Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

Authors Organisations
  • Sebastian Köhler(Author)
    Chairité-Universitatsmedizin Berlin
  • Sandra C Doelken(Author)
    Chairité-Universitatsmedizin Berlin
  • Barbara J Ruef(Author)
    University of Oregon
  • Sebastian Bauer(Author)
    Chairité-Universitatsmedizin Berlin
  • Nicole Washington(Author)
    Lawrence Berkeley National Laboratory
  • Monte Westerfield(Author)
    University of Oregon
  • Georgios Gkoutos(Author)
  • Paul Schofield(Author)
    University of Cambridge
  • Damian Smedley(Author)
    Wellcome Trust Sanger Institute
  • Suzanna E Lewis(Author)
    Lawrence Berkeley National Laboratory
  • Peter N Robinson(Author)
    Chairité-Universitatsmedizin Berlin
  • Christopher J Mungall(Author)
    Lawrence Berkeley National Laboratory
Type Article
Original languageEnglish
Article number30
JournalF1000Research
Volume2
DOI
Publication statusPublished - 2013
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Abstract

Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of phenotype information between species. We have generated a cross-species phenotype ontology for human, mouse and zebra fish that contains zebrafish phenotypes. We also provide up-to-date annotation data connecting human genes to phenotype classes from the generated ontology. We have included the data generation pipeline into our continuous integration system ensuring stable and up-to-date releases. This article describes the data generation process and is intended to help interested researchers access both the phenotype annotation data and the associated cross-species phenotype ontology. The resource described here can be used in sophisticated semantic similarity and gene set enrichment analyses for phenotype data across species. The stable releases of this resource can be obtained from http://purl.obolibrary.org/obo/hp/uberpheno/.