diff --git a/lang/R/inst/extdata/airr-schema-openapi3.yaml b/lang/R/inst/extdata/airr-schema-openapi3.yaml index ff0e5753..f49eebaf 100644 --- a/lang/R/inst/extdata/airr-schema-openapi3.yaml +++ b/lang/R/inst/extdata/airr-schema-openapi3.yaml @@ -92,11 +92,19 @@ CURIEMap: IEDB_RECEPTOR: type: identifier default: - map: IEDB - provider: IEDB + map: IEDB_RECEPTOR + provider: IEDB_RECEPTOR map: - IEDB: + IEDB_RECEPTOR: iri_prefix: "https://www.iedb.org/receptor/" + IEDB_EPITOPE: + type: identifier + default: + map: IEDB_EPITOPE + provider: IEDB_EPITOPE + map: + IEDB_EPITOPE: + iri_prefix: "https://www.iedb.org/epitope/" MRO: type: ontology default: @@ -176,9 +184,15 @@ InformationProvider: request: url: "{iri}" response: text/html - IEDB: + IEDB_RECEPTOR: + request: + url: + - 'https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}' + - 'https://query-api.iedb.org/bcr_search?receptor_group_id=eq.{local_id}' + response: application/json + IEDB_EPITOPE: request: - url: "https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}" + url: "https://query-api.iedb.org/epitope_search?structure_id=eq.{local_id}" response: application/json OLS: request: @@ -4669,6 +4683,21 @@ Rearrangement: x-airr: adc-query-support: true identifier: true + reactivity_id: + type: string + nullable: true + description: > + Comma separated list of unique identifiers for Reactivity objects associated with this Rearrangement. + Order and length of reactivity_id and reactivity_ref are independent. + x-airr: + identifier: true + reactivity_ref: + type: string + nullable: true + description: > + Comma separated list of CURIE identifiers of external reactivity records (e.g. IEDB_RECEPTOR:182992, https://www.iedb.org/receptor/182992) + associated with this Rearrangement. Order and length of reactivity_id and reactivity_ref are independent. + example: "IEDB_RECEPTOR:182992, IEDB_RECEPTOR:36336" repertoire_id: type: string nullable: true @@ -5270,7 +5299,7 @@ Reactivity: adc-query-support: true cell_id: type: string - nullable: false + nullable: true description: > Identifier of the Cell in the context of which the reactivity measurement was conducted. title: Cell ID @@ -5304,7 +5333,7 @@ Reactivity: - peptide - non-peptidic description: Classification of ligand binding to the cell - example: non-peptide + example: "MHC:peptide" x-airr: format: controlled_vocabulary adc-query-support: true @@ -5330,8 +5359,8 @@ Reactivity: or by T cell activation after presentation via an MHC molecule. title: Antigen example: - id: UNIPROT:P19597 - label: Circumsporozoite protein + id: UNIPROT:P01308 + label: Insulin x-airr: adc-query-support: true format: ontology @@ -5341,8 +5370,8 @@ Reactivity: description: The species from which the antigen was isolated title: Source species of antigen example: - id: NCBITAXON:5843 - label: Plasmodium falciparum NF54 + id: NCBITAXON:9606 + label: Homo sapiens x-airr: adc-query-support: true format: ontology @@ -5354,14 +5383,17 @@ Reactivity: peptide_start: type: integer nullable: true + example: 87 description: Start position of the peptide within the reference protein sequence peptide_end: type: integer nullable: true + example: 101 description: End position of the peptide within the reference protein sequence peptide_sequence_aa: type: string nullable: true + example: QKRGIVEQCCTSICS 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`. @@ -5430,24 +5462,25 @@ Reactivity: reactivity_method: type: string nullable: false - enum: - - native_protein - - MHC_peptide_multimer - description: The methodology used to assess expression (assay implemented in experiment) + description: > + The methodology used to assess/classify reactivity. This should be either the assay utlizied in the experiment, + delineated as "annotated" if annotated from an external source (e.g. IEDB), or inferred if imputed using + a computational method. In future versions we anticipate this field being an enumerated type, and it is