| Title: |
The Unified Phenotype Ontology : a framework for cross-species integrative phenomics |
| Authors: |
Matentzoglu, Nicolas; Bello, Susan M; Stefancsik, Ray; Alghamdi, Sarah M; Anagnostopoulos, Anna V; Balhoff, James P; Balk, Meghan A; Bradford, Yvonne M; Bridges, Yasemin; Callahan, Tiffany J; Caufield, Harry; Cuzick, Alayne; Carmody, Leigh C; Caron, Anita R; de Souza, Vinicius; Engel, Stacia R; Fey, Petra; Fisher, Malcolm; Gehrke, Sarah; Grove, Christian; Hansen, Peter; Harris, Nomi L; Harris, Midori A; Harris, Laura; Ibrahim, Arwa; Jacobsen, Julius O B; Köhler, Sebastian; McMurry, Julie A; Munoz-Fuentes, Violeta; Munoz-Torres, Monica C; Parkinson, Helen; Pendlington, Zoë M; Pilgrim, Clare; Robb, Sofia M C; Robinson, Peter N; Seager, James; Segerdell, Erik; Smedley, Damian; Sollis, Elliot; Toro, Sabrina; Vasilevsky, Nicole; Wood, Valerie; Haendel, Melissa A; Mungall, Christopher J; McLaughlin, James A; Osumi-Sutherland, David |
| Contributors: |
Baryshnikova, A; NIH National Human Genome Research Institute Phenomics First Resource; Center of Excellence in Genomic Science; Office of the Director; National Institutes of Health; Office of Science; Office of Basic Energy Sciences; US Department of Energy; National Human Genome Research Institute; BBSRC Growing Health; Delivering Sustainable Wheat; Gene Ontology Consortium; Alliance of Genome Resources; Dicty database and Stock Center; NICHD; NIH; EMBL-EBI Core Funds; Wellcome Grant; Open Targets; Biogen; Celgene; EMBL-EBI; GSK; Takeda; Sanofi; Wellcome Trust Sanger Institute |
| Source: |
GENETICS ; volume 229, issue 3 ; ISSN 1943-2631 |
| Publisher Information: |
Oxford University Press (OUP) |
| Publication Year: |
2025 |
| Description: |
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 interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1093/genetics/iyaf027 |
| DOI: |
10.1093/genetics/iyaf027/62308580/iyaf027.pdf |
| Availability: |
https://doi.org/10.1093/genetics/iyaf027; https://academic.oup.com/genetics/advance-article-pdf/doi/10.1093/genetics/iyaf027/62308580/iyaf027.pdf; https://academic.oup.com/genetics/article-pdf/229/3/iyaf027/62308580/iyaf027.pdf |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ |
| Accession Number: |
edsbas.EE7E9414 |
| Database: |
BASE |