The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.

Journal: Mammalian genome : official journal of the International Mammalian Genome Society
Published Date:

Abstract

Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.

Authors

  • Ray Stefancsik
    Samples Phenotypes and Ontologies Team (SPOT), European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • James P Balhoff
    National Evolutionary Synthesis Center, Durham, NC 27705, USA; University of North Carolina, Chapel Hill, NC 27599, USA;
  • Meghan A Balk
    Natural History Museum, University of Oslo, Oslo, Norway.
  • Robyn L Ball
    From the Department of Radiology, Stanford University School of Medicine, Stanford University Medical Center, 725 Welch Rd, Room 1675, Stanford, Calif 94305-5913 (M.C.C., N.M., D.B.L., C.P.L., M.P.L.); Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, Calif (R.L.B., L.Y.); Department of Bioinformatics, University of Utah Medical Center, Salt Lake City, Utah (B.E.C.); and Department of Radiology, Duke University Medical Center, Durham, NC (T.J.A.).
  • Susan M Bello
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
  • Anita R Caron
    Samples Phenotypes and Ontologies Team (SPOT), European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Elissa J Chesler
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
  • Vinicius de Souza
    European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Sarah Gehrke
    Anschutz Medical Campus, University of Colorado, Aurora, CO, 80045, USA.
  • Melissa Haendel
    Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
  • Laura W Harris
    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Nomi L Harris
    Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
  • Arwa Ibrahim
    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Sebastian Koehler
    Ada Health GmbH, Berlin, Germany.
  • Nicolas Matentzoglu
    School of Computer Science, University of Manchester, Oxford Road, Manchester, UK. nicolas.matentzoglu@manchester.ac.uk.
  • Julie A McMurry
    Monarch Initiative, monarchinitiative.org.
  • Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Monica C Munoz-Torres
    Monarch Initiative.
  • Tim Putman
    Anschutz Medical Campus, University of Colorado, Aurora, CO, 80045, USA.
  • Peter Robinson
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
  • Damian Smedley
    School of ITEE, The University of Queensland, St. Lucia, QLD 4072, Australia, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, National Institute of Informatics, Hitotsubashi, Tokyo, Japan, Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK, LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, Genetic Services of Western Australia, King Edward Memorial Hospital, WA 6008, Australia, School of Paediatrics and Child Health, University of Western Australia, WA 6008, Australia, Institute for Immunology and Infectious Diseases, Murdoch University, WA 6150, Australia, Office of Population Health, Public Health and Clinical Services Division, Western Australian Department of Health, WA 6004, Australia, Academic Department of Medical Genetics, Sydney Children's Hospitals Network (Westmead), NSW 2145, Australia, Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, NSW 2006, Australia, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany and Berlin Brandenburg Center for Regenerative Therapies, 13353 Berlin, Germany.
  • Elliot Sollis
    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Anne E Thessen
    Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America.
  • Nicole Vasilevsky
    Library, Oregon Health & Science University, Portland, OR 97239, USA.
  • David O Walton
    The Jackson Laboratory, Bar Harbor, ME, United States of America.
  • David Osumi-Sutherland
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.