Data sources

We collect evidence (E) from various data sources (e.g. Reactome, SLAPenrich, PROGENy, CRISPR, and SysBio) to allow for target identification and prioritisation when using the Open Targets Platform.

To associate targets (T) with diseases (D), we group similar data sources into broader categories called data types:

Evidence data sources

Data type category

Data source

Reference(s)

Genetic associations

Open Targets Genetics Portal

Mountjoy E. et al, 2020

Genetic associations

PheWAS Catalog

Denny, J. et al, 2013

Genetic associations

ClinVar (via EVA)

Cook, C. et al, 2016; Landrum, M. et al, 2017

Genetic associations

Genomics England PanelApp

Martin, A. et al, 2019

Genetic associations

Gene2Phenotype

Thormann, A. et al, 2019

Genetic associations

UniProt

The UniProt Consortium, 2019

Known drugs

ChEMBL

Mendez, D. et al, 2019

Pathways & Sys Bio

Reactome

Jassal, B. et al, 2020

Pathways & Sys Bio

CRISPR (via Project Score)

Behan, F. et al, 2019

Pathways & Sys Bio

SLAPenrich

Iorio, F. et al, 2018

Pathways & Sys Bio

SysBio

Peters, L. A. et al, 2017; Huan, T. et al, 2013; Zhang, B. et al, 2013; Mostafavi, S. et al, 2018

Pathways & Sys Bio

PROGENy

Schubert, M. et al, 2018

RNA expression

Expression Atlas

Papatheodorou, I. et al, 2020

Somatic mutations

Cancer Gene Census

Sondka, Z. et al, 2018

Somatic mutations

intOGen

Martínez-Jiménez, F. et al, 2020

Somatic mutations

UniProt (somatic)

The UniProt Consortium, 2019

Somatic mutations

ClinVar (via EVA)

Cook, C. et al, 2016; Landrum, M. et al, 2017

Literature

Europe PMC

The Europe PMC Consortium, 2015; Kafkas, Ş. et al, 2017

Animal Models

Phenodigm

Smedley, D. et al, 2013

Evidence from an individual data source can contribute to different data types. For example, data from ClinVar from EVA is used as evidence for both Genetic associations and Somatic mutations, depending on whether the evidence is germline or somatic mutation.

Entity annotation data sources

Entity

Annotation data

Data source

Target

Protein, positional, and structural information; functional annotation; Gene Ontology

UniProt

Target

Protein Interactions

OmniPath

Target

Pathways

Reactome

Target

Baseline expression

Expression Atlas; GTEx; Human Protein Atlas

Target

Variants, isoforms, and genomic context

Ensembl

Target

Comparative genomics

Ensembl Compara

Target

Mouse phenotypes

MGI

Target

Cancer hallmarks

Cancer Gene Census

Target

Cancer biomarkers

Cancer Genome Interpreter

Target

Chemical Probes

SGC; Chemical Probes Portal; Open Science Probe Project; Probe Miner

Target

Bibliography

Open Targets LINK

Target

Target tractability

ChEMBL and others

Target

Target safety

HeCaTos, Tox21, eTox, and others

Target

Target Enabling Packages

SGC

Target

Drugs

ChEMBL

Target

CRISPR-Cas9 cancer cell line dependency

Project Score

Target

Protein structure

PDBe

Disease

Description; cross-references; synonyms; ontology and classification

EFO

Disease

Phenotypes

EFO

Disease

Bibliography

Open Targets LINK

Disease

Drugs

ChEMBL

Drug

Molecule information, including structure (if available), modality, withdrawal notice, and mechanism of action

ChEMBL

Drug

Clinical trial information

ChEMBL

Drug

Bibliography

Open Targets LINK