strongly + recommended that users utilize one of the following keywords in this field if appropriate: + native_protein, MHC_peptide_multimer, annotated, inferred. x-airr: adc-query-support: true - format: controlled_vocabulary reactivity_readout: type: string nullable: false - enum: - - fluorescence_intensity - - barcode_count - description: Reactivity measurement read-out + description: > + Reactivity measurement read-out. For physical assays, this should describe what was measured. For inferred + and annotated methods this should indicate a confidence/quality level for the inference/annotation. In future + versions we anticipate this field being an enumerated type, and it is strongly recommended that users utilize + one of the following keywords in this field if appropriate: fluorescence_intensity, barcode_count, confidence. example: barcode_count x-airr: adc-query-support: true - format: controlled_vocabulary reactivity_value: type: number nullable: false @@ -5462,3 +5495,13 @@ Reactivity: example: read count x-airr: adc-query-support: true + reactivity_ref: + type: array + nullable: true + description: Array of cross references to external epitope reactivity records + title: Epitope reactivity cross-references + items: + type: string + example: ["IEDB_EPITOPE:1616345"] + x-airr: + adc-query-support: true diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml index 5d4097b5..0eec0747 100644 --- a/lang/R/inst/extdata/airr-schema.yaml +++ b/lang/R/inst/extdata/airr-schema.yaml @@ -90,11 +90,19 @@ CURIEMap: IEDB_RECEPTOR: type: identifier default: - map: IEDB - provider: IEDB + map: IEDB_RECEPTOR + provider: IEDB_RECEPTOR map: - IEDB: + IEDB_RECEPTOR: iri_prefix: "https://www.iedb.org/receptor/" + IEDB_EPITOPE: + type: identifier + default: + map: IEDB_EPITOPE + provider: IEDB_EPITOPE + map: + IEDB_EPITOPE: + iri_prefix: "https://www.iedb.org/epitope/" MRO: type: ontology default: @@ -174,9 +182,15 @@ InformationProvider: request: url: "{iri}" response: text/html - IEDB: + IEDB_RECEPTOR: + request: + url: + - 'https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}' + - 'https://query-api.iedb.org/bcr_search?receptor_group_id=eq.{local_id}' + response: application/json + IEDB_EPITOPE: request: - url: "https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}" + url: "https://query-api.iedb.org/epitope_search?structure_id=eq.{local_id}" response: application/json OLS: request: @@ -4402,6 +4416,22 @@ Rearrangement: nullable: true adc-query-support: true identifier: true + reactivity_id: + type: string + description: > + Comma separated list of unique identifiers for Reactivity objects associated with this Rearrangement. + Order and length of reactivity_id and reactivity_ref are independent. + x-airr: + nullable: true + identifier: true + reactivity_ref: + type: string + description: > + Comma separated list of CURIE identifiers of external reactivity records (e.g. IEDB_RECEPTOR:182992, https://www.iedb.org/receptor/182992) + associated with this Rearrangement. Order and length of reactivity_id and reactivity_ref are independent. + example: "IEDB_RECEPTOR:182992, IEDB_RECEPTOR:36336" + x-airr: + nullable: true sample_processing_id: type: string description: > @@ -4968,7 +4998,7 @@ Reactivity: Identifier of the Cell in the context of which the reactivity measurement was conducted. title: Cell ID x-airr: - nullable: false + nullable: true adc-query-support: true repertoire_id: type: string @@ -4997,7 +5027,7 @@ Reactivity: - peptide - non-peptidic description: Classification of ligand binding to the cell - example: non-peptide + example: "MHC:peptide" x-airr: format: controlled_vocabulary nullable: false @@ -5023,8 +5053,8 @@ Reactivity: or by T cell activation after presentation via an MHC molecule. title: Antigen example: - id: UNIPROT:P19597 - label: Circumsporozoite protein + id: UNIPROT:P01308 + label: Insulin x-airr: nullable: false adc-query-support: true @@ -5034,8 +5064,8 @@ Reactivity: description: The species from which the antigen was isolated title: Source species of antigen example: - id: NCBITAXON:5843 - label: Plasmodium falciparum NF54 + id: NCBITAXON:9606 + label: Homo sapiens x-airr: nullable: true adc-query-support: true @@ -5048,11 +5078,13 @@ Reactivity: peptide_start: type: integer description: Start position of the peptide within the reference protein sequence + example: 87 x-airr: nullable: true peptide_end: type: integer description: End position of the peptide within the reference protein sequence + example: 101 x-airr: nullable: true peptide_sequence_aa: @@ -5060,6 +5092,7 @@ Reactivity: 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`. + example: QKRGIVEQCCTSICS x-airr: nullable: true adc-query-support: true @@ -5125,23 +5158,24 @@ Reactivity: adc-query-support: true reactivity_method: type: string - enum: - - native_protein - - MHC_peptide_multimer - description: The methodology used to assess expression (assay implemented in experiment) + description: > + The methodology used to assess/classify reactivity. This should be either the assay utlizied in the experiment, + delineated as "annotated" if annotated from an external source (e.g. IEDB), or inferred if imputed using + a computational method. In future versions we anticipate this field being an enumerated type, and it is strongly + recommended that users utilize one of the following keywords in this field if appropriate: + native_protein, MHC_peptide_multimer, annotated, inferred. x-airr: - format: controlled_vocabulary nullable: false adc-query-support: true reactivity_readout: type: string - enum: - - fluorescence_intensity - - barcode_count - description: Reactivity measurement read-out + description: > + Reactivity measurement read-out. For physical assays, this should describe what was measured. For inferred + and annotated methods this should indicate a confidence/quality level for the inference/annotation. In future + versions we anticipate this field being an enumerated type, and it is strongly recommended that users utilize + one of the following keywords in this field if appropriate: fluorescence_intensity, barcode_count, confidence. example: barcode_count x-airr: - format: controlled_vocabulary nullable: false adc-query-support: true reactivity_value: @@ -5158,3 +5192,13 @@ Reactivity: x-airr: nullable: false adc-query-support: true + reactivity_ref: + type: array + description: Array of cross references to external epitope reactivity records + title: Epitope reactivity cross-references + items: + type: string + example: ["IEDB_EPITOPE:1616345"] + x-airr: + nullable: true + adc-query-support: true diff --git a/lang/python/airr/specs/airr-schema-openapi3.yaml b/lang/python/airr/specs/airr-schema-openapi3.yaml index ff0e5753..f49eebaf 100644 --- a/lang/python/airr/specs/airr-schema-openapi3.yaml +++ b/lang/python/airr/specs/airr-schema-openapi3.yaml @@ -92,11 +92,19 @@ CURIEMap: IEDB_RECEPTOR: type: identifier default: - map: IEDB - provider: IEDB + map: IEDB_RECEPTOR + provider: IEDB_RECEPTOR map: - IEDB: + IEDB_RECEPTOR: iri_prefix: "https://www.iedb.org/receptor/" + IEDB_EPITOPE: + type: identifier + default: + map: IEDB_EPITOPE + provider: IEDB_EPITOPE + map: + IEDB_EPITOPE: + iri_prefix: "https://www.iedb.org/epitope/" MRO: type: ontology default: @@ -176,9 +184,15 @@ InformationProvider: request: url: "{iri}" response: text/html - IEDB: + IEDB_RECEPTOR: + request: + url: + - 'https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}' + - 'https://query-api.iedb.org/bcr_search?receptor_group_id=eq.{local_id}' + response: application/json + IEDB_EPITOPE: request: - url: "https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}" + url: "https://query-api.iedb.org/epitope_search?structure_id=eq.