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Peer-Reviewed Publication
bioRxiv2024September 22, 2024Journal Article

The Unified Phenotype Ontology (uPheno): 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 Mc 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, Athens, Greece.
2The Jackson Laboratory, Bar Harbor, ME.
3EMBL-EBI, Hinxton, UK.
4King Abdullah University of Science and Technology (KAUST).
5Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC USA.
6Natural History Museum, University of Oslo, Oslo, Norway.
7University of Oregon, Eugene, OR.
8Queen Mary University of London.
9Department of Biomedical Informatics, Columbia University Irving Medical Center.
10Lawrence Berkeley National. Laboratory, Berkeley, CA, USA.
11Rothamsted Research.
12Stanford University, Palo Alto, CA, 94304.
13Northwestern University, Chicago.
14Cincinnati Children's Hospital Medical Center, Cincinnati, OH, US.
15University of North Carolina at Chapel Hill.
16California Institute of Technology, Pasadena, CA 91125.
17Berlin Institute of Health at Charité.
18University of Cambridge.
19Ada Health GmbH.
20UNEP-WCMC.
21University of Colorado Anschutz Medical Campus.
22Stowers Institute for Medical Research.
23Critical Path Institute.
24Wellcome Sanger Institute.
PubMed PMC DOI PDF

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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