Are you working on biomedical research, studying associations of human genes with diseases? Or are you trying to identify a biological target for a new therapy? Perhaps you’d like to access drug targets that have been validated by genome-scale experiments and cutting edge analysis? Would you like to have open and free access to all this data?
If you answer yes to any or all of the above, then Open Targets is the project for you.
What we are: Open Targets is a public-private partnership that uses human genetics and genomics data for systematic drug target identification and prioritisation.
Who we are: Open Targets was founded by three global leading institutions in the fields of pharmaceuticals, bioinformatics and genomics, GSK, EMBL-EBI, the Wellcome Sanger Institute, and joined by Biogen in 2016, Takeda in 2017, and Celgene and Sanofi in 2018. We welcome future partnerships with other groups, both in academia and elsewhere. For more details on Open Targets, contact us.
Which methods are we using: Open Targets combines large-scale genomic experiments with objective statistical and computational techniques to identify and validate the causal links between targets, pathways and diseases. Cross-cutting several therapeutic areas, we generate cellular models of disease through gene editing technologies or single cell analysis. In addition to clinical samples, iPS cells and cellular organoids are resourced to provide cellular phenotyping with high physiological relevance.
What data is available: Open Targets integrates comprehensive datasets from a myriad of public databases, such as UniProt, ChEMBL, NHGRI-EBI GWAS, EuropePMC, Cancer Gene Census, among others to calculate, rank and score gene-disease associations. The data and analytical processes are developed by a set of interlinking projects. The latest data sources included in our Platform are Genomics England PanelApp, PheWAS and pathway information in cancer from SLAPenrich and PROGENy. Check our release blog posts for all the details. We also include the Ensembl annotation of alternatively spliced transcripts, RNA baseline expression from GTEx, protein baseline expression from Human Protein Atlas, and protein structure from PDBe (whenever available) for all human genes, e.g. BRAF.
How to access our data: You can use the Open Targets Platform GUI, the REST-API (with our without our Python and unofficial R clients, or get the entire data from our Downloads page. There is plenty of tutorials and webinars on our YouTube channel.
What our users have to say?
"Great platform!" (ICESI Colombia, April 2017).
"Great to see that the challenge of assessing target validation is being addressed - openly presenting an unbiased holistic view of each target and disease linkage is important. This should also include negative and/or conflicting data as well as highlighting what data is missing (as well as a warning, this might also prompt the community to carry out experiments to fill the gaps)" (lifeArc, formerly MRC Technology, June 2017).
"The website look, feel and loading time are awesome" (Perdana University, July 2017).
"A fascinating and ambitious undertaking. Wonderful to learn more. (Certara, October 2017).
"The open target platform is very useful especially for my gene report project. It can sort the disease by related genes and vice versa. It also linked with the evidence like literature. Very user friendly." (UCL Human genetics in Disease MSc course, December 2017).
"Comprehensive one-stop platform for non-programmatic researcher" (University of Cambridge, June 2018).
"Overall found Open Targets very useful; was previously looking separately at NCBI and UniProt to look up individual protein targets (well-studied!) but will use Open Targets from now on." (Structural Genomics Consortium, September 2018).
Get in touch via Twitter, Facebook, LinkedIN or email to know more.
It seems https://github.com/CTTV, as shown in the NAR2016 paper (doi: 10.1093/nar/gkw1055), is unavailable on GitHub now.
The new GitHub for our project is called Open Targets now. There are links to our repo from the Open Targets Platform in every single footer of our pages.