Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research [v1; ref status: indexed, http://f1000r.es/p5]
Sebastian Köhler,
Sandra C Doelken,
Barbara J Ruef,
Sebastian Bauer,
Nicole Washington,
Monte Westerfield,
George Gkoutos,
Paul Schofield,
Damian Smedley,
Suzanna E Lewis,
Peter N Robinson,
Christopher J Mungall
Affiliations
Sebastian Köhler
Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13352, Germany
Sandra C Doelken
Institute for Medical and Human Genetics, Chairité-Universitatsmedizin Berlin, Berlin, 13353, Germany
Barbara J Ruef
ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
Sebastian Bauer
Institute for Medical and Human Genetics, Chairité-Universitatsmedizin Berlin, Berlin, 13353, Germany
Nicole Washington
Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA
Monte Westerfield
ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
George Gkoutos
Department of Computer Science, University of Aberystwyth, Aberystwyth, SY23 2AX, UK
Paul Schofield
Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
Damian Smedley
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
Suzanna E Lewis
Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA
Peter N Robinson
Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
Christopher J Mungall
Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA
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/.
