Skip to content

Commit

Permalink
Add gene expression trait related pattern templates
Browse files Browse the repository at this point in the history
This commit intends to
1. gene expression trait
2. gene expression in location
trait pattern templates.
Addresses #223.
  • Loading branch information
rays22 committed Mar 3, 2023
1 parent 4ec7348 commit ac3331e
Show file tree
Hide file tree
Showing 4 changed files with 190 additions and 0 deletions.
2 changes: 2 additions & 0 deletions src/patterns/data/default/gene_expression_in_location.tsv
Original file line number Diff line number Diff line change
@@ -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
2 changes: 2 additions & 0 deletions src/patterns/data/default/gene_expression_trait.tsv
Original file line number Diff line number Diff line change
@@ -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
101 changes: 101 additions & 0 deletions src/patterns/dosdp-patterns/gene_expression_in_location.yaml
Original file line number Diff line number Diff line change
@@ -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
85 changes: 85 additions & 0 deletions src/patterns/dosdp-patterns/gene_expression_trait.yaml
Original file line number Diff line number Diff line change
@@ -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

0 comments on commit ac3331e

Please sign in to comment.