Merge pull request #206 from alliance-genome/secondary_ids_update

Secondary IDs update
alliance-genome · May 15, 2023 · 862cff5 · 862cff5
2 parents c3f4af4 + 499ad6b
commit 862cff5
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Showing 10 changed files with 373 additions and 202 deletions.
diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json
diff --git a/model/schema/affectedGenomicModel.yaml b/model/schema/affectedGenomicModel.yaml
@@ -43,6 +43,7 @@ classes:
     slots:
       - name
       - subtype
+      - agm_secondary_ids
       - components
       - sequence_targeting_reagents
       - parental_populations
@@ -54,10 +55,22 @@ classes:
     slots:
       - name
       - subtype_name
+      - agm_secondary_id_dtos
       - reference_curies
       - sequence_targeting_reagent_curies
       - component_dtos
 
+  AgmSecondaryIdSlotAnnotation:
+    is_a: SlotAnnotation
+    slots:
+      - single_agm
+      - secondary_id
+    slot_usage:
+      single_agm:
+        required: true
+      secondary_id:
+        required: true
+
   AffectedGenomicModelComponent:
     is_a: AuditedObject
     description: >-
@@ -86,6 +99,10 @@ slots:
     range: string
     required: true
 
+  single_agm:
+    range: AffectedGenomicModel
+    multivalued: false
+
   subtype:
     description: >-
       Subtype of affected genomic model - permissible values: strain / genotype
@@ -102,6 +119,19 @@ slots:
     range: string
     required: true
 
+  agm_secondary_ids:
+    description: Secondary IDs of a given AGM
+    domain: AffectedGenomicModel
+    range: AgmSecondaryIdSlotAnnotation
+    multivalued: true
+
+  agm_secondary_id_dtos:
+    domain: AffectedGenomicModelDTO
+    range: SecondaryIdSlotAnnotationDTO
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+
   components:
     singular_name: component
     description: >-

diff --git a/model/schema/allele.yaml b/model/schema/allele.yaml
@@ -289,15 +289,12 @@ classes:
         required: true
 
   AlleleSecondaryIdSlotAnnotation:
-    is_a: SlotAnnotation
+    is_a: SecondaryIdSlotAnnotation
     slots:
       - single_allele
-      - secondary_id
     slot_usage:
       single_allele:
         required: true
-      secondary_id:
-        required: true
 
   AlleleSymbolSlotAnnotation:
     description: >-

diff --git a/model/schema/alleleDTO.yaml b/model/schema/alleleDTO.yaml
@@ -170,14 +170,6 @@ classes:
       note_dto:
         required: true
 
-  AlleleSecondaryIdSlotAnnotationDTO:
-    is_a: SlotAnnotationDTO
-    slots:
-      - secondary_id
-    slot_usage:
-      secondary_id:
-        required: true
-
 
 ## ------------
 ## ALLELE DTO ASSOCIATION CLASSES
@@ -376,7 +368,7 @@ slots:
 
   allele_secondary_id_dtos:
     domain: AlleleDTO
-    range: AlleleSecondaryIdSlotAnnotationDTO
+    range: SecondaryIdSlotAnnotationDTO
     multivalued: true
     inlined: true
     inlined_as_list: true

diff --git a/model/schema/core.yaml b/model/schema/core.yaml
@@ -120,14 +120,12 @@ classes:
       RNA transcript translation).
     slots:
       - cross_references
-      - secondary_identifiers
       - genomic_location_associations
 
   GenomicEntityDTO:
     is_a: BiologicalEntityDTO
     slots:
       - cross_reference_dtos
-      - secondary_identifiers
       - genomic_location_association_dtos
 
   Transcript:
@@ -277,6 +275,22 @@ classes:
         any_of:
           - equals_string: systematic_name
 
+  SecondaryIdSlotAnnotation:
+    is_a: SlotAnnotation
+    slots:
+      - secondary_id
+    slot_usage:
+      secondary_id:
+        required: true
+
+  SecondaryIdSlotAnnotationDTO:
+    is_a: SlotAnnotationDTO
+    slots:
+      - secondary_id
+    slot_usage:
+      secondary_id:
+        required: true
+
 
   Association:
     is_a: AuditedObject

diff --git a/model/schema/gene.yaml b/model/schema/gene.yaml
@@ -54,6 +54,7 @@ classes:
       - gene_full_name
       - gene_systematic_name
       - gene_synonyms
+      - gene_secondary_ids
       - related_notes
       - gene_type
       - gene_types_secondary
@@ -91,6 +92,7 @@ classes:
       - gene_full_name_dto
       - gene_systematic_name_dto
       - gene_synonym_dtos
+      - gene_secondary_id_dtos
       - gene_type_curie
 
   GeneSymbolSlotAnnotation:
@@ -119,6 +121,14 @@ classes:
         notes: >-
           permissible_values: full_name (VocabularyTerm)
 
+  GeneSecondaryIdSlotAnnotation:
+    is_a: SecondaryIdSlotAnnotation
+    slots:
+      - single_gene
+    slot_usage:
+      single_gene:
+        required: true
+
   GeneSystematicNameSlotAnnotation:
     is_a: NameSlotAnnotation
     description: >-
@@ -239,6 +249,19 @@ slots:
     required: false
     inlined: true
 
+  gene_secondary_ids:
+    description: Secondary IDs of a given gene
+    domain: Gene
+    range: GeneSecondaryIdSlotAnnotation
+    multivalued: true
+
+  gene_secondary_id_dtos:
+    domain: GeneDTO
+    range: SecondaryIdSlotAnnotationDTO
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+
   gene_systematic_name:
     description: >-
       The one current systematic name for a gene: e.g., YHR084W, R09F10.2.

diff --git a/test/data/agm_test.json b/test/data/agm_test.json
@@ -8,8 +8,14 @@
       "updated_by_curie": "ZFIN",
       "internal": false,
       "name": "TL + MO1-hars",
-      "secondary_identifiers": [
-        "ZFIN:ZDB-FISH-123456-1"
+      "agm_secondary_id_dtos": [
+        {
+          "secondary_id": "ZFIN:ZDB-FISH-123456-1",
+          "evidence_curies": [
+            "PMID:00020012"
+          ],
+          "internal": false
+        }
       ],
       "reference_curies": [],
       "sequence_targeting_reagent_curies": [
@@ -35,8 +41,14 @@
       "updated_by_curie": "ZFIN",
       "internal": false,
       "name": "pax2a<sup>tb21/tb21</sup>",
-      "secondary_identifiers": [
-        "ZFIN:ZDB-FISH-123456-1"
+      "agm_secondary_id_dtos": [
+        {
+          "secondary_id": "ZFIN:ZDB-FISH-123456-1",
+          "evidence_curies": [
+            "PMID:00020012"
+          ],
+          "internal": false
+        }
       ],
       "reference_curies": [],
       "component_dtos": [

diff --git a/test/data/allele_test.json b/test/data/allele_test.json
@@ -39,7 +39,16 @@
           "PMID:01231002"
         ],
         "internal": false
-      }
+      },
+      "allele_secondary_id_dtos": [
+        {
+          "secondary_id": "scnd_id",
+          "evidence_curies": [
+            "PMID:00020012"
+          ],
+          "internal": false
+        }
+      ]
     },
     {
       "curie": "ZFIN:ZDB-ALT-130411-947",

diff --git a/test/data/gene_test.json b/test/data/gene_test.json
@@ -64,6 +64,15 @@
           "internal": false
         }
       ],
+      "gene_secondary_id_dtos": [
+        {
+          "secondary_id": "scnd_id",
+          "evidence_curies": [
+            "PMID:00020012"
+          ],
+          "internal": false
+        }
+      ],
       "cross_reference_dtos": [
         {
           "referenced_curie": "ZFIN:ZDB-GENE-010226-1",

diff --git a/test/data/sqtr_test.json b/test/data/sqtr_test.json
@@ -7,9 +7,6 @@
       "created_by_curie": "ZFIN",
       "updated_by_curie": "ZFIN",
       "internal": false,
-      "secondary_identifiers": [
-        "ZFIN:ZDB-MRPHLNO-123456-1"
-      ],
       "reference_curies": [
         "PMID:19648295"
       ],
@@ -42,9 +39,6 @@
       "created_by_curie": "ZFIN",
       "updated_by_curie": "ZFIN",
       "internal": false,
-      "secondary_identifiers": [
-        "ZFIN:ZDB-MRPHLNO-123456-1"
-      ],
       "reference_curies": [
         "PMID:19648295"
       ]
@@ -66,9 +60,6 @@
       "created_by_curie": "ZFIN",
       "updated_by_curie": "ZFIN",
       "internal": false,
-      "secondary_identifiers": [
-        "ZFIN:ZDB-MRPHLNO-123456-1"
-      ],
       "reference_curies": [
         "PMID:19648295"
       ]