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

Gary Schindelman,Carol A Bastiani,Jolene S Fernandes,Paul W Sternberg,Karen Yook

doi:10.1186/1471-2105-12-32

Gary Schindelman, Carol A Bastiani + Show 3 more

Open Access

https://doi.org/10.1186/1471-2105-12-32

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Abstract

BackgroundCaenorhabditis 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.ResultsWe 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.ConclusionsWe 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.

Highlights

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
C. elegans is amenable to various other methods of genetic or physical manipulation, and the phenotypic outcomes of these modifications are useful to discern gene function
The Worm Phenotype Ontology (WPO) was initially aimed at the curation of C. elegans phenotypes, we have extended its application to include phenotypic data from other nematode species

Summary

Introduction

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 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. C. elegans is amenable to various other methods of genetic or physical manipulation, and the phenotypic outcomes of these modifications are useful to discern gene function. These manipulations include transgene overexpression, cell ablation, pharmacological treatment, and genetic mosaic analysis. The phenotypic consequence of multiple modifications within the same strain describes a genetic interaction, instrumental in defining whether genes act in parallel or intersecting genetic pathways [11]

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