Changed cardinality of primary identifier to 1- closes #37

biocaddie · Sep 10, 2016 · 26565c1 · 26565c1
1 parent dbeea90
commit 26565c1
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Showing 31 changed files with 100 additions and 218 deletions.
diff --git a/json-instances/ClinicalTrials.gov-NCT00001372.json b/json-instances/ClinicalTrials.gov-NCT00001372.json
@@ -1,10 +1,8 @@
 {
-  "identifiers": [
-    {
+  "identifier": {
       "identifier": "https://clinicaltrials.gov/show/NCT00001372",
       "identifierSource": "https://clinicaltrials.gov/show/NCT/\\d+"
-    }
-  ],
+   },
   "relatedIdentifiers": [
     {
       "identifier": "940066",
@@ -125,12 +123,10 @@
       ]
     },
     {
-      "identifiers": [
-        {
+      "identifier": {
           "identifier": "7511686",
           "identifierSource": "pubmed"
-        }
-      ],
+      },
       "title": "Autoantigens targeted in systemic lupus erythematosus are clustered in two populations of surface structures on apoptotic keratinocytes.",
       "type" : {
         "value" : "article",
@@ -177,12 +173,10 @@
     "isAboutBiologicalEntity": [
       {
         "name": "Systemic Lupus Erythematosus",
-        "identifiers": [
-          {
+        "identifier": {
             "identifier": "HP_0002725",
             "identifierSource": "hpo"
           }
-        ]
       }
     ],
     "selectionCriteria": [
@@ -265,13 +259,10 @@
 
   "distributions" : [
     {
-      "identifiers":
-      [
-        {
+      "identifier": {
           "identifier" : "1",
           "identifierSource": ""
-        }
-      ],
+      },
       "dates": [
         {
           "date": "1999-11-03",
@@ -294,25 +285,21 @@
       },
       "conformsTo": [
         {
-          "identifiers": [
-            {
+          "identifier": {
               "identifier": "https://clinicaltrials.gov/ct2/html/images/info/public.xsd",
               "identifierSource": ""
-            }
-          ],
+          },
           "name": "XSD",
           "type": {
             "value": "xml schema",
             "valueIRI" : ""
           }
         },
         {
-          "identifiers": [
-            {
+          "identifier": {
               "identifier": "https://clinicaltrials.gov/ct2/html/images/info/public.xsd",
               "identifierSource": ""
-            }
-          ],
+          },
           "name": "XML",
           "type": {
             "value": "format",
@@ -321,12 +308,10 @@
         }
       ],
       "storedIn" : {
-          "identifiers": [
-            {
+          "identifier": {
               "identifier": "https://clinicaltrials.gov/ct2/home",
               "identifierSource": "http"
-            }
-          ],
+          },
           "relatedIdentifiers": [
             {
               "identifier": "https://biosharing.org/biodbcore-000470",

diff --git a/json-instances/PDB-5AEM.json b/json-instances/PDB-5AEM.json
@@ -1,10 +1,9 @@
 {
-  "identifiers": [
-    {
+  "identifier": {
       "identifier": "5AEM",
       "identifierSource": "PDB"
-    },
-    {
+  },
+  "alternateIdentifiers": [ {
       "identifier": "http://identifiers.org/pdb/5AEM",
       "identifierSource": "http://identifiers.org"
     }

