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:
​Genetic associations​
​Somatic mutations​
​Drugs​
​Pathways & systems biology​
​RNA expression​
​Text mining​
​Animal models​
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
​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​
​
​
​

Last updated 2 months ago

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	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

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