Merge changes for issue 781 (Reactivity)

lang/R/inst/extdata/airr-schema.yaml

@@ -4403,6 +4403,12 @@ Rearrangement:
                 nullable: true
                 adc-query-support: true
                 identifier: true
+        reactivity_id:
+            type: string
+            description: Unique identifier of reactivity record associated with this Rearrangement.
+            x-airr:
+                nullable: true
+                identifier: true
         sample_processing_id:
             type: string
             description: >
@@ -4738,7 +4744,7 @@ Cell:
 
 # The Expression 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
+# data_processing_id 
 Expression:
     type: object
     required:
@@ -4969,7 +4975,7 @@ 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
@@ -4998,7 +5004,7 @@ 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
@@ -5024,8 +5030,8 @@ 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
@@ -5035,8 +5041,8 @@ 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
@@ -5049,18 +5055,21 @@ 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:
             type: string
             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
@@ -5126,23 +5135,24 @@ 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:
@@ -5159,3 +5169,13 @@ 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

lang/python/airr/specs/airr-schema.yaml

@@ -4403,6 +4403,12 @@ Rearrangement:
                 nullable: true
                 adc-query-support: true
                 identifier: true
+        reactivity_id:
+            type: string
+            description: Unique identifier of reactivity record associated with this Rearrangement.
+            x-airr:
+                nullable: true
+                identifier: true
         sample_processing_id:
             type: string
             description: >
@@ -4738,7 +4744,7 @@ Cell:
 
 # The Expression 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
+# data_processing_id 
 Expression:
     type: object
     required:
@@ -4969,7 +4975,7 @@ 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
@@ -4998,7 +5004,7 @@ 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
@@ -5024,8 +5030,8 @@ 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
@@ -5035,8 +5041,8 @@ 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
@@ -5049,18 +5055,21 @@ 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:
             type: string
             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
@@ -5126,23 +5135,24 @@ 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:
@@ -5159,3 +5169,13 @@ 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

specs/airr-schema-openapi3.yaml

@@ -4669,6 +4669,12 @@ Rearrangement:
             x-airr:
                 adc-query-support: true
                 identifier: true
+        reactivity_id:
+            type: string
+            nullable: true
+            description: Unique identifier of reactivity record associated with this Rearrangement.
+            x-airr:
+                identifier: true
         repertoire_id:
             type: string
             nullable: true
@@ -5270,7 +5276,7 @@ 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 +5310,7 @@ 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 +5336,8 @@ 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 +5347,8 @@ 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 +5360,17 @@ 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 +5439,25 @@ 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 +5472,13 @@ 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