{local_id}" response: application/json OLS: request: @@ -4669,6 +4683,21 @@ Rearrangement: x-airr: adc-query-support: true identifier: true + reactivity_id: + type: string + nullable: true + description: > + Comma separated list of unique identifiers for Reactivity objects associated with this Rearrangement. + Order and length of reactivity_id and reactivity_ref are independent. + x-airr: + identifier: true + reactivity_ref: + type: string + nullable: true + description: > + Comma separated list of CURIE identifiers of external reactivity records (e.g. IEDB_RECEPTOR:182992, https://www.iedb.org/receptor/182992) + associated with this Rearrangement. Order and length of reactivity_id and reactivity_ref are independent. + example: "IEDB_RECEPTOR:182992, IEDB_RECEPTOR:36336" repertoire_id: type: string nullable: true @@ -5270,7 +5299,7 @@ Reactivity: adc-query-support: true cell_id: type: string - nullable: false + nullable: true description: > Identifier of the Cell in the context of which the reactivity measurement was conducted. title: Cell ID @@ -5304,7 +5333,7 @@ Reactivity: - peptide - non-peptidic description: Classification of ligand binding to the cell - example: non-peptide + example: "MHC:peptide" x-airr: format: controlled_vocabulary adc-query-support: true @@ -5330,8 +5359,8 @@ Reactivity: or by T cell activation after presentation via an MHC molecule. title: Antigen example: - id: UNIPROT:P19597 - label: Circumsporozoite protein + id: UNIPROT:P01308 + label: Insulin x-airr: adc-query-support: true format: ontology @@ -5341,8 +5370,8 @@ Reactivity: description: The species from which the antigen was isolated title: Source species of antigen example: - id: NCBITAXON:5843 - label: Plasmodium falciparum NF54 + id: NCBITAXON:9606 + label: Homo sapiens x-airr: adc-query-support: true format: ontology @@ -5354,14 +5383,17 @@ Reactivity: peptide_start: type: integer nullable: true + example: 87 description: Start position of the peptide within the reference protein sequence peptide_end: type: integer nullable: true + example: 101 description: End position of the peptide within the reference protein sequence peptide_sequence_aa: type: string nullable: true + example: QKRGIVEQCCTSICS 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`. @@ -5430,24 +5462,25 @@ Reactivity: reactivity_method: type: string nullable: false - enum: - - native_protein - - MHC_peptide_multimer - description: The methodology used to assess expression (assay implemented in experiment) + description: > + The methodology used to assess/classify reactivity. This should be either the assay utlizied in the experiment, + delineated as "annotated" if annotated from an external source (e.g. IEDB), or inferred if imputed using + a computational method. In future versions we anticipate this field being an enumerated type, and it is strongly + recommended that users utilize one of the following keywords in this field if appropriate: + native_protein, MHC_peptide_multimer, annotated, inferred. x-airr: adc-query-support: true - format: controlled_vocabulary reactivity_readout: type: string nullable: false - enum: - - fluorescence_intensity - - barcode_count - description: Reactivity measurement read-out + description: > + Reactivity measurement read-out. For physical assays, this should describe what was measured. For inferred + and annotated methods this should indicate a confidence/quality level for the inference/annotation. In future + versions we anticipate this field being an enumerated type, and it is strongly recommended that users utilize + one of the following keywords in this field if appropriate: fluorescence_intensity, barcode_count, confidence. example: barcode_count x-airr: adc-query-support: true - format: controlled_vocabulary reactivity_value: type: number nullable: false @@ -5462,3 +5495,13 @@ Reactivity: example: read count x-airr: adc-query-support: true + reactivity_ref: + type: array + nullable: true + description: Array of cross references to external epitope reactivity records + title: Epitope reactivity cross-references + items: + type: string + example: ["IEDB_EPITOPE:1616345"] + x-airr: + adc-query-support: true diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml index 5d4097b5..0eec0747 100644 --- a/lang/python/airr/specs/airr-schema.yaml +++ b/lang/python/airr/specs/airr-schema.yaml @@ -90,11 +90,19 @@ CURIEMap: IEDB_RECEPTOR: type: identifier default: - map: IEDB - provider: IEDB + map: IEDB_RECEPTOR + provider: IEDB_RECEPTOR map: - IEDB: + IEDB_RECEPTOR: iri_prefix: "https://www.iedb.org/receptor/" + IEDB_EPITOPE: + type: identifier + default: + map: IEDB_EPITOPE + provider: IEDB_EPITOPE + map: + IEDB_EPITOPE: + iri_prefix: "https://www.iedb.org/epitope/" MRO: type: ontology default: @@ -174,9 +182,15 @@ InformationProvider: request: url: "{iri}" response: text/html - IEDB: + IEDB_RECEPTOR: + request: + url: + - 'https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}' + - 'https://query-api.iedb.org/bcr_search?receptor_group_id=eq.{local_id}' + response: application/json + IEDB_EPITOPE: request: - url: "https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}" + url: "https://query-api.iedb.org/epitope_search?structure_id=eq.{local_id}" response: application/json OLS: request: @@ -4402,6 +4416,22 @@ Rearrangement: nullable: true adc-query-support: true identifier: true + reactivity_id: + type: string + description: > + Comma separated list of unique identifiers for Reactivity objects associated with this Rearrangement. + Order and length of reactivity_id and reactivity_ref are independent. + x-airr: + nullable: true + identifier: true + reactivity_ref: + type: string + description: > + Comma separated list of CURIE identifiers of external reactivity records (e.g. IEDB_RECEPTOR:182992, https://www.iedb.org/receptor/182992) + associated with this Rearrangement. Order and length of reactivity_id and reactivity_ref are independent. + example: "IEDB_RECEPTOR:182992, IEDB_RECEPTOR:36336" + x-airr: + nullable: true sample_processing_id: type: string description: > @@ -4968,7 +4998,7 @@ Reactivity: Identifier of the Cell in the context of which the reactivity measurement was conducted. title: Cell ID x-airr: - nullable: false + nullable: true adc-query-support: true repertoire_id: type: string @@ -4997,7 +5027,7 @@ Reactivity: - peptide - non-peptidic description: Classification of ligand binding to the cell - example: non-peptide + example: "MHC:peptide" x-airr: format: controlled_vocabulary nullable: false @@ -5023,8 +5053,8 @@ Reactivity: or by T cell activation after presentation via an MHC molecule. title: Antigen example: - id: UNIPROT:P19597 - label: Circumsporozoite protein + id: UNIPROT:P01308 + label: Insulin x-airr: nullable: false adc-query-support: true @@ -5034,8 +5064,8 @@ Reactivity: description: The species from which the antigen was isolated title: Source species of antigen example: - id: NCBITAXON:5843 - label: Plasmodium falciparum NF54 + id: NCBITAXON:9606 + label: Homo sapiens x-airr: nullable: true adc-query-support: true @@ -5048,11 +5078,13 @@ Reactivity: peptide_start: type: integer description: Start position of the peptide within the reference protein sequence + example: 87 x-airr: nullable: true peptide_end: type: integer description: End position of the peptide within the reference protein sequence + example: 101 x-airr: nullable: true peptide_sequence_aa: @@ -5060,6 +5092,7 @@ Reactivity: 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`. + example: QKRGIVEQCCTSICS x-airr: nullable: true adc-query-support: true @@ -5125,23 +5158,24 @@ Reactivity: adc-query-support: true reactivity_method: type: string - enum: - - native_protein - - MHC_peptide_multimer - description: The methodology used to assess expression (assay implemented in experiment) + description: > + The methodology used to assess/classify reactivity. This should be either the assay utlizied in the experiment, + delineated as "annotated" if annotated from an external source (e.g. IEDB), or inferred if imputed using + a computational method. In