An ontology for Xenopus anatomy and development.
BACKGROUND
The 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.


RESULTS
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.


CONCLUSIONS
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.
Segerdell
Erik
E
Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada. esegerde@ucalgary.ca
Bowes
Jeff B
JB
Pollet
Nicolas
N
Vize
Peter D
PD
D000715:Anatomy; D000818:Animals; D030541:Databases, Genetic; D004625:Embryo, Nonmammalian / Q000033:anatomy & histology* / Q000196:embryology*; D009626:Terminology as Topic; D014982:Xenopus laevis / Q000033:anatomy & histology* / Q000235:genetics / Q000254:growth & development*