diff --git a/json-instances/SBGrid-179.json b/json-instances/SBGrid-179.json
@@ -1,8 +1,6 @@
 {
-	"identifiers":
-	[
-		{"identifier" : "10.15785/SBGRID/179","identifierSource" : "DOI"}
-	],
+	"identifier": { "identifier" : "10.15785/SBGRID/179","identifierSource" : "DOI"},
+
 	"title":"X-Ray Diffraction data from Nup37-Nup120 full-length complex from Schizosaccharomyces pombe, source of 4FHN structure",
 	"types":
 	[
@@ -39,14 +37,14 @@
 			"storedIn":
 			{
 				"name": "Structural Biology Data Grid",
-				"identifiers": [
-					{
-						"identifier": "https://data.sbgrid.org",
-						"identifierSource": "HTTP"
-					},
+				"identifier": {
+					"identifier": "https://data.sbgrid.org",
+					"identifierSource": "HTTP"
+				},
+				"alternateIdentifiers":	[
 					{
-						"identifier": "https://www.biosharing.org/biodbcore-000683",
-						"identifierSource": "BioSharing"
+					"identifier": "https://www.biosharing.org/biodbcore-000683",
+					"identifierSource": "BioSharing"
 					}
 				]
 			}
@@ -59,13 +57,13 @@
 			"storedIn":
 			{
 				"name": "Structural Biology Data Grid",
-				"identifiers": [
-					{
+				"identifier": {
 						"identifier": "https://data.sbgrid.org",
 						"identifierSource": "HTTP"
-					},
+				},
+				"alternateIdentifiers":[
 					{
-						"identifier": "https://www.biosharing.org/biodbcore-000683",
+						"idenfifier": "https://www.biosharing.org/biodbcore-000683",
 						"identifierSource": "BioSharing"
 					}
 				]
@@ -79,11 +77,11 @@
 			"storedIn":
 			{
 				"name": "Structural Biology Data Grid",
-				"identifiers": [
-					{
+				"identifier": {
 						"identifier": "https://data.sbgrid.org",
 						"identifierSource": "HTTP"
-					},
+				},
+				"alternateIdentifiers":[
 					{
 						"identifier": "https://www.biosharing.org/biodbcore-000683",
 						"identifierSource": "BioSharing"
@@ -99,11 +97,11 @@
 			"storedIn":
 			{
 				"name": "Structural Biology Data Grid",
-				"identifiers": [
-					{
+				"identifier": {
 						"identifier": "https://data.sbgrid.org",
 						"identifierSource": "HTTP"
-					},
+				},
+				"alternateIdentifiers":[
 					{
 						"identifier": "https://www.biosharing.org/biodbcore-000683",
 						"identifierSource": "BioSharing"

diff --git a/json-instances/Uniprot-P77967.json b/json-instances/Uniprot-P77967.json
@@ -1,16 +1,14 @@
 {
-  "identifiers":
-  [
-    {
-      "identifier": "P77967",
-      "identifierSource": "uniprot"
-    },
+  "identifier":
+  {
+    "identifier": "P77967",
+    "identifierSource": "uniprot"
+  },
+  "alternateIdentifiers":[
     {
       "identifier": "http://identifiers.org/uniprot/P77967",
       "identifierSource": "http://identifiers.org"
-    }
-  ],
-  "alternateIdentifiers":[
+    },
     {
       "alternateIdentifier": "BA000022",
       "alternateIdentifierSource": "embl"

diff --git a/json-schemas/access_schema.json b/json-schemas/access_schema.json
@@ -6,11 +6,8 @@
   "properties": {
     "@context": { "type": "object"},
     "@type": { "type": "string", "enum": [ "Access" ]},
-    "identifiers": {
-      "type": "array",
-      "items": {
-        "$ref": "identifier_info_schema.json#"
-      }
+    "identifier": {
+      "$ref": "identifier_info_schema.json#"
     },
     "alternateIdentifiers": {
       "type": "array",

diff --git a/json-schemas/activity_schema.json b/json-schemas/activity_schema.json
@@ -6,12 +6,8 @@
   "properties": {
     "@context": { "type": "object"},
     "@type": { "type": "string", "enum": [ "Activity" ]},
-    "identifiers": {
-      "description": "Primary identifiers for the activity.",
-      "type": "array",
-      "items": {
-        "$ref": "identifier_info_schema.json#"
-      }
+    "identifier": {
+      "$ref": "identifier_info_schema.json#"
     },
     "alternateIdentifiers": {
       "description": "Alternate identifiers for the activity.",

diff --git a/json-schemas/alt_identifier_info_schema.json → ...mas/alternate_identifier_info_schema.json b/json-schemas/alt_identifier_info_schema.json → ...mas/alternate_identifier_info_schema.json
@@ -5,13 +5,13 @@
   "type": "object",
   "properties": {
     "@context": { "type": "object"},
-    "@type": { "type": "string", "enum": [ "AlternativeIdentifier" ]},
-    "alternateIdentifier": {
+    "@type": { "type": "string", "enum": [ "AlternateIdentifier" ]},
+    "identifier": {
       "description": "An identifier or identifiers other than the primary Identifier applied to the resource being registered. (definition from DataCite)",
       "type" : "string",
       "format": "uri"
     },
-    "alternateIdentifierSource": {
+    "identifierSource": {
       "description": "The identifier source represents information about the organisation/namespace responsible for minting the identifiers. It must be provided if the identifier is provided.",
       "type" : "string"
     }

