Abstract
BackgroundThe frogs Xenopus laevis and Xenopus (Silurana) tropicalis are model systems that have produced a wealth of genetic, genomic, and developmental information. Xenbase is a model organism database that provides centralized access to this information, including gene function data from high-throughput screens and the scientific literature. A controlled, structured vocabulary for Xenopus anatomy and development is essential for organizing these data.ResultsWe have constructed a Xenopus anatomical ontology that represents the lineage of tissues and the timing of their development. We have classified many anatomical features in a common framework that has been adopted by several model organism database communities. The ontology is available for download at the Open Biomedical Ontologies Foundry .ConclusionThe Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. We encourage community recommendations for updates and improvements to the ontology.
Highlights
The frogs Xenopus laevis and Xenopus (Silurana) tropicalis are model systems that have produced a wealth of genetic, genomic, and developmental information
The African clawed frog, Xenopus laevis, is a widely used model organism in developmental biology and the related species Xenopus (Silurana) tropicalis has emerged as an important model for genetics
The Xenopus Anatomical Ontology In the Xenopus Anatomical Ontology (XAO) we have described X. laevis anatomy as a controlled, structured vocabulary of the set of structures and tissues that exists throughout development
Summary
The frogs Xenopus laevis and Xenopus (Silurana) tropicalis are model systems that have produced a wealth of genetic, genomic, and developmental information. High throughput screens of gene expression patterns by whole mount in situ hybridization in X. laevis [2,3] and morpholino-based geneknockdown experiments [4,5] have generated a vast set of gene function data. Biomedical ontologies offer distinct advantages for annotating and disseminating biological data, representing areas of knowledge such as gene function, genetic sequence features and anatomy as structured, controlled vocabularies [6] and giving researchers and informaticians the ability to query and communicate across biological and human (page number not for citation purposes)
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