Document Type
Article
Publication Date
3-17-2025
Publication Title
Genetics
Keywords
JMG, Phenomics, Animals, Phenotype, Humans, Biological Ontologies
JAX Source
Genetics. 2025;229(3):iyaf027.
Volume
229
Issue
3
ISSN
1943-2631
PMID
40048704
DOI
https://doi.org/10.1093/genetics/iyaf027
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 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.
Recommended Citation
Matentzoglu N,
Bello SM,
Stefancsik R,
Alghamdi S,
Anagnostopoulos A,
Balhoff J,
Balk M,
Bradford Y,
Bridges Y,
Callahan T,
Caufield H,
Cuzick A,
Carmody L,
Caron A,
de Souza V,
Engel S,
Fey P,
Fisher M,
Gehrke S,
Grove C,
Hansen P,
Harris N,
Harris M,
Harris L,
Ibrahim A,
Jacobsen J,
Köhler S,
McMurry J,
Munoz-Fuentes V,
Munoz-Torres M,
Parkinson H,
Pendlington Z,
Pilgrim C,
Robb S,
Robinson P,
Seager J,
Segerdell E,
Smedley D,
Sollis E,
Toro S,
Vasilevsky N,
Wood V,
Haendel M,
Mungall C,
McLaughlin J,
Osumi-Sutherland D.
The Unified Phenotype Ontology : a framework for cross-species integrative phenomics. Genetics. 2025;229(3):iyaf027.
Comments
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited