title: Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research.
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 zebrafish that contains classes from the Human Phenotype Ontology, Mammalian Phenotype Ontology, and generated classes for 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/.
authors.affiliation: Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Köhler
authors.affiliation: Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany.
authors.forename: Sandra C
authors.initials: SC
authors.lastname: Doelken
authors.affiliation: ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA.
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Ruef
authors.affiliation: Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bauer
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Washington
authors.affiliation: ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA.
authors.forename: Monte
authors.initials: M
authors.lastname: Westerfield
authors.affiliation: Department of Computer Science, University of Aberystwyth, Aberystwyth, SY23 2AX, UK.
authors.forename: George
authors.initials: G
authors.lastname: Gkoutos
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Schofield
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.
authors.forename: Damian
authors.initials: D
authors.lastname: Smedley
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA.
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
authors.affiliation: Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Robinson
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall