diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml index be4608414..4db181c85 100644 --- a/lang/R/inst/extdata/airr-schema.yaml +++ b/lang/R/inst/extdata/airr-schema.yaml @@ -1213,7 +1213,7 @@ GenotypeSet: items: $ref: '#/Genotype' -# This enumerates the alleles and gene deletions inferred in a single subject. Included alleles may either be listed by reference to a GermlineSet, or +# This enumerates the alleles and gene deletions inferred in a single subject. Included alleles may either be listed by reference to a GermlineSet, or # listed as 'undocumented', in which case the inferred sequence is provided # Genotype of adaptive immune receptors @@ -3353,6 +3353,28 @@ Rearrangement: adc-query-support: true name: Gene locus format: controlled_vocabulary + locus_species: + $ref: '#/Ontology' + description: > + Binomial designation of the species from which the locus originates. Typically, this value should be + identical to `organism`, if which case it SHOULD NOT be set explicitly. However, there are valid + experimental setups in which the two might differ, e.g. transgenic animal models. If set, this key + will overwrite the `organism` information for all lower layers of the schema. + title: Locus species + example: + id: NCBITAXON:9606 + label: Homo sapiens + x-airr: + miairr: defined + nullable: true + adc-query-support: true + name: Locus species + format: ontology + ontology: + draft: false + top_node: + id: NCBITAXON:7776 + label: Gnathostomata v_call: type: string description: > @@ -4346,8 +4368,8 @@ Cell: name: Virtual pairing # The CellExpression object acts as a container to hold a single expression level measurement from -# an experiment. Expression data is associated with a cell_id and the related repertoire_id and -# data_processing_id as cell_id is not guaranteed to be unique outside the data processing for +# an experiment. Expression data is associated with a cell_id and the related repertoire_id and +# data_processing_id as cell_id is not guaranteed to be unique outside the data processing for # a single repertoire. CellExpression: type: object diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml index be4608414..4db181c85 100644 --- a/lang/python/airr/specs/airr-schema.yaml +++ b/lang/python/airr/specs/airr-schema.yaml @@ -1213,7 +1213,7 @@ GenotypeSet: items: $ref: '#/Genotype' -# This enumerates the alleles and gene deletions inferred in a single subject. Included alleles may either be listed by reference to a GermlineSet, or +# This enumerates the alleles and gene deletions inferred in a single subject. Included alleles may either be listed by reference to a GermlineSet, or # listed as 'undocumented', in which case the inferred sequence is provided # Genotype of adaptive immune receptors @@ -3353,6 +3353,28 @@ Rearrangement: adc-query-support: true name: Gene locus format: controlled_vocabulary + locus_species: + $ref: '#/Ontology' + description: > + Binomial designation of the species from which the locus originates. Typically, this value should be + identical to `organism`, if which case it SHOULD NOT be set explicitly. However, there are valid + experimental setups in which the two might differ, e.g. transgenic animal models. If set, this key + will overwrite the `organism` information for all lower layers of the schema. + title: Locus species + example: + id: NCBITAXON:9606 + label: Homo sapiens + x-airr: + miairr: defined + nullable: true + adc-query-support: true + name: Locus species + format: ontology + ontology: + draft: false + top_node: + id: NCBITAXON:7776 + label: Gnathostomata v_call: type: string description: > @@ -4346,8 +4368,8 @@ Cell: name: Virtual pairing # The CellExpression object acts as a container to hold a single expression level measurement from -# an experiment. Expression data is associated with a cell_id and the related repertoire_id and -# data_processing_id as cell_id is not guaranteed to be unique outside the data processing for +# an experiment. Expression data is associated with a cell_id and the related repertoire_id and +# data_processing_id as cell_id is not guaranteed to be unique outside the data processing for # a single repertoire. CellExpression: type: object diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml index bf470cca1..340a6c5a7 100644 --- a/specs/airr-schema-openapi3.yaml +++ b/specs/airr-schema-openapi3.yaml @@ -3483,6 +3483,28 @@ Rearrangement: adc-query-support: true name: Gene locus format: controlled_vocabulary + locus_species: + $ref: '#/Ontology' + nullable: true + description: > + Binomial designation of the species from which the locus originates. Typically, this value should be + identical to `organism`, if which case it SHOULD NOT be set explicitly. However, there are valid + experimental setups in which the two might differ, e.g. transgenic animal models. If set, this key + will overwrite the `organism` information for all lower layers of the schema. + title: Locus species + example: + id: NCBITAXON:9606 + label: Homo sapiens + x-airr: + miairr: defined + adc-query-support: true + name: Locus species + format: ontology + ontology: + draft: false + top_node: + id: NCBITAXON:7776 + label: Gnathostomata v_call: type: string nullable: true diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index be4608414..4c972f261 100644 --- a/specs/airr-schema.yaml +++ b/specs/airr-schema.yaml @@ -3353,6 +3353,28 @@ Rearrangement: adc-query-support: true name: Gene locus format: controlled_vocabulary + locus_species: + $ref: '#/Ontology' + description: > + Binomial designation of the species from which the locus originates. Typically, this value should be + identical to `organism`, if which case it SHOULD NOT be set explicitly. However, there are valid + experimental setups in which the two might differ, e.g. transgenic animal models. If set, this key + will overwrite the `organism` information for all lower layers of the schema. + title: Locus species + example: + id: NCBITAXON:9606 + label: Homo sapiens + x-airr: + miairr: defined + nullable: true + adc-query-support: true + name: Locus species + format: ontology + ontology: + draft: false + top_node: + id: NCBITAXON:7776 + label: Gnathostomata v_call: type: string description: >