Switch references between objects, introduce study_id to ReceptorReac…

…tivity
airr-community · Jan 14, 2024 · 54a63e8 · 54a63e8
1 parent c007313
commit 54a63e8
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Showing 4 changed files with 102 additions and 57 deletions.
diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml
@@ -4266,7 +4266,7 @@ Cell:
             title: Cell-associated rearrangements
             items:
                 type: string
-            example: [id1, id2] #empty vs NULL?
+            example: [id1, id2]
             x-airr:
                 miairr: defined
                 nullable: true
@@ -4279,7 +4279,7 @@ Cell:
             title: Cell-associated receptors
             items:
                 type: string
-            example: [id1, id2] #empty vs NULL?
+            example: [id1, id2]
             x-airr:
                 miairr: defined
                 nullable: true
@@ -4436,7 +4436,7 @@ CellExpression:
                 name: Property value
 
 
-# The Receptor object hold information about a receptor and its reactivity.
+# The Receptor object holds information about a receptor (immunoglobulin or TCR)
 #
 Receptor:
     type: object
@@ -4536,22 +4536,15 @@ Receptor:
             x-airr:
                 nullable: true
                 adc-query-support: true
-        reactivity_measurements:
-            type: array
-            description: >
-                Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Receptor
-            title: Reactivity measurements
-            items:
-                type: string
-            example: [id1, id2]
-            x-airr:
-                nullable: true
-                adc-query-support: true
 
+# The ReceptorReactivity object holds information about the reactivity exhibited by a given receptor
+#
 ReceptorReactivity:
     type: object
     required:
         - receptor_reactivity_id
+        - receptor_hash
+        - study_id
         - ligand_type
         - antigen_type
         - antigen
@@ -4568,6 +4561,25 @@ ReceptorReactivity:
                 identifier: true
                 nullable: false
                 adc-query-support: true
+        receptor_hash:
+            type: string
+            description: >
+                The hash of the receptor that the record refers to, calculated as described for the Receptor.receptor_hash
+                property.
+            title: Receptor hash ID
+            example: aa1c4b77a6f4927611ab39f5267415beaa0ba07a952c233d803b07e52261f026
+            x-airr:
+                nullable: false
+                adc-query-support: true
+        study_id:
+            type: string
+            description: >
+                Identifier of the study in the context of which the reactivity measurement was conducted.
+            title: Study ID
+            example: PRJNA001
+            x-airr:
+                nullable: false
+                adc-query-support: true
         ligand_type:
             type: string
             enum:

diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml
@@ -4266,7 +4266,7 @@ Cell:
             title: Cell-associated rearrangements
             items:
                 type: string
-            example: [id1, id2] #empty vs NULL?
+            example: [id1, id2]
             x-airr:
                 miairr: defined
                 nullable: true
@@ -4279,7 +4279,7 @@ Cell:
             title: Cell-associated receptors
             items:
                 type: string
-            example: [id1, id2] #empty vs NULL?
+            example: [id1, id2]
             x-airr:
                 miairr: defined
                 nullable: true
@@ -4436,7 +4436,7 @@ CellExpression:
                 name: Property value
 
 
-# The Receptor object hold information about a receptor and its reactivity.
+# The Receptor object holds information about a receptor (immunoglobulin or TCR)
 #
 Receptor:
     type: object
@@ -4536,22 +4536,15 @@ Receptor:
             x-airr:
                 nullable: true
                 adc-query-support: true
-        reactivity_measurements:
-            type: array
-            description: >
-                Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Receptor
-            title: Reactivity measurements
-            items:
-                type: string
-            example: [id1, id2]
-            x-airr:
-                nullable: true
-                adc-query-support: true
 
+# The ReceptorReactivity object holds information about the reactivity exhibited by a given receptor
+#
 ReceptorReactivity:
     type: object
     required:
         - receptor_reactivity_id
+        - receptor_hash
+        - study_id
         - ligand_type
         - antigen_type
         - antigen
@@ -4568,6 +4561,25 @@ ReceptorReactivity:
                 identifier: true
                 nullable: false
                 adc-query-support: true
+        receptor_hash:
+            type: string
+            description: >
+                The hash of the receptor that the record refers to, calculated as described for the Receptor.receptor_hash
+                property.
+            title: Receptor hash ID
+            example: aa1c4b77a6f4927611ab39f5267415beaa0ba07a952c233d803b07e52261f026
+            x-airr:
+                nullable: false
+                adc-query-support: true
+        study_id:
+            type: string
+            description: >
+                Identifier of the study in the context of which the reactivity measurement was conducted.
+            title: Study ID
+            example: PRJNA001
+            x-airr:
+                nullable: false
+                adc-query-support: true
         ligand_type:
             type: string
             enum:

diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml
@@ -4560,7 +4560,7 @@ Cell:
             title: Cell-associated rearrangements
             items:
                 type: string
-            example: [id1, id2] #empty vs NULL?
+            example: [id1, id2]
             x-airr:
                 miairr: defined
                 adc-query-support: true
@@ -4573,7 +4573,7 @@ Cell:
             title: Cell-associated receptors
             items:
                 type: string
-            example: [id1, id2] #empty vs NULL?
+            example: [id1, id2]
             x-airr:
                 miairr: defined
                 adc-query-support: true
@@ -4730,7 +4730,7 @@ CellExpression:
                 name: Property value
 
 
-# The Receptor object hold information about a receptor and its reactivity.
+# The Receptor object holds information about a receptor (immunoglobulin or TCR)
 #
 Receptor:
     type: object
@@ -4830,22 +4830,13 @@ Receptor:
             example: ["IEDB_RECEPTOR:10"]
             x-airr:
                 adc-query-support: true
-        reactivity_measurements:
-            type: array
-            nullable: true
-            description: >
-                Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Receptor
-            title: Reactivity measurements
-            items:
-                type: string
-            example: [id1, id2]
-            x-airr:
-                adc-query-support: true
 
 ReceptorReactivity:
     type: object
     required:
         - receptor_reactivity_id
+        - receptor_hash
+        - study_id
         - ligand_type
         - antigen_type
         - antigen
@@ -4862,6 +4853,25 @@ ReceptorReactivity:
             x-airr:
                 identifier: true
                 adc-query-support: true
+        receptor_hash:
+            type: string
+            nullable: false
+            description: >
+                The hash of the receptor that the record refers to, calculated as described for the Receptor.receptor_hash
+                property.
+            title: Receptor hash ID
+            example: aa1c4b77a6f4927611ab39f5267415beaa0ba07a952c233d803b07e52261f026
+            x-airr:
+                adc-query-support: true
+        study_id:
+            type: string
+            nullable: false
+            description: >
+                Identifier of the study in the context of which the reactivity measurement was conducted.
+            title: Study ID
+            example: PRJNA001
+            x-airr:
+                adc-query-support: true
         ligand_type:
             type: string
             nullable: false
@@ -5039,4 +5049,3 @@ ReceptorReactivity:
             example: pg/ml
             x-airr:
                 adc-query-support: true
-
diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml
@@ -4266,7 +4266,7 @@ Cell:
             title: Cell-associated rearrangements
             items:
                 type: string
-            example: [id1, id2] #empty vs NULL?
+            example: [id1, id2]
             x-airr:
                 miairr: defined
                 nullable: true
@@ -4279,7 +4279,7 @@ Cell:
             title: Cell-associated receptors
             items:
                 type: string
-            example: [id1, id2] #empty vs NULL?
+            example: [id1, id2]
             x-airr:
                 miairr: defined
                 nullable: true
@@ -4436,7 +4436,7 @@ CellExpression:
                 name: Property value
 
 
-# The Receptor object hold information about a receptor and its reactivity.
+# The Receptor object holds information about a receptor (immunoglobulin or TCR)
 #
 Receptor:
     type: object
@@ -4536,22 +4536,15 @@ Receptor:
             x-airr:
                 nullable: true
                 adc-query-support: true
-        reactivity_measurements:
-            type: array
-            description: >
-                Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Receptor
-            title: Reactivity measurements
-            items:
-                type: string
-            example: [id1, id2]
-            x-airr:
-                nullable: true
-                adc-query-support: true
 
+# The ReceptorReactivity object holds information about the reactivity exhibited by a given receptor
+#
 ReceptorReactivity:
     type: object
     required:
         - receptor_reactivity_id
+        - receptor_hash
+        - study_id
         - ligand_type
         - antigen_type
         - antigen
@@ -4568,6 +4561,25 @@ ReceptorReactivity:
                 identifier: true
                 nullable: false
                 adc-query-support: true
+        receptor_hash:
+            type: string
+            description: >
+                The hash of the receptor that the record refers to, calculated as described for the Receptor.receptor_hash
+                property.
+            title: Receptor hash ID
+            example: aa1c4b77a6f4927611ab39f5267415beaa0ba07a952c233d803b07e52261f026
+            x-airr:
+                nullable: false
+                adc-query-support: true
+        study_id:
+            type: string
+            description: >
+                Identifier of the study in the context of which the reactivity measurement was conducted.
+            title: Study ID
+            example: PRJNA001
+            x-airr:
+                nullable: false
+                adc-query-support: true
         ligand_type:
             type: string
             enum: