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Add gene expression trait related pattern templates
This commit intends to 1. gene expression trait 2. gene expression in location trait pattern templates. Addresses #223.
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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 |
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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 |
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src/patterns/dosdp-patterns/gene_expression_in_location.yaml
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--- | ||
pattern_name: gene_expression_in_location.yaml | ||
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pattern_iri: gene_expression_in_location.yaml | ||
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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.' | ||
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contributors: | ||
- https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik | ||
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classes: | ||
entity: owl:Thing # preferably a gene or gene product | ||
location: UBERON:0001062 # anatomical entity | ||
process_quality: PATO:0001236 | ||
gene_expression: GO:0010467 | ||
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relations: | ||
characteristic_of: RO:0000052 | ||
has_participant: RO:0000057 | ||
has_part_that_occurs_in: RO:0002479 | ||
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annotationProperties: | ||
exact_synonym: oio:hasExactSynonym | ||
related_synonym: oio:hasRelatedSynonym | ||
contributor: dct:contributor # contributor: dcterms:contributor | ||
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vars: | ||
gene_product: "'entity'" | ||
location: "'location'" | ||
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data_list_vars: | ||
orcid: xsd:anyURI # ORCID of contributor | ||
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name: | ||
text: "%s expression in %s quality" | ||
vars: | ||
- gene_product | ||
- location | ||
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annotations: | ||
- annotationProperty: exact_synonym | ||
text: "%s gene expression in %s quality" | ||
vars: | ||
- gene_product | ||
- location | ||
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- annotationProperty: exact_synonym | ||
text: "%s gene expression in %s attribute" | ||
vars: | ||
- gene_product | ||
- location | ||
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- annotationProperty: exact_synonym | ||
text: "expression of %s in %s quality" | ||
vars: | ||
- gene_product | ||
- location | ||
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- annotationProperty: exact_synonym | ||
text: "expression of %s in %s attribute" | ||
vars: | ||
- gene_product | ||
- location | ||
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- annotationProperty: related_synonym | ||
text: "%s expression in %s" | ||
vars: | ||
- gene_product | ||
- location | ||
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- annotationProperty: related_synonym | ||
text: "expression of %s in %s" | ||
vars: | ||
- gene_product | ||
- location | ||
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- annotationProperty: contributor | ||
value: orcid | ||
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def: | ||
text: "A gene expression trait that affects the process of %s expression in | ||
%s." | ||
vars: | ||
- gene_product | ||
- location | ||
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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 |
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--- | ||
pattern_name: gene_expression_trait.yaml | ||
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pattern_iri: gene_expression_trait.yaml | ||
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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.' | ||
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contributors: | ||
- https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik | ||
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classes: | ||
entity: owl:Thing # preferably a gene or gene product | ||
process_quality: PATO:0001236 | ||
gene_expression: GO:0010467 | ||
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relations: | ||
characteristic_of: RO:0000052 | ||
has_participant: RO:0000057 | ||
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annotationProperties: | ||
exact_synonym: oio:hasExactSynonym | ||
related_synonym: oio:hasRelatedSynonym | ||
contributor: dct:contributor # contributor: dcterms:contributor | ||
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vars: | ||
gene_product: "'entity'" | ||
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data_list_vars: | ||
orcid: xsd:anyURI # ORCID of contributor | ||
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name: | ||
text: "%s expression quality" | ||
vars: | ||
- gene_product | ||
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annotations: | ||
- annotationProperty: exact_synonym | ||
text: "%s gene expression quality" | ||
vars: | ||
- gene_product | ||
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- annotationProperty: exact_synonym | ||
text: "%s gene expression attribute" | ||
vars: | ||
- gene_product | ||
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- annotationProperty: exact_synonym | ||
text: "%s expression attribute" | ||
vars: | ||
- gene_product | ||
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- annotationProperty: related_synonym | ||
text: "%s expression" | ||
vars: | ||
- gene_product | ||
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- annotationProperty: related_synonym | ||
text: "expression of %s" | ||
vars: | ||
- gene_product | ||
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- annotationProperty: contributor | ||
value: orcid | ||
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def: | ||
text: "A gene expression trait that affects the process of %s expression." | ||
vars: | ||
- gene_product | ||
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equivalentTo: | ||
text: "'process_quality' and | ||
('characteristic_of' some | ||
('gene_expression' and | ||
('has_participant' some %s)))" | ||
vars: | ||
- gene_product |