diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml index 03a638611..125bab627 100644 --- a/specs/airr-schema-openapi3.yaml +++ b/specs/airr-schema-openapi3.yaml @@ -4578,19 +4578,6 @@ Cell: miairr: defined adc-query-support: true name: Cell-associated receptors - reactivity_measurements: - type: array - nullable: true - description: > - Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Cell - title: Reactivity measurements - items: - type: string - example: [id1, id2] - x-airr: - miairr: defined - adc-query-support: true - name: Cell-associated reactivity measurements repertoire_id: type: string nullable: true @@ -5049,3 +5036,210 @@ ReceptorReactivity: example: pg/ml x-airr: adc-query-support: true + +CellReactivity: + type: object + required: + - cell_reactivity_id + - cell_id + - ligand_type + - antigen_type + - antigen + - reactivity_method + - reactivity_readout + - reactivity_value + - reactivity_unit + properties: + cell_reactivity_id: + type: string + nullable: false + description: ID of this CellReactivity object, globally unique. + title: Cell Reactivity ID + x-airr: + identifier: true + adc-query-support: true + cell_id: + type: string + nullable: false + description: > + Identifier of the cell in the context of which the reactivity measurement was conducted. + title: Cell ID + x-airr: + adc-query-support: true + ligand_type: + type: string + nullable: false + enum: + - "MHC:peptide" + - "MHC:non-peptide" + - protein + - peptide + - non-peptidic + description: Classification of ligand binding to receptor + example: non-peptide + x-airr: + format: controlled_vocabulary + adc-query-support: true + antigen_type: + type: string + nullable: false + enum: + - protein + - peptide + - non-peptidic + description: > + The type of antigen before processing by the immune system. + example: protein + x-airr: + format: controlled_vocabulary + adc-query-support: true + antigen: + $ref: '#/Ontology' + nullable: false + description: > + The substance against which the receptor was tested. This can be any substance that + stimulates an adaptive immune response in the host, either through antibody production + or by T cell activation after presentation via an MHC molecule. + title: Antigen + example: + id: UNIPROT:P19597 + label: Circumsporozoite protein + x-airr: + adc-query-support: true + format: ontology + antigen_source_species: + $ref: '#/Ontology' + nullable: true + description: The species from which the antigen was isolated + title: Source species of antigen + example: + id: NCBITAXON:5843 + label: Plasmodium falciparum NF54 + x-airr: + adc-query-support: true + format: ontology + ontology: + draft: true + top_node: + id: NCBITAXON:1 + label: root + peptide_start: + type: integer + nullable: true + description: Start position of the peptide within the reference protein sequence + peptide_end: + type: integer + nullable: true + description: End position of the peptide within the reference protein sequence + peptide_sequence_aa: + type: string + nullable: true + description: > + The actual peptide sequence against which the receptor reactivity was measured. This field should be + used as a convenience for antigens of antigen_type `protein` or `peptide`. + x-airr: + adc-query-support: true + mhc_class: + type: string + nullable: true + enum: + - MHC-I + - MHC-II + - MHC-nonclassical + - null + description: Class of MHC molecule, only present for MHC:x ligand types + example: MHC-II + x-airr: + format: controlled_vocabulary + adc-query-support: true + mhc_gene_1: + $ref: '#/Ontology' + nullable: true + description: The MHC gene to which the mhc_allele_1 belongs + title: MHC gene 1 + example: + id: MRO:0000055 + label: HLA-DRA + x-airr: + adc-query-support: true + format: ontology + ontology: + draft: true + top_node: + id: MRO:0000004 + label: MHC gene + mhc_allele_1: + type: string + nullable: true + description: Allele designation of the MHC alpha chain + example: HLA-DRA + x-airr: + adc-query-support: true + mhc_gene_2: + $ref: '#/Ontology' + nullable: true + description: The MHC gene to which the mhc_allele_2 belongs + title: MHC gene 2 + example: + id: MRO:0000057 + label: HLA-DRB1 + x-airr: + adc-query-support: true + format: ontology + ontology: + draft: true + top_node: + id: MRO:0000004 + label: MHC gene + mhc_allele_2: + type: string + nullable: true + description: > + Allele designation of the MHC class II beta chain or the invariant beta2-microglobin chain + example: HLA-DRB1*04:01 + x-airr: + adc-query-support: true + reactivity_method: + type: string + nullable: false + enum: + - SPR + - ITC + - ELISA + - cytometry + - biological_activity + - MHC_peptide_multimer + description: The methodology used to assess expression (assay implemented in experiment) + x-airr: + adc-query-support: true + format: controlled_vocabulary + reactivity_readout: + type: string + nullable: false + enum: + - binding_strength + - cytokine_release + - dissociation_constant_kd + - on_rate + - off_rate + - pathogen_inhibition + - barcode_count + description: Reactivity measurement read-out + example: cytokine release + x-airr: + adc-query-support: true + format: controlled_vocabulary + reactivity_value: + type: number + nullable: false + description: The absolute (processed) value of the measurement + example: 162.26 + x-airr: + adc-query-support: true + reactivity_unit: + type: string + nullable: false + description: The unit of the measurement + example: pg/ml + x-airr: + adc-query-support: true