future versions we anticipate this field being an enumerated type, and it is strongly + recommended that users utilize one of the following keywords in this field if appropriate: + native_protein, MHC_peptide_multimer, annotated, inferred. x-airr: - format: controlled_vocabulary nullable: false adc-query-support: true reactivity_readout: type: string - enum: - - fluorescence_intensity - - barcode_count - description: Reactivity measurement read-out + description: > + Reactivity measurement read-out. For physical assays, this should describe what was measured. For inferred + and annotated methods this should indicate a confidence/quality level for the inference/annotation. In future + versions we anticipate this field being an enumerated type, and it is strongly recommended that users utilize + one of the following keywords in this field if appropriate: fluorescence_intensity, barcode_count, confidence. example: barcode_count x-airr: - format: controlled_vocabulary nullable: false adc-query-support: true reactivity_value: @@ -5158,3 +5192,13 @@ Reactivity: x-airr: nullable: false adc-query-support: true + reactivity_ref: + type: array + description: Array of cross references to external epitope reactivity records + title: Epitope reactivity cross-references + items: + type: string + example: ["IEDB_EPITOPE:1616345"] + x-airr: + nullable: true + adc-query-support: true diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml index ff0e5753..f49eebaf 100644 --- a/specs/airr-schema-openapi3.yaml +++ b/specs/airr-schema-openapi3.yaml @@ -92,11 +92,19 @@ CURIEMap: IEDB_RECEPTOR: type: identifier default: - map: IEDB - provider: IEDB + map: IEDB_RECEPTOR + provider: IEDB_RECEPTOR map: - IEDB: + IEDB_RECEPTOR: iri_prefix: "https://www.iedb.org/receptor/" + IEDB_EPITOPE: + type: identifier + default: + map: IEDB_EPITOPE + provider: IEDB_EPITOPE + map: + IEDB_EPITOPE: + iri_prefix: "https://www.iedb.org/epitope/" MRO: type: ontology default: @@ -176,9 +184,15 @@ InformationProvider: request: url: "{iri}" response: text/html - IEDB: + IEDB_RECEPTOR: + request: + url: + - 'https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}' + - 'https://query-api.iedb.org/bcr_search?receptor_group_id=eq.{local_id}' + response: application/json + IEDB_EPITOPE: request: - url: "https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}" + url: "https://query-api.iedb.org/epitope_search?structure_id=eq.{local_id}" response: application/json OLS: request: @@ -4669,6 +4683,21 @@ Rearrangement: x-airr: adc-query-support: true identifier: true + reactivity_id: + type: string + nullable: true + description: > + Comma separated list of unique identifiers for Reactivity objects associated with this Rearrangement. + Order and length of reactivity_id and reactivity_ref are independent. + x-airr: + identifier: true + reactivity_ref: + type: string + nullable: true + description: > + Comma separated list of CURIE identifiers of external reactivity records (e.g. IEDB_RECEPTOR:182992, https://www.iedb.org/receptor/182992) + associated with this Rearrangement. Order and length of reactivity_id and reactivity_ref are independent. + example: "IEDB_RECEPTOR:182992, IEDB_RECEPTOR:36336" repertoire_id: type: string nullable: true @@ -5270,7 +5299,7 @@ Reactivity: adc-query-support: true cell_id: type: string - nullable: false + nullable: true description: > Identifier of the Cell in the context of which the reactivity measurement was conducted. title: Cell ID @@ -5304,7 +5333,7 @@ Reactivity: - peptide - non-peptidic description: Classification of ligand binding to the cell - example: non-peptide + example: "MHC:peptide" x-airr: format: controlled_vocabulary adc-query-support: true @@ -5330,8 +5359,8 @@ Reactivity: or by T cell activation after presentation via an MHC molecule. title: Antigen example: - id: UNIPROT:P19597 - label: Circumsporozoite protein + id: UNIPROT:P01308 + label: Insulin x-airr: adc-query-support: true