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Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

Schindelman, Gary and Fernandes, Jolene S. and Bastiani, Carol A. and Yook, Karen and Sternberg, Paul W. (2011) Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics, 12 . Art. No. 32. ISSN 1471-2105. PMCID PMC3039574. https://resolver.caltech.edu/CaltechAUTHORS:20110222-110252067

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Abstract

Background: Caenorhabditis elegans 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 C. elegans 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 C. elegans 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. Results: We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, 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 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans 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. Conclusions: 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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1186/1471-2105-12-32DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039574/PubMed CentralArticle
ORCID:
AuthorORCID
Yook, Karen0000-0002-4457-6787
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:© 2011 Schindelman et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 12 August 2010 Accepted: 24 January 2011. Published: 24 January 2011. We thank Raymond Lee and Christian Grove for helpful discussions and advice; Igor Antoshechkin for assistance with RNAi phenotype curation tools and advice; Juancarlos Chan for assistance with curation tools for alleles and transgene overexpression; Chris Mungall and Amina Abdullah for the impetus to include equivalences for the WPO; Kris Gunsalus for input on early embryonic lethal phenotype suggestions; Norie de la Cruz for his work on the phenotype ontology search tool and fellow curators at WormBase for their valuable input. We also thank Christian Grove, Ranjana Kishore, Raymond Lee, Chris Mungall, Kimberly Van Auken, Cheryl Van Buskirk, and Xiaodong Wang for comments on the manuscript. Supported by U.S.P.H.S grant P41HG0223 to PWS, an investigator of the Howard Hughes Medical Institute. Authors’ contributions: CAB and PWS initiated this project. CAB, GS, JSF and KY further developed the WPO, namely creating, defining and placing terms in the ontology. JSF and GS generated and maintained the WPO-GO XP ontology. GS, JSF and CAB wrote the paper with valuable discussions and critical contributions at all stages of the project from KY and PWS. All authors read and approved the final manuscript.
Funders:
Funding AgencyGrant Number
NIHP41HG0223
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
PubMed Central ID:PMC3039574
Record Number:CaltechAUTHORS:20110222-110252067
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20110222-110252067
Official Citation:Schindelman et al.: Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics 2011 12:32
Usage Policy:This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
ID Code:22420
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:08 Mar 2011 23:29
Last Modified:29 Oct 2019 20:09

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