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. 2017 Jan 4;45(D1):D985-D994.
doi: 10.1093/nar/gkw1055. Epub 2016 Nov 29.

Open Targets: a platform for therapeutic target identification and validation

Gautier Koscielny  1   2 , Peter An  3   4 , Denise Carvalho-Silva  3   5 , Jennifer A Cham  3   5 , Luca Fumis  3   5 , Rippa Gasparyan  3   4 , Samiul Hasan  3   2 , Nikiforos Karamanis  3   5 , Michael Maguire  3   5 , Eliseo Papa  3   4 , Andrea Pierleoni  3   5 , Miguel Pignatelli  3   5 , Theo Platt  3   4 , Francis Rowland  3   5 , Priyanka Wankar  3   4 , A Patrícia Bento  3   5 , Tony Burdett  3   5 , Antonio Fabregat  3   5 , Simon Forbes  3   6 , Anna Gaulton  3   5 , Cristina Yenyxe Gonzalez  3   5 , Henning Hermjakob  3   5   7 , Anne Hersey  3   5 , Steven Jupe  3   5 , Şenay Kafkas  3   5 , Maria Keays  3   5 , Catherine Leroy  3   5 , Francisco-Javier Lopez  3   5 , Maria Paula Magarinos  3   5 , James Malone  3   5 , Johanna McEntyre  3   5 , Alfonso Munoz-Pomer Fuentes  3   5 , Claire O'Donovan  3   5 , Irene Papatheodorou  3   5 , Helen Parkinson  3   5 , Barbara Palka  3   5 , Justin Paschall  3   5 , Robert Petryszak  3   5 , Naruemon Pratanwanich  3   5 , Sirarat Sarntivijal  3   5 , Gary Saunders  3   5 , Konstantinos Sidiropoulos  3   5 , Thomas Smith  3   5 , Zbyslaw Sondka  3   6 , Oliver Stegle  3   5 , Y Amy Tang  3   5 , Edward Turner  3   5 , Brendan Vaughan  3   5 , Olga Vrousgou  3   5 , Xavier Watkins  3   5 , Maria-Jesus Martin  3   5 , Philippe Sanseau  3   2 , Jessica Vamathevan  5 , Ewan Birney  3   5 , Jeffrey Barrett  3   5   6 , Ian Dunham  8   5
Affiliations

Open Targets: a platform for therapeutic target identification and validation

Gautier Koscielny et al. Nucleic Acids Res. .

Abstract

We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows. The Open Targets Validation Platform is accessible at https://www.targetvalidation.org.

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Figures

Figure 1.
Figure 1.
Workflows of the application. (A) Platform workflow for PDE4D: the user has searched for the gene name ‘PDE4D’ and is presented with all the diseases associated with this gene including asthma. Diseases are presented as ‘bubbles’ grouped into therapeutic areas using their EFO relationships. The size and shade of blue color of each bubble is proportional to the strength of association between the disease and PDE4D. Diseases can also be presented as a table or a tree (based on the EFO (17)) by clicking on the corresponding tabs. Selecting the ‘Respiratory system disease’ filter, displays the diseases in this therapeutic area which are associated with PDE4D. (B) Platform workflow for asthma: conversely, the user can enter the disease term ‘asthma’ and will be presented with all the associated targets for asthma including PDE4D. (C) Evidence for PDE4D in asthma: Clicking on asthma in panel A or on PDE4D in panel B shows the types of evidence which support the association between PDE4D and asthma. The evidence ‘flower’ provides an overview of the strength of the association for each type of evidence. Details of the available evidence are presented as summary tables or graphical displays. For example, the red pin in the gene browser below shows the position of a SNP in PDE4D associated with asthma.
Figure 2.
Figure 2.
Schematic representation of the Open Targets evidence object associating a Target (T) with a disease (D). Evidence (E) is provided as JSON objects according to a JSON schema. Database icons are clockwise from bottom left IntOGen (32), Cancer Gene Census (31), Europe PMC (21), ChEMBL (49), PhenoDigm (50), GWAS Catalog (51), European Variation Archive (http://www.ebi.ac.uk/eva/), Gene2Phenotype (52), UniProt (23), Expression Atlas (53) and Reactome (47). Specific ontology terms have been defined to describe evidence and are part of the Open Targets evidence ontology, included in the experimental factor ontology (EFO).
See this image and copyright information in PMC

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