format: ontology @@ -5341,8 +5370,8 @@ Reactivity: description: The species from which the antigen was isolated title: Source species of antigen example: - id: NCBITAXON:5843 - label: Plasmodium falciparum NF54 + id: NCBITAXON:9606 + label: Homo sapiens x-airr: adc-query-support: true format: ontology @@ -5354,14 +5383,17 @@ Reactivity: peptide_start: type: integer nullable: true + example: 87 description: Start position of the peptide within the reference protein sequence peptide_end: type: integer nullable: true + example: 101 description: End position of the peptide within the reference protein sequence peptide_sequence_aa: type: string nullable: true + example: QKRGIVEQCCTSICS 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`. @@ -5430,24 +5462,25 @@ Reactivity: reactivity_method: type: string nullable: false - enum: - - native_protein - - MHC_peptide_multimer - description: The methodology used to assess expression (assay implemented in experiment) + description: > + The methodology used to assess/classify reactivity. This should be either the assay utlizied in the experiment, + delineated as "annotated" if annotated from an external source (e.g. IEDB), or inferred if imputed using + a computational method. In future versions we anticipate this field being an enumerated type, and it is strongly + recommended that users utilize one of the following keywords in this field if appropriate: + native_protein, MHC_peptide_multimer, annotated, inferred. x-airr: adc-query-support: true - format: controlled_vocabulary reactivity_readout: type: string nullable: false - enum: - - fluorescence_intensity - - barcode_count - description: Reactivity measurement read-out + description: > + Reactivity measurement read-out. For physical assays, this should describe what was measured. For inferred + and annotated methods this should indicate a confidence/quality level for the inference/annotation. In future + versions we anticipate this field being an enumerated type, and it is strongly recommended that users utilize + one of the following keywords in this field if appropriate: fluorescence_intensity, barcode_count, confidence. example: barcode_count x-airr: adc-query-support: true - format: controlled_vocabulary reactivity_value: type: number nullable: false @@ -5462,3 +5495,13 @@ Reactivity: example: read count x-airr: adc-query-support: true + reactivity_ref: + type: array + nullable: true + description: Array of cross references to external epitope reactivity records + title: Epitope reactivity cross-references + items: + type: string + example: ["IEDB_EPITOPE:1616345"] + x-airr: + adc-query-support: true diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index 5d4097b5..0eec0747 100644 --- a/specs/airr-schema.yaml +++ b/specs/airr-schema.yaml @@ -90,11 +90,19 @@ CURIEMap: IEDB_RECEPTOR: type: identifier default: - map: IEDB - provider: IEDB + map: IEDB_RECEPTOR + provider: IEDB_RECEPTOR map: - IEDB: + IEDB_RECEPTOR: iri_prefix: "https://www.iedb.org/receptor/" + IEDB_EPITOPE: + type: identifier + default: + map: IEDB_EPITOPE + provider: IEDB_EPITOPE + map: + IEDB_EPITOPE: + iri_prefix: "https://www.iedb.org/epitope/" MRO: type: ontology default: @@ -174,9 +182,15 @@ InformationProvider: request: url: "{iri}" response: text/html - IEDB: + IEDB_RECEPTOR: + request: + url: + - 'https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}' + - 'https://query-api.iedb.org/bcr_search?receptor_group_id=eq.{local_id}' + response: application/json + IEDB_EPITOPE: request: - url: "https://query-api.iedb.org/tcr_search?receptor_group_id=eq.{local_id}" + url: "https://query-api.iedb.org/epitope_search?structure_id=eq.