From eec8f33e4bfc401f3d2e8b94c092174a7ea37e96 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Irene=20L=C3=B3pez?= <45119610+ireneisdoomed@users.noreply.github.com> Date: Thu, 16 Jun 2022 17:03:59 +0100 Subject: [PATCH 1/5] Burden: Remove `literature` from required field The publication supporting Genebass associations hasn't been peer reviewed yet, therefore we don't have a suitable ID for it. As discussed, we want to include an additional field in the schema to accommodate PPR IDs - especially to get EPMC evidence, however we don't want to do this right now as it would imply changes in the API and so on. So for the time being, Genebass evidence will only be referenced with a linkout to their app and not with a publication. --- opentargets.json | 1 - 1 file changed, 1 deletion(-) diff --git a/opentargets.json b/opentargets.json index 2e21ac0..e199b52 100644 --- a/opentargets.json +++ b/opentargets.json @@ -678,7 +678,6 @@ }, "required": [ "datasourceId", - "literature", "pValueMantissa", "resourceScore", "statisticalMethod", From a731bcc1bc35c883bd986c83adb0451461c2fb67 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Irene=20L=C3=B3pez?= <45119610+ireneisdoomed@users.noreply.github.com> Date: Thu, 16 Jun 2022 17:43:15 +0100 Subject: [PATCH 2/5] Add `diseaseFromSourceId` to the gene_burden schema To accommodate the Phenocodes --- opentargets.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/opentargets.json b/opentargets.json index e199b52..33c3af1 100644 --- a/opentargets.json +++ b/opentargets.json @@ -627,6 +627,9 @@ "diseaseFromSource": { "$ref": "#/definitions/diseaseFromSource" }, + "diseaseFromSourceId": { + "$ref": "#/definitions/diseaseFromSourceId" + }, "diseaseFromSourceMappedId": { "$ref": "#/definitions/diseaseFromSourceMappedId" }, From fe854292a588a6d923e042b9654ce26543f60a86 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Irene=20L=C3=B3pez?= <45119610+ireneisdoomed@users.noreply.github.com> Date: Thu, 21 Jul 2022 19:46:19 +0200 Subject: [PATCH 3/5] Remove `inchiKey` from the probes schema After discussion, we've decided to drop the field referring to the inchikey from the definition of a chemical probe. This is primarily used to being able to map from a probe to a ChEMBL ID. The reason for the drop is that it was introducing some bugs when for the same probe we had a row with an inchikey and another one without. This is the case for Talazoparib, a probe of PARP1. The data was not being aggregated because of this discrepancy, leading to [duplicated rows in the FE](https://platform.opentargets.org/target/ENSG00000143799). ``` { "id": "TALAZOPARIB", "control": null, "drugId": null, "isHighQuality": false, "mechanismOfAction": [ "inhibitor" ], "origin": [ "calculated", "experimental" ], "probeMinerScore": null, "probesDrugScore": null, "scoreInCells": null, "scoreInOrganisms": null, "targetFromSourceId": "P09874", "urls": [ { "niceName": "Chemical Probes.org (legacy)", "url": "https://new.chemicalprobes.org/?q=TALAZOPARIB" } ] }, { "id": "TALAZOPARIB", "control": null, "drugId": "CHEMBL3137320", "isHighQuality": true, "mechanismOfAction": [ "inhibitor" ], "origin": [ "experimental" ], "probeMinerScore": "53.0", "probesDrugScore": null, "scoreInCells": "83.25", "scoreInOrganisms": "91.75", "targetFromSourceId": "P09874", "urls": [ { "niceName": "Probes & Drugs Portal", "url": "https://www.probes-drugs.org" } ] }, ``` --- opentargets_chemical_probe.json | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/opentargets_chemical_probe.json b/opentargets_chemical_probe.json index 355ca75..c34bfec 100644 --- a/opentargets_chemical_probe.json +++ b/opentargets_chemical_probe.json @@ -23,11 +23,6 @@ "examples": ["CHEMBL1651534"], "type": "string" }, - "inchiKey": { - "description": "ID that identifies the probe.", - "examples": ["JGRPKOGHYBAVMW-UHFFFAOYSA-N"], - "type": "string" - }, "urls": { "type": "array", "items": { @@ -89,7 +84,6 @@ "required": [ "targetFromSourceId", "id", - "inchiKey", "urls", "isHighQuality", "origin" @@ -112,4 +106,4 @@ "additionalProperties": false } } - } \ No newline at end of file + } From b529809d16d4bec86b030076605f9d36a7c639d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Irene=20L=C3=B3pez?= <45119610+ireneisdoomed@users.noreply.github.com> Date: Thu, 11 Aug 2022 16:43:01 +0100 Subject: [PATCH 4/5] Add `publicationYear` to the EPMC evidence This field is always present in EPMC evidence. --- opentargets.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/opentargets.json b/opentargets.json index 33c3af1..80e3b5c 100644 --- a/opentargets.json +++ b/opentargets.json @@ -334,6 +334,9 @@ "literature": { "$ref": "#/definitions/literature" }, + "publicationYear": { + "$ref": "#/definitions/publicationYear" + }, "resourceScore": { "$ref": "#/definitions/resourceScore" }, @@ -350,6 +353,7 @@ "required": [ "datasourceId", "diseaseFromSourceMappedId", + "publicationYear", "resourceScore", "targetFromSourceId", "textMiningSentences" From eb7b0e6d772ef1c835a9b9066a3803f1c59b7c26 Mon Sep 17 00:00:00 2001 From: Daniel Suveges Date: Thu, 25 Aug 2022 10:02:41 +0100 Subject: [PATCH 5/5] Adding new clinical significance terms. --- opentargets.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/opentargets.json b/opentargets.json index 80e3b5c..44fb088 100644 --- a/opentargets.json +++ b/opentargets.json @@ -1565,14 +1565,17 @@ "conflicting data from submitters", "conflicting interpretations of pathogenicity", "drug response", + "established risk allele", "likely benign", "likely risk allele", "likely pathogenic", + "low penetrance", "not provided", "other", "pathogenic", "protective", "risk factor", + "uncertain risk allele", "uncertain significance" ] },