties diff --git a/src/ontology/efo-edit.owl b/src/ontology/efo-edit.owl index 059d56dc..e859db10 100644 --- a/src/ontology/efo-edit.owl +++ b/src/ontology/efo-edit.owl @@ -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)) @@ -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.") diff --git a/src/ontology/efo-edit.properties b/src/ontology/efo-edit.properties new file mode 100644 index 00000000..2d091942 --- /dev/null +++ b/src/ontology/efo-edit.properties @@ -0,0 +1,5 @@ +#Fri Jan 14 12:42:00 CET 2022 +jdbc.url= +jdbc.driver= +jdbc.user= +jdbc.password=