Worm Phenotype Ontology: Integrating phenotype data within and beyond the <it>C. elegans </it>community

• Main Authors: Yook Karen, Bastiani Carol A, Fernandes Jolene S, Schindelman Gary, Sternberg Paul W
• Format: Article
• Language: English
• Published: BMC 2011-01-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/12/32

<p>Abstract</p> <p>Background</p> <p><it>Caenorhabditis elegans </it>gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then <it>C. elegans </it>has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of <it>C. elegans </it>as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form.</p> <p>Results</p> <p>We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in <it>C. elegans</it>, namely the Worm Phenotype Ontology (WPO). The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 <it>C. elegans </it>genes. The scope of the WPO is not exclusively limited to <it>C. elegans </it>biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor.</p> <p>Conclusions</p> <p>We provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and interoperability across the different Model Organism Databases (MODs) and other biological databases. This standardized phenotype ontology will therefore allow for more complex data queries and enhance bioinformatic analyses.</p>