MAY 25, 2017 10:30 AM PDT

Open Targets Platform: mining gene and disease evidence for improved drug target selection.

Presented at: Lab Automation 2017
Speaker
  • Scientific Outreach Officer - Open Targets, EMBL-EBI
    Biography
      Denise joined EMBL-EBI's Open Targets team in June 2016, where she delivers workshops, provides user support and creates online training materials for the Open Targets projects. Denise holds a PhD in Biochemistry from the Universidade Federal de Minas Gerais, Belo Horizonte, Brazil, and completed her postdoctoral training in Genetics at the Australian National University, Canberra, Australia. Before coming to Open Targets, she worked in Ensembl at EMBL-EBI, at the Wellcome Trust Sanger Institute as a Research Associate in Human Evolution, and as a Senior Computer Biologist in the HAVANA team on the GENCODE, EUCOMM and Pig genome projects.

    Abstract

    Open Targets is a public-private partnership made up of four global leading institutions in the fields of pharmaceuticals, bioinformatics and genomics, GSK, EMBL-EBI, the Wellcome Trust Sanger Institute, and Biogen. We combine large-scale genomic experiments with objective statistical and computational techniques to identify and validate the causal links between targets, pathways and diseases. We have designed and developed the Open Targets Platform, a web application for data integration and visualisation, which supports both target- and disease-centric workflows. Our Platform enables biomedical researchers to discover and prioritise biological targets for new therapies. Targets may be a protein, protein complex or RNA molecule, and we integrate evidence through the target gene. Phenotypes and diseases are integrated through the Experimental Factor Ontology, so that we can include both Mendelian (rare) and common diseases and their phenotypes. We derive evidence of association between a target and a disease from multiple public domain resources, including germline and somatic genetics, known drugs, differential gene expression profiling, reaction pathways, murine genetic models and the scientific literature. We also provide an association score, which takes into account the observed frequency, the experiment confidence, and the likely strength of the effect of the target on the disease. By drawing on expertise in product and platform development including product testing, UX design and site development, we have created this comprehensive and robust data integration for access and visualisation. In addition, programmatic retrieval of data via REST services is also available as well as dumps of our entire datasets. In this talk, I will introduce the Open Targets Consortium and focus on our Open Targets Platform. I will demonstrate how the Platform can be used to visualise and interpret target and disease associations based on the different datasets available.


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