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Comparative Study
. 2008 Sep 25:8:92.
doi: 10.1186/1471-213X-8-92.

An ontology for Xenopus anatomy and development

Erik Segerdell  1 , Jeff B Bowes, Nicolas Pollet, Peter D Vize
Affiliations
Comparative Study

An ontology for Xenopus anatomy and development

Erik Segerdell et al. BMC Dev Biol. .

Abstract

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.

Conclusion: 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.

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Figures

Figure 1
Figure 1
A portion of the Xenopus Anatomical Ontology's developmental map. Shown are the anatomical features to which the sensorial layer of the ectoderm gives rise. Types in green boxes have develops_from relationships to their parents. Also shown here are examples of the other two anatomical relationships that are integral to the XAO: ectoderm is_a primary germ layer; and the auditory ossicle, etc., are parts_of the auditory apparatus. The develops_from relationships are transitive: given that the lens develops from the lens placode and the lens placode develops from the sensorial layer, it is implied that the lens develops from the sensorial layer (and more generally from ectoderm). Transitivity operates over is_a relationships as well, e.g. the lens may be inferred to develop from a primary germ layer.
Figure 2
Figure 2
Annotation of X. laevis gene expression in the Phenote tool with the XAO. Images of a Nieuwkoop-Faber stage 25 embryo from the XDB3 in situ gene expression database (top) show pax8 expression in the developing pronephros (arrowheads), information that can easily be captured with the ontology-aware Phenote application. The XAO provides a controlled vocabulary for recording stage and anatomical information in the Phenote interface (drop-down menus, at left), while a separate ontology is used for assertions of evidence; data is recorded in a spreadsheet-like panel (bottom-left). The term viewer at right displays information about the current anatomy selection ("pronephric mesenchyme") including its unique XAO identifier, synonyms and definition, relationships to other types in the ontology, and the stage range during which it exists during development. Related types are hyperlinked to give annotators the ability to rapidly browse the ontology for contextual information or to seek a more appropriate item with which to populate an annotation.
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References

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