Peer-Reviewed Publication
Genetics2025;229(3)March 17, 2025Journal Article
The Unified Phenotype Ontology : a framework for cross-species integrative phenomics.
Nicolas Matentzoglu1, Susan M Bello2, Ray Stefancsik3, Sarah M Alghamdi4, Anna V Anagnostopoulos2, James P Balhoff5, Meghan A Balk6, Yvonne M Bradford7, Yasemin Bridges8, Tiffany J Callahan9, Harry Caufield10, Alayne Cuzick11, Leigh C Carmody2, Anita R Caron3, Vinicius de Souza3, Stacia R Engel12, Petra Fey13, Malcolm Fisher14, Sarah Gehrke15, Christian Grove16, Peter Hansen17, Nomi L Harris10, Midori A Harris18, Laura Harris3, Arwa Ibrahim3, Julius O B Jacobsen8, Sebastian Köhler19, Julie A McMurry15, Violeta Munoz-Fuentes20, Monica C Munoz-Torres21, Helen Parkinson3, Zoë M Pendlington3, Clare Pilgrim18, Sofia M C Robb22, Peter N Robinson17, James Seager11, Erik Segerdell14, Damian Smedley8, Elliot Sollis3, Sabrina Toro15, Nicole Vasilevsky23, Valerie Wood18, Melissa A Haendel15, Christopher J Mungall10, James A McLaughlin3, David Osumi-Sutherland24
1Semanticly, Ermou 56, Athens, 10563, Attiki, Greece.
2The Jackson Laboratory, Bar Harbor, ME 04609, USA.
3European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK.
4King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, 23955-6900, Saudi Arabia.
5Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA.
6Natural History Museum, University of Oslo, Oslo 0562, Norway.
7The Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
8William Harvey Research Institute, Queen Mary University of London, London, E14 NS, UK.
9Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY 10032, USA.
10Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
11Department of Biointeractions and Crop Protection, Rothamsted Research, West Common, Harpenden, AL52 JQ, UK.
12Department of Genetics, Stanford University, Palo Alto, CA 94304, USA.
13Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
14Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
15Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
16Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
17Universitätsmedizin Berlin, Berlin Institute of Health at Charité, Anna-Louisa-Karsch-Straße 2, Berlin 10178, Germany.
18Department of Biochemistry, University of Cambridge, Cambridge, CB21 TN, UK.
19Ada Health GmbH, Neue Grünstraße 17, Berlin 10179, Germany.
20UNEP-WCMC, Cambridge CB3 0DL, UK.
21Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA.
22Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
23Critical Path Institute, Tucson, AZ 85718, USA.
24Wellcome Sanger Institute, Hinxton, Saffron Walden CB10 1RQ, UK.
Abstract
Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and inter…
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