• The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research

    • Joseline Ratnam
    • Grupo BioFarma-USEF, Departamento de Farmacología, Universidade de Santiago de Compostela
    • Barbara Zdrazil
    • Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna
    • Daniela Digles
    • Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna
    • Emiliano Cuadrado-Rodriguez
    • Grupo BioFarma-USEF, Departamento de Farmacología, Universidade de Santiago de Compostela
    • Jean-Marc Neefs
    • Janssen Research & Development
    • Hannah Tipney
    • GSK Medicines Research Centre
    • Ronald Siebes
    • Division of Math. and Computer Science, Faculty of Sciences, Vrije Universiteit
    • Andra Waagmeester
    • Department of Bioinformatics – BiGCaT, Maastricht University
    • Glyn Bradley
    • GSK Medicines Research Centre
    • Chau Han Chau
    • GSK Medicines Research Centre
    • Lars Richter
    • Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna
    • Jose Brea
    • Grupo BioFarma-USEF, Departamento de Farmacología, Universidade de Santiago de Compostela
    • Chris T. Evelo
    • Department of Bioinformatics – BiGCaT, Maastricht University
    • Edgar Jacoby
    • Janssen Research & Development
    • Stefan Senger
    • GSK Medicines Research Centre
    • Maria Isabel Loza
    • Grupo BioFarma-USEF, Departamento de Farmacología, Universidade de Santiago de Compostela
    • Gerhard F. Ecker
    • Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna
    • Christine Chichester
    • CALIPHO Group, Swiss Institute of Bioinformatics
  • Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers used in different resources and the absence of a simple mechanism to link them, gathering and combining relevant, comprehensive information from diverse databases remains a challenge. The Open Pharmacological Concepts Triple Store (Open PHACTS) is an Innovative Medicines Initiative project that uses semantic web technology approaches to enable scientists to easily access and process data from multiple sources to solve real-world drug discovery problems. The project draws together sources of publicly-available pharmacological, physicochemical and biomolecular data, represents it in a stable infrastructure and provides well-defined information exploration and retrieval methods. Here, we highlight the utility of this platform in conjunction with workflow tools to solve pharmacological research questions that require interoperability between target, compound, and pathway data. Use cases presented herein cover 1) the comprehensive identification of chemical matter for a dopamine receptor drug discovery program 2) the identification of compounds active against all targets in the Epidermal growth factor receptor (ErbB) signaling pathway that have a relevance to disease and 3) the evaluation of established targets in the Vitamin D metabolism pathway to aid novel Vitamin D analogue design. The example workflows presented illustrate how the Open PHACTS Discovery Platform can be used to exploit existing knowledge and generate new hypotheses in the process of drug discovery.

  • PDF

  • http://phaidra.univie.ac.at/o:467542

  • Article

  • Published Version

  • PLoS ONE

  • 2014

  • 9

  • 12

  • Public Library of Science (PLoS)

  • English

  • Open access

  • 1932-6203

  • Pharmacology; Vitamin D; Drug discovery; Protein kinases; Database searching; Calcitriol; Drug research and development; Gene ontologies