diff --git a/src/patterns/data/default/gene_expression_in_location.tsv b/src/patterns/data/default/gene_expression_in_location.tsv new file mode 100644 index 00000000..ff766662 --- /dev/null +++ b/src/patterns/data/default/gene_expression_in_location.tsv @@ -0,0 +1,2 @@ +defined_class defined_class_name entity entity_name location location_name orcid +OBA:2040176 troponin T, fast skeletal muscle protein isoform expression quality in fast skeletal muscle tissue PR:000016510 troponin T, fast skeletal muscle UBERON:0006908 fast muscle tissue https://orcid.org/0000-0001-8314-2140 diff --git a/src/patterns/data/default/gene_expression_trait.tsv b/src/patterns/data/default/gene_expression_trait.tsv new file mode 100644 index 00000000..967bb763 --- /dev/null +++ b/src/patterns/data/default/gene_expression_trait.tsv @@ -0,0 +1,2 @@ +defined_class defined_class_name entity entity_name orcid +OBA:2040175 troponin T, fast skeletal muscle protein expression quality PR:000016510 troponin T, fast skeletal muscle https://orcid.org/0000-0001-8314-2140 diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index e353e4dd..f6b6ac3f 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2025-05-20") + +Annotation(owl:versionInfo "2025-05-21") Declaration(Class()) Declaration(Class()) @@ -182283,4 +182283,8 @@ SubClassOf(ObjectIntersectionOf( Ob SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") +AnnotationAssertion(rdfs:label "troponin T, fast skeletal muscle protein expression quality") +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") +AnnotationAssertion(rdfs:label "troponin T, fast skeletal muscle protein isoform expression quality in fast skeletal muscle tissue") ) \ No newline at end of file diff --git a/src/patterns/dosdp-patterns/gene_expression_in_location.yaml b/src/patterns/dosdp-patterns/gene_expression_in_location.yaml new file mode 100644 index 00000000..e57876e5 --- /dev/null +++ b/src/patterns/dosdp-patterns/gene_expression_in_location.yaml @@ -0,0 +1,101 @@ +--- +pattern_name: gene_expression_in_location.yaml + +pattern_iri: gene_expression_in_location.yaml + +description: 'Use this pattern to annotate gene expression in location traits + where the quality of the process of the expression of a gene, gene complex or + gene family is observed or measured, but no judgement is made whether the + quality deviates or not from a reference. In contrast to gene expression + related phenotypes, the gene expression trait is indifferent about the + quality of the process being normal or abnormal. You should specify the + genetically most relevant participant or participant category for this trait + pattern, i.e. the gene(s) being expressed or the products of those genes, and + not any other participant (e.g. ribosomes or ribonucleotides) in the gene + expression process. The location must be an anatomical entity.' + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + +classes: + entity: owl:Thing # preferably a gene or gene product + location: UBERON:0001062 # anatomical entity + process_quality: PATO:0001236 + gene_expression: GO:0010467 + +relations: + characteristic_of: RO:0000052 + has_participant: RO:0000057 + has_part_that_occurs_in: RO:0002479 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + related_synonym: oio:hasRelatedSynonym + contributor: dct:contributor # contributor: dcterms:contributor + +vars: + gene_product: "'entity'" + location: "'location'" + +data_list_vars: + orcid: xsd:anyURI # ORCID of contributor + +name: + text: "%s expression in %s quality" + vars: + - gene_product + - location + +annotations: + - annotationProperty: exact_synonym + text: "%s gene expression in %s quality" + vars: + - gene_product + - location + + - annotationProperty: exact_synonym + text: "%s gene expression in %s attribute" + vars: + - gene_product + - location + + - annotationProperty: exact_synonym + text: "expression of %s in %s quality" + vars: + - gene_product + - location + + - annotationProperty: exact_synonym + text: "expression of %s in %s attribute" + vars: + - gene_product + - location + + - annotationProperty: related_synonym + text: "%s expression in %s" + vars: + - gene_product + - location + + - annotationProperty: related_synonym + text: "expression of %s in %s" + vars: + - gene_product + - location + + - annotationProperty: contributor + value: orcid + +def: + text: "A gene expression trait that affects the process of %s expression in + %s." + vars: + - gene_product + - location + +equivalentTo: + text: "'process_quality' and ('characteristic_of' some ('gene_expression' and + ( ('has_participant' some %s) and ('has_part_that_occurs_in' some %s))))" + vars: + - gene_product + - location diff --git a/src/patterns/dosdp-patterns/gene_expression_trait.yaml b/src/patterns/dosdp-patterns/gene_expression_trait.yaml new file mode 100644 index 00000000..78b19ab5 --- /dev/null +++ b/src/patterns/dosdp-patterns/gene_expression_trait.yaml @@ -0,0 +1,85 @@ +--- +pattern_name: gene_expression_trait.yaml + +pattern_iri: gene_expression_trait.yaml + +description: 'Use this pattern to annotate gene expression traits where the + quality of the process of the expression of a gene, gene complex or gene + family is observed or measured, but no judgement is made whether the quality + deviates or not from a reference. In contrast to gene expression related + phenotypes, the gene expression trait is indifferent about the quality of the + process being normal or abnormal. You should specify the genetically most + relevant participant or participant category for this trait pattern, i.e. the + gene(s) being expressed or the products of those genes, and not any other + participant (e.g. ribosomes or ribonucleotides) in the gene expression + process.' + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + +classes: + entity: owl:Thing # preferably a gene or gene product + process_quality: PATO:0001236 + gene_expression: GO:0010467 + +relations: + characteristic_of: RO:0000052 + has_participant: RO:0000057 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + related_synonym: oio:hasRelatedSynonym + contributor: dct:contributor # contributor: dcterms:contributor + +vars: + gene_product: "'entity'" + +data_list_vars: + orcid: xsd:anyURI # ORCID of contributor + +name: + text: "%s expression quality" + vars: + - gene_product + +annotations: + - annotationProperty: exact_synonym + text: "%s gene expression quality" + vars: + - gene_product + + - annotationProperty: exact_synonym + text: "%s gene expression attribute" + vars: + - gene_product + + - annotationProperty: exact_synonym + text: "%s expression attribute" + vars: + - gene_product + + - annotationProperty: related_synonym + text: "%s expression" + vars: + - gene_product + + - annotationProperty: related_synonym + text: "expression of %s" + vars: + - gene_product + + - annotationProperty: contributor + value: orcid + +def: + text: "A gene expression trait that affects the process of %s expression." + vars: + - gene_product + +equivalentTo: + text: "'process_quality' and + ('characteristic_of' some + ('gene_expression' and + ('has_participant' some %s)))" + vars: + - gene_product