From 90b8e4795038ddbb7e711a1840c25d122092ce53 Mon Sep 17 00:00:00 2001 From: John Erol Evangelista Date: Thu, 2 May 2019 15:40:17 -0400 Subject: [PATCH] Added v1.1 meta schema --- .../entity/{draft-1.json => draft-1.1.json} | 2 +- meta-1.1/entity/ilincs-compound.json | 0 meta-1.1/entity/ilincs-gene.json | 0 .../library/{draft-1.json => draft-1.1.json} | 5 +- meta-1.1/library/ilincs.json | 0 meta-1.1/signature/clue-io.json | 0 meta-1.1/signature/creeds.json | 73 +++++++++++++++---- .../{draft-1.json => draft-1.1.json} | 6 +- meta-1.1/signature/ilincs.json | 0 meta-1.1/signature/l1000-fwd.json | 0 meta-1.1/signature/pert.test.json | 53 +++++++++++++- meta-1.1/signature/perturbation/disease.json | 0 meta-1.1/signature/perturbation/gene.json | 8 ++ meta-1.1/signature/perturbation/other.json | 0 .../signature/perturbation/phenotype.json | 0 .../perturbation/small-molecule.json | 0 16 files changed, 125 insertions(+), 22 deletions(-) rename meta-1.1/entity/{draft-1.json => draft-1.1.json} (98%) mode change 100644 => 100755 mode change 100644 => 100755 meta-1.1/entity/ilincs-compound.json mode change 100644 => 100755 meta-1.1/entity/ilincs-gene.json rename meta-1.1/library/{draft-1.json => draft-1.1.json} (98%) mode change 100644 => 100755 mode change 100644 => 100755 meta-1.1/library/ilincs.json mode change 100644 => 100755 meta-1.1/signature/clue-io.json mode change 100644 => 100755 meta-1.1/signature/creeds.json rename meta-1.1/signature/{draft-1.json => draft-1.1.json} (99%) mode change 100644 => 100755 mode change 100644 => 100755 meta-1.1/signature/ilincs.json mode change 100644 => 100755 meta-1.1/signature/l1000-fwd.json mode change 100644 => 100755 meta-1.1/signature/pert.test.json mode change 100644 => 100755 meta-1.1/signature/perturbation/disease.json mode change 100644 => 100755 meta-1.1/signature/perturbation/gene.json mode change 100644 => 100755 meta-1.1/signature/perturbation/other.json mode change 100644 => 100755 meta-1.1/signature/perturbation/phenotype.json mode change 100644 => 100755 meta-1.1/signature/perturbation/small-molecule.json diff --git a/meta-1.1/entity/draft-1.json b/meta-1.1/entity/draft-1.1.json old mode 100644 new mode 100755 similarity index 98% rename from meta-1.1/entity/draft-1.json rename to meta-1.1/entity/draft-1.1.json index 163c446..bd44023 --- a/meta-1.1/entity/draft-1.json +++ b/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", "$schema": "http://json-schema.org/draft-04/schema#", "allOf": [ { diff --git a/meta-1.1/entity/ilincs-compound.json b/meta-1.1/entity/ilincs-compound.json old mode 100644 new mode 100755 diff --git a/meta-1.1/entity/ilincs-gene.json b/meta-1.1/entity/ilincs-gene.json old mode 100644 new mode 100755 diff --git a/meta-1.1/library/draft-1.json b/meta-1.1/library/draft-1.1.json old mode 100644 new mode 100755 similarity index 98% rename from meta-1.1/library/draft-1.json rename to meta-1.1/library/draft-1.1.json index 0478caa..fa1e348 --- a/meta-1.1/library/draft-1.json +++ b/meta-1.1/library/draft-1.1.json @@ -1,5 +1,5 @@ { - "$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" diff --git a/meta-1.1/library/ilincs.json b/meta-1.1/library/ilincs.json old mode 100644 new mode 100755 diff --git a/meta-1.1/signature/clue-io.json b/meta-1.1/signature/clue-io.json old mode 100644 new mode 100755 diff --git a/meta-1.1/signature/creeds.json b/meta-1.1/signature/creeds.json old mode 100644 new mode 100755 index e1b8d19..7660bf3 --- a/meta-1.1/signature/creeds.json +++ b/meta-1.1/signature/creeds.json @@ -9,10 +9,6 @@ { "type": "object", "properties": { - "cell_type": { - "type": "string", - "example": "Ganglioneuroblastoma" - }, "ctrl_ids": { "type": "array", "items": { @@ -20,6 +16,26 @@ "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", diff --git a/meta-1.1/signature/draft-1.json b/meta-1.1/signature/draft-1.1.json old mode 100644 new mode 100755 similarity index 99% rename from meta-1.1/signature/draft-1.json rename to meta-1.1/signature/draft-1.1.json index 9a00d51..6f3e9f2 --- a/meta-1.1/signature/draft-1.json +++ b/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", "$schema": "http://json-schema.org/draft-04/schema#", "allOf": [ { @@ -308,7 +308,9 @@ "description": "the sex of the sample", "enum": [ "female", - "male" + "male", + "male v female", + "mixed sex" ], "type": "string" }, diff --git a/meta-1.1/signature/ilincs.json b/meta-1.1/signature/ilincs.json old mode 100644 new mode 100755 diff --git a/meta-1.1/signature/l1000-fwd.json b/meta-1.1/signature/l1000-fwd.json old mode 100644 new mode 100755 diff --git a/meta-1.1/signature/pert.test.json b/meta-1.1/signature/pert.test.json old mode 100644 new mode 100755 index cdb8cf2..3f7dfd9 --- a/meta-1.1/signature/pert.test.json +++ b/meta-1.1/signature/pert.test.json @@ -10,7 +10,7 @@ "id": "1", "library": "0", "meta": { - "$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 + } + ] + } } ] } \ No newline at end of file diff --git a/meta-1.1/signature/perturbation/disease.json b/meta-1.1/signature/perturbation/disease.json old mode 100644 new mode 100755 diff --git a/meta-1.1/signature/perturbation/gene.json b/meta-1.1/signature/perturbation/gene.json old mode 100644 new mode 100755 index c4e753e..f1e7381 --- a/meta-1.1/signature/perturbation/gene.json +++ b/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" diff --git a/meta-1.1/signature/perturbation/other.json b/meta-1.1/signature/perturbation/other.json old mode 100644 new mode 100755 diff --git a/meta-1.1/signature/perturbation/phenotype.json b/meta-1.1/signature/perturbation/phenotype.json old mode 100644 new mode 100755 diff --git a/meta-1.1/signature/perturbation/small-molecule.json b/meta-1.1/signature/perturbation/small-molecule.json old mode 100644 new mode 100755