Add gene expression trait related pattern templates

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

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

src/patterns/definitions.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/oba/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/oba/releases/2023-02-16/patterns/definitions.owl>
-Annotation(owl:versionInfo "2023-02-16"^^xsd:string)
+<http://purl.obolibrary.org/obo/oba/releases/2023-03-03/patterns/definitions.owl>
+Annotation(owl:versionInfo "2023-03-03"^^xsd:string)
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10033>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10112>))
@@ -71616,4 +71616,8 @@ SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0015007> Ob
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0015007> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001691>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0015007> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001691>))))
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0015007> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001847>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0015007> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001847>))))
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0015026> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000468>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0015026> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0000468>))))
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2040175> "https://orcid.org/0000-0001-8314-2140"^^xsd:string)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2040175> "troponin T, fast skeletal muscle protein expression quality"^^xsd:string)
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2040176> "https://orcid.org/0000-0001-8314-2140"^^xsd:string)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2040176> "troponin T, fast skeletal muscle protein isoform expression quality in fast skeletal muscle tissue"^^xsd:string)
 )

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

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