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An ontology for Xenopus anatomy and development

DOI: 10.1186/1471-213x-8-92

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We 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 http://obofoundry.org webcite.The 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.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 quickly developing embryos of Xenopus, which form a full set of differentiated tissues within days of fertilization, have been described in fine detail [1] and are highly amenable to analysis of embryonic gene function. High throughput screens of gene expression patterns by whole mount in situ hybridization in X. laevis [2,3] and morpholino-based gene-knockdown experiments [4,5] have generated a vast set of gene function data. These data are crucial to ongoing Xenopus research efforts and they complement the gene expression and gene function information that is available for other model systems. Consequentially a need has emerged for a centralized database of Xenopus information, and with it, in order to organize tissue-specific data, a formalized specification of knowledge about Xenopus anatomy throughout the organism's development. 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

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