Target

Overview

A target in the Platform is understood as any naturally-occurring molecule that can be targeted by a medicinal product. EMBL-EBI Ensembl database is used as source for human targets in the Platform, with the Ensembl gene ID as the primary identifier. The criteria for target inclusion is the next:

• Genes from all biotypes encoded in canonical chromosomes

• Genes in alternative assemblies encoding for a reviewed protein product.

This definition accounts for some of the complexities of human targets. Not only protein coding genes can act as targets, as RNAs or pseudogenes are also considered. However, the current definition has some potential drawbacks. Some drug targets are the result of interactions between genes (e.g. gene fusion) or proteins (e.g. protein complexes). The current target entity does not yet consider these cases, which will be addressed in the future.

Target annotation data sources

Annotation data	Data source
Protein, positional, and structural information (ProtVista); Subcellular location; Gene Ontology	UniProt
Molecular interactions	Open Targets
Pathways	Reactome
Baseline expression	Expression Atlas; GTEx; Human Protein Atlas
Comparative genomics	Ensembl Compara
Mouse phenotypes	MGI
Cancer hallmarks	Cancer Gene Census
Chemical Probes	Probes & Drugs
Bibliography	Open Targets
Target tractability	Open Targets
Target safety	ToxCast, AOPWiki, PharmGKB and selected publications
Target Enabling Packages (TEPs)	SGC
Known drugs	ChEMBL
CRISPR-Cas9 cancer cell line dependency	Project Score
Core Gene Essentiality	DepMap Portal
Pharmacogenetics	PharmGKB
Genetic constraint	gnomAD