Merge pull request #88 from alliance-genome/da_updates

Minor disease annotation updates
alliance-genome · Feb 22, 2022 · 83b9799 · 83b9799
2 parents fdc73c4 + f46df1a
commit 83b9799
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Showing 8 changed files with 20 additions and 29 deletions.
diff --git a/model/schema/core.yaml b/model/schema/core.yaml
@@ -148,19 +148,19 @@ classes:
   Note:
     description: >-
       Note object for capturing free-text describing some attribute of an entity,
-      coupled with a 'note type', private boolean, and an optional list of
+      coupled with a 'note type', internal boolean, and an optional list of
       references.
     slots:
       - free_text
       - note_type
-      - private
+      - internal
       - references
     slot_usage:
       free_text:
         required: true
       note_type:              # Permissible values currently: disease_summary, disease_note
         required: true
-      private:
+      internal:
         required: true
 
   EntityStatement:
@@ -325,7 +325,7 @@ slots:
       The type of note: e.g., cytology, comment, summary.
     range: VocabularyTerm
 
-  private:
+  internal:
     description: >-
       Classifies the entity as private (for internal use) or not (for public use).
     notes: >-
@@ -475,12 +475,12 @@ slots:
 
   data_provider:
     description: Organization (e.g. MOD) from which the data was sourced
-    multivalued: true
+    multivalued: false
     range: string
 
   secondary_data_provider:
     description: Organization (e.g. MOD) that provided the data directly to the Alliance, but not the original source
-    multivalued: true
+    multivalued: false
     range: string
 
   association_slot:

diff --git a/model/schema/phenotypeAndDiseaseAnnotation.yaml b/model/schema/phenotypeAndDiseaseAnnotation.yaml
@@ -501,6 +501,7 @@ slots:
     range: Allele
 
   disease_qualifiers:
+    multivalued: true
     range: disease_annotation_qualifier_enum
 
   genetic_sex:

diff --git a/test/data/disease_agm_test.json b/test/data/disease_agm_test.json
@@ -5,9 +5,7 @@
         "ECO:0000305"
       ],
       "single_reference": "PMID:0012345",
-      "data_provider": [
-        "ZFIN"
-      ],
+      "data_provider": "ZFIN",
       "object": "DOID:9452",
       "created_by": "ZFIN",
       "modified_by": "ZFIN",

diff --git a/test/data/disease_allele_test.json b/test/data/disease_allele_test.json
@@ -3,7 +3,7 @@
     {
       "evidence_codes": ["ECO:0000305"],
       "single_reference": "PMID:0012345",
-      "data_provider": ["ZFIN"],
+      "data_provider": "ZFIN",
       "subject": "ZFIN:ZDB-ALT-001122-1",
       "predicate": "is_implicated_in",
       "object": "DOID:0001234",

diff --git a/test/data/disease_gene_test.json b/test/data/disease_gene_test.json
@@ -3,7 +3,7 @@
     {
       "evidence_codes": ["ECO:0000305"],
       "single_reference": "PMID:0012345",
-      "data_provider": ["ZFIN"],
+      "data_provider": "ZFIN",
       "object": "DOID:9452",
 	"created_by": "ZFIN",
       "modified_by": "ZFIN",

diff --git a/test/data/fb_disease_test.json b/test/data/fb_disease_test.json
@@ -9,7 +9,7 @@
       "single_reference": "FB:FBrf0227496",
       "annotation_type": "manually_curated",
       "inferred_gene": "FB:FBgn0000047",
-      "data_provider": ["FB"],
+      "data_provider": "FB",
       "created_by": "FB:FB_curator",
       "creation_date": "2022-01-12T09:57:42-05:00",
       "modified_by": "FB:FB_curator",
@@ -25,7 +25,7 @@
       "evidence_codes": ["ECO:0007013"],
       "single_reference": "FB:FBrf0211153",
       "annotation_type": "manually_curated",
-      "data_provider": ["FB"],
+      "data_provider": "FB",
       "created_by": "FB:FB_curator",
       "creation_date": "2022-01-12T09:57:42-05:00",
       "modified_by": "FB:FB_curator",

diff --git a/test/data/invalid/disease_allele_invalid.json b/test/data/invalid/disease_allele_invalid.json
@@ -5,7 +5,7 @@
         "TAS"
       ],
       "single_reference": "PMID:0012345",
-      "data_provider": "ZFIN",
+      "data_provider": ["ZFIN"],
       "subjectTO": "ZFIN:ZDB-ALT-001122-1",
       "predicate": "is model of",
       "object": "DOID:0001234",

diff --git a/test/data/wb_disease_test.json b/test/data/wb_disease_test.json
@@ -13,16 +13,14 @@
           ]
         }
       ],
-      "data_provider": [
-        "WB"
-      ],
+      "data_provider": "WB",
       "created_by": "WB:WBPerson324",
       "date_last_modified": "2021-09-01T00:00:00+00:00",
       "related_notes": [
         {
           "free_text": "summary statement",
           "note_type": "disease_summary",
-          "private": false
+          "internal": false
         }
       ],
       "evidence_codes": [
@@ -53,16 +51,14 @@
           ]
         }
       ],
-      "data_provider": [
-        "WB"
-      ],
+      "data_provider": "WB",
       "created_by": "WB:WBPerson324",
       "date_last_modified": "2021-08-24T00:00:00+00:00",
       "related_notes": [
         {
           "free_text": "summary statement",
           "note_type": "disease_summary",
-          "private": false
+          "internal": false
         }
       ],
       "disease_genetic_modifier": "WB:WBStrain00035193",
@@ -84,9 +80,7 @@
   "disease_agm_ingest_set": [
     {
       "created_by": "WB:WBPerson324",
-      "data_provider": [
-        "WB"
-      ],
+      "data_provider": "WB",
       "date_last_modified": "2019-03-08T00:00:00+00:00",
       "disease_genetic_modifier": "WB:WBVar00250993",
       "disease_genetic_modifier_relation": "exacerbated_by",
@@ -121,15 +115,13 @@
         }
       ],
       "created_by": "WB:WBPerson324",
-      "data_provider": [
-        "WB"
-      ],
+      "data_provider": "WB",
       "date_last_modified": "2017-05-22T00:00:00+00:00",
       "related_notes": [
         {
           "free_text": "Mutations in human dystrophin are associated with the Duchenne and Becker types of muscular dystrophy, that affect skeletal muscles used for movement, and heart (cardiac) muscle; the genetic model for progressive myopathy in C. elegans is a mutant of the elegans dystrophin ortholog, dys-1, combined with a mutation in hlh-1, the MyoD ortholog, (dys-1(cx18);hlh-1(cc561ts), these animals display time-dependent muscle degeneration; a screen of approximately 1000 compounds on the dys-1(cx18),hlh-1(cc561) model, identified several substances that ameliorated the dystrophic phenotype, with the top hits being the sulfonamides, methazolamide (MTZ) and dichlorphenamide (DCPM), known inhibitors of carbonic anydrase (CA) enymes; knock-down of the elegans CA ortholog, cah-4, via RNAi interference, significantly reduced muscle degeneration in the dys-1(cx18),hlh-1(cc561) strain; further, the effects of MTZ and DCPM have been validated in the mdx mouse model for Duchenne muscular dystrophy (DMD).",
           "note_type": "disease_summary",
-          "private": false
+          "internal": false
         }
       ],
       "evidence_codes": [