diff --git a/json-schemas/anatomical_part_schema.json b/json-schemas/anatomical_part_schema.json
@@ -4,14 +4,10 @@
   "description": "A structure that is part of a multicellular organism.",
   "type": "object",
   "properties": {
-     "@context": { "type": "object"},
-     "@type": { "type": "string", "enum": [ "AnatomicalPart" ]},
-    "identifiers": {
-      "description": "Primary identifiers for the anatomical part.",
-      "type": "array",
-      "items": {
-        "$ref": "identifier_info_schema.json#"
-      }
+    "@context": { "type": "object"},
+    "@type": { "type": "string", "enum": [ "AnatomicalPart" ]},
+    "identifier": {
+      "$ref": "identifier_info_schema.json#"
     },
     "alternateIdentifiers": {
       "description": "Alternate identifiers for the anatomical part.",

diff --git a/json-schemas/biological_entity_schema.json b/json-schemas/biological_entity_schema.json
@@ -5,13 +5,9 @@
   "type": "object",
   "properties": {
     "@context": { "type": "object"},
-     "@type": { "type": "string", "enum": [ "BiologicalEntity" ]},
-    "identifiers": {
-      "description": "Primary identifiers for the biological entity.",
-      "type": "array",
-      "items": {
-        "$ref": "identifier_info_schema.json#"
-      }
+    "@type": { "type": "string", "enum": [ "BiologicalEntity" ]},
+    "identifier": {
+      "$ref": "identifier_info_schema.json#"
     },
     "alternateIdentifiers": {
       "description": "Alternate identifiers for the biological entity.",

diff --git a/json-schemas/data_acquisition_schema.json b/json-schemas/data_acquisition_schema.json
@@ -6,12 +6,8 @@
     "properties": {
         "@context": { "type": "object"},
         "@type": { "type": "string", "enum": [ "DataAcquisition" ]},
-        "identifiers": {
-            "description": "Primary identifiers for the activity.",
-            "type": "array",
-            "items": {
-                "$ref": "identifier_info_schema.json#"
-            }
+        "identifier": {
+            "$ref": "identifier_info_schema.json#"
         },
         "alternateIdentifiers": {
             "description": "Alternate identifiers for the activity.",

diff --git a/json-schemas/data_analysis_schema.json b/json-schemas/data_analysis_schema.json
@@ -6,12 +6,8 @@
   "properties": {
     "@context": { "type": "object"},
     "@type": { "type": "string", "enum": [ "DataAnalysis" ]},
-    "identifiers": {
-      "description": "Primary identifiers for the activity.",
-      "type": "array",
-      "items": {
-        "$ref": "identifier_info_schema.json#"
-      }
+    "identifier": {
+      "$ref": "identifier_info_schema.json#"
     },
     "alternateIdentifiers": {
       "description": "Alternate identifiers for the activity.",

diff --git a/json-schemas/data_repository_schema.json b/json-schemas/data_repository_schema.json
@@ -7,12 +7,8 @@
   "properties": {
     "@context": { "type": "object"},
     "@type": { "type": "string", "enum": [ "DataRepository" ]},
-    "identifiers": {
-      "description": "Primary identifiers for the data repository.",
-      "type": "array",
-      "items": {
-        "$ref": "identifier_info_schema.json#"
-      }
+    "identifier": {
+      "$ref": "identifier_info_schema.json#"
     },
     "alternateIdentifiers": {
       "description": "Alternate identifiers for the data repository.",

diff --git a/json-schemas/data_standard_schema.json b/json-schemas/data_standard_schema.json
@@ -6,12 +6,8 @@
   "properties": {
     "@context": { "type": "object"},
     "@type": { "type": "string", "enum": [ "DataStandard" ]},
-    "identifiers": {
-      "description": "Primary identifiers for the standard.",
-      "type": "array",
-      "items": {
-        "$ref": "identifier_info_schema.json#"
-      }
+    "identifier": {
+      "$ref": "identifier_info_schema.json#"
     },
     "alternateIdentifiers": {
       "description": "Alternate identifiers for the standard.",

diff --git a/json-schemas/dataset_distribution_schema.json b/json-schemas/dataset_distribution_schema.json
@@ -6,12 +6,8 @@
   "properties": {
     "@context": { "type": "object"},
     "@type": { "type": "string", "enum": [ "DatasetDistribution" ]},
-    "identifiers": {
-      "description": "Primary identifiers for the dataset distribution.",
-      "type": "array",
-      "items": {
-        "$ref": "identifier_info_schema.json#"
-      }
+    "identifier": {
+      "$ref": "identifier_info_schema.json#"
     },
     "alternateIdentifiers": {
       "description": "Alternate identifiers for the dataset distribution.",