{local_id}" response: application/json OLS: request: @@ -4402,6 +4416,22 @@ Rearrangement: nullable: true adc-query-support: true identifier: true + reactivity_id: + type: string + description: > + Comma separated list of unique identifiers for Reactivity objects associated with this Rearrangement. + Order and length of reactivity_id and reactivity_ref are independent. + x-airr: + nullable: true + identifier: true + reactivity_ref: + type: string + description: > + Comma separated list of CURIE identifiers of external reactivity records (e.g. IEDB_RECEPTOR:182992, https://www.iedb.org/receptor/182992) + associated with this Rearrangement. Order and length of reactivity_id and reactivity_ref are independent. + example: "IEDB_RECEPTOR:182992, IEDB_RECEPTOR:36336" + x-airr: + nullable: true sample_processing_id: type: string description: > @@ -4968,7 +4998,7 @@ Reactivity: Identifier of the Cell in the context of which the reactivity measurement was conducted. title: Cell ID x-airr: - nullable: false + nullable: true adc-query-support: true repertoire_id: type: string @@ -4997,7 +5027,7 @@ Reactivity: - peptide - non-peptidic description: Classification of ligand binding to the cell - example: non-peptide + example: "MHC:peptide" x-airr: format: controlled_vocabulary nullable: false @@ -5023,8 +5053,8 @@ Reactivity: or by T cell activation after presentation via an MHC molecule. title: Antigen example: - id: UNIPROT:P19597 - label: Circumsporozoite protein + id: UNIPROT:P01308 + label: Insulin x-airr: nullable: false adc-query-support: true @@ -5034,8 +5064,8 @@ Reactivity: description: The species from which the antigen was isolated title: Source species of antigen example: - id: NCBITAXON:5843 - label: Plasmodium falciparum NF54 + id: NCBITAXON:9606 + label: Homo sapiens x-airr: nullable: true adc-query-support: true @@ -5048,11 +5078,13 @@ Reactivity: peptide_start: type: integer description: Start position of the peptide within the reference protein sequence + example: 87 x-airr: nullable: true peptide_end: type: integer description: End position of the peptide within the reference protein sequence + example: 101 x-airr: nullable: true peptide_sequence_aa: @@ -5060,6 +5092,7 @@ Reactivity: 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`. + example: QKRGIVEQCCTSICS x-airr: nullable: true adc-query-support: true @@ -5125,23 +5158,24 @@ Reactivity: adc-query-support: true reactivity_method: type: string - enum: - - native_protein - - MHC_peptide_multimer - description: The methodology used to assess expression (assay implemented in experiment) + description: > + The methodology used to assess/classify reactivity. This should be either the assay utlizied in the experiment, + delineated as "annotated" if annotated from an external source (e.g. IEDB), or inferred if imputed using + a computational method. In future versions we anticipate this field being an enumerated type, and it is strongly + recommended that users utilize one of the following keywords in this field if appropriate: + native_protein, MHC_peptide_multimer, annotated, inferred. x-airr: - format: controlled_vocabulary nullable: false adc-query-support: true reactivity_readout: type: string - enum: - - fluorescence_intensity - - barcode_count - description: Reactivity measurement read-out + description: > + Reactivity measurement read-out. For physical assays, this should describe what was measured. For inferred + and annotated methods this should indicate a confidence/quality level for the inference/annotation. In future + versions we anticipate this field being an enumerated type, and it is strongly recommended that users utilize + one of the following keywords in this field if appropriate: fluorescence_intensity, barcode_count, confidence. example: barcode_count x-airr: - format: controlled_vocabulary nullable: false adc-query-support: true reactivity_value: @@ -5158,3 +5192,13 @@ Reactivity: x-airr: nullable: false adc-query-support: true + reactivity_ref: + type: array + description: Array of cross references to external epitope reactivity records + title: Epitope reactivity cross-references + items: + type: string + example: ["IEDB_EPITOPE:1616345"] + x-airr: + nullable: true + adc-query-support: true