Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.

Journal: Journal of biomedical semantics
Published Date: Mar 23, 2016

Abstract

BACKGROUND: The Centre for Therapeutic Target Validation (CTTV - https://www.targetvalidation.org/) was established to generate therapeutic target evidence from genome-scale experiments and analyses. CTTV aims to support the validity of therapeutic targets by integrating existing and newly-generated data. Data integration has been achieved in some resources by mapping metadata such as disease and phenotypes to the Experimental Factor Ontology (EFO). Additionally, the relationship between ontology descriptions of rare and common diseases and their phenotypes can offer insights into shared biological mechanisms and potential drug targets. Ontologies are not ideal for representing the sometimes associated type relationship required. This work addresses two challenges; annotation of diverse big data, and representation of complex, sometimes associated relationships between concepts.

Authors

  • Sirarat Sarntivijai
    European Bioinformatics Institute (EMBL-EBI),European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • Drashtti Vasant
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Simon Jupp
    European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK.
  • Gary Saunders
    European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK.
  • A Patrícia Bento
    European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK.
  • Daniel Gonzalez
    European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK.
  • Joanna Betts
    Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; GSK, Medicine Research Centre, Stevenage, SG1 2NY UK.
  • Samiul Hasan
    Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; GSK, Medicine Research Centre, Stevenage, SG1 2NY UK.
  • Gautier Koscielny
    Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; GSK, Medicine Research Centre, Stevenage, SG1 2NY UK.
  • Ian Dunham
    European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK.
  • Helen Parkinson
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • James Malone
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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