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Version 2. F1000Res. 2013 Feb 1 [revised 2014 Jan 21];2:30. doi: 10.12688/f1000research.2-30.v2. eCollection 2013.

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

Author information

1
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.
2
Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany.
3
ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA.
4
Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA.
5
Department of Computer Science, University of Aberystwyth, Aberystwyth, SY23 2AX, UK.
6
Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
7
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.
8
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.

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/.

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