Added v1.1 meta schema

meta-1.1/entity/draft-1.json → meta-1.1/entity/draft-1.1.json

@@ -1,5 +1,5 @@
 {
-  "$id": "/@dcic/signature-commons-schema/meta-1.1/entity/draft-1.json",
+  "$id": "/@dcic/signature-commons-schema/meta-1.1/entity/draft-1.1.json",
   "$schema": "http://json-schema.org/draft-04/schema#",
   "allOf": [
     {

meta-1.1/library/draft-1.json → meta-1.1/library/draft-1.1.json

@@ -1,5 +1,5 @@
 {
-  "$id": "/@dcic/signature-commons-schema/meta-1.1/library/draft-1.json",
+  "$id": "/@dcic/signature-commons-schema/meta-1.1/library/draft-1.1.json",
   "$schema": "http://json-schema.org/draft-04/schema#",
   "allOf": [
     {
@@ -76,7 +76,6 @@
         },
         "Link_to_processing_scripts_on_GitHub": {
           "description": "Link to the script used to process the library",
-          "format": "uri",
           "type": "string"
         },
         "Link_to_resource": {
@@ -142,7 +141,6 @@
         "Access_URL",
         "Assay",
         "Description",
-        "Filename",
         "Icon",
         "Library_created_by",
         "Library_name",
@@ -152,7 +150,6 @@
         "Perturbation_Type",
         "Primary_Resource",
         "Readout",
-        "Spec",
         "Version"
       ],
       "type": "object"

meta-1.1/signature/creeds.json

@@ -9,17 +9,33 @@
     {
       "type": "object",
       "properties": {
-        "cell_type": {
-          "type": "string",
-          "example": "Ganglioneuroblastoma"
-        },
         "ctrl_ids": {
           "type": "array",
           "items": {
             "type": "string",
             "example": "GSM282582"
           }
         },
+        "Cell_Line": {
+          "description": "The cell line context",
+          "items": {
+            "properties": {
+              "Accession": {
+                "description": "Ontology accession",
+                "type": "string"
+              },
+              "Name": {
+                "description": "Official name of cell line",
+                "type": "string"
+              }
+            },
+            "required": [
+              "Name"
+            ],
+            "type": "object"
+          },
+          "type": "array"
+        },
         "curator": {
           "type": "string"
         },
@@ -50,6 +66,10 @@
           "type": "string",
           "example": "GPL570"
         },
+        "umls_cui": {
+          "type": "string",
+          "example": "C0028043"
+        },
         "version": {
           "type": "string",
           "example": "1.0"
@@ -58,25 +78,52 @@
           "$ref": "/@dcic/signature-commons-schema/meta-1.1/signature/perturbation/small-molecule.json",
           "description": "Small Molecule used in the study"
         },
-        "chdir_norm": {
+        "drug_name": {
           "type": "string",
-          "example": "C1=C(C(=O)NC(=O)N1)F"
+          "example": "Fluorouracil"
         },
-        "hs_gene_symbol": {
+        "drugbank_id": {
           "type": "string",
-          "example": "FOX01"
+          "example": "DB00544"
         },
-        "mm_gene_symbol": {
+        "pubchem_cid": {
+          "type": "number",
+          "example": 3385
+        },
+        "smiles": {
           "type": "string",
-          "example": "Foxo1"
+          "example": "C1=C(C(=O)NC(=O)N1)F"
         },
-        "pert_type": {
+        "chdir_norm": {
           "type": "string",
-          "example": "KO"
+          "example": "C1=C(C(=O)NC(=O)N1)F"
+        },
+        "Tissue": {
+          "description": "The tissue context",
+          "items": {
+            "properties": {
+              "Accession": {
+                "description": "Ontology accession",
+                "type": "string"
+              },
+              "Name": {
+                "description": "Name of the tissue",
+                "type": "string"
+              }
+            },
+            "required": [
+              "Name"
+            ],
+            "type": "object"
+          },
+          "type": "array"
+        },
+        "Gene": {
+          "$ref": "/@dcic/signature-commons-schema/meta-1.1/signature/perturbation/gene.json",
+          "description": "Gene involved"
         }
       },
       "required": [
-        "cell_type",
         "ctrl_ids",
         "geo_id",
         "id",

meta-1.1/signature/draft-1.json → meta-1.1/signature/draft-1.1.json

@@ -1,5 +1,5 @@
 {
-  "$id": "/@dcic/signature-commons-schema/meta-1.1/signature/draft-1.json",
+  "$id": "/@dcic/signature-commons-schema/meta-1.1/signature/draft-1.1.json",
   "$schema": "http://json-schema.org/draft-04/schema#",
   "allOf": [
     {
@@ -308,7 +308,9 @@
           "description": "the sex of the sample",
           "enum": [
             "female",
-            "male"
+            "male",
+            "male v female",
+            "mixed sex"
           ],
           "type": "string"
         },

meta-1.1/signature/pert.test.json

@@ -10,7 +10,7 @@
         "id": "1",
         "library": "0",
         "meta": {
-          "$validator": "/@dcic/signature-commons-schema/meta-1.1/signature/draft-1.json",
+          "$validator": "/@dcic/signature-commons-schema/meta-1.1/signature/draft-1.1.json",
           "Perturbation_Type": "gene",
           "Readout" : "mRNA",
           "Number_of_genes": 0,
@@ -40,7 +40,7 @@
         "id": "1",
         "library": "0",
         "meta": {
-          "$validator": "/@dcic/signature-commons-schema/meta-1.1/signature/draft-1.json",
+          "$validator": "/@dcic/signature-commons-schema/meta-1.1/signature/draft-1.1.json",
           "Readout" : "mRNA",
           "Number_of_genes": 0,
           "Perturbation_Type": "gene",
@@ -61,6 +61,55 @@
           }
         ]
       }
+    },
+    {
+      "name": "Signature Creeds (CL)",
+      "valid": true,
+      "schema": "/@dcic/signature-commons-schema/core/signature.json",
+      "data": {
+        "$validator": "/@dcic/signature-commons-schema/core/signature.json",
+        "id": "1",
+        "library": "4",
+        "meta": {
+          "id": "drug:3323",
+          "Tissue": [
+            {
+              "Name": "liver",
+              "Remarks": "Liver *other remarks*",
+              "Accession": "BTO:0000759"
+            }
+          ],
+          "geo_id": "GSE2328",
+          "curator": "cadimo",
+          "version": "1.0",
+          "Organism": "Mus musculus",
+          "ctrl_ids": [
+            "GSM59",
+            "GSM12"
+          ],
+          "pert_ids": [
+            "GSM123",
+            "GSM55",
+            "GSM597"
+          ],
+          "platform": "GPL712",
+          "$validator": "/@dcic/signature-commons-schema/meta-1.1/signature/creeds.json",
+          "Small_Molecule": [
+            {
+              "Name": "Trichloroethylene",
+              "Smiles": "C(=C(Cl)Cl)Cl",
+              "PubChemID": "6575"
+            }
+          ],
+          "Perturbation_Type": "gene; drug; disease"
+        },
+        "entities": [
+          {
+            "entity": "2",
+            "value": 0.1
+          }
+        ]
+      }
     }
   ]
 }

meta-1.1/signature/perturbation/gene.json

@@ -13,6 +13,14 @@
               "description": "The name of the gene",
               "type": "string"
             },
+            "Human_Symbol": {
+              "description": "Human symbol of gene",
+              "type": "string"
+            },
+            "Mouse_Symbol": {
+              "description": "Mouse symbol of gene",
+              "type": "string"
+            },
             "Accession": {
               "description": "The ontology accession of the gene",
               "type": "string"