Click here to close Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly. We suggest using a current version of Chrome, FireFox, or Safari.
Summary Download XAO Search Anatomy Search Stages
 

Xenopus Anatomical Ontology

The Xenopus Anatomical Ontology, aka the XAO, describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. Xenbase curators use XAO terms to describe gene expression, and the XAO is constantly being updated in response to the latest published Xenopus research.

The XAO contains 1000's of terms and relationships. Each anatomical system (eg; central nervous system, alimentary/biliary system), tissue and structure (eg; neural fold, mesoderm, blastpore) and many cell types (eg., clilated epidermal cell, migrating neural crest cell) are separate terms; each term is fully defined and related to other terms by is_a, part_of , develops_from and develops_into relationships.

All growth/life cycles stages (eg blastula, gastrula, tadpole) and Nieuwkoop & Faber stages (NF stages) are also XAO terms (e.g., gastrula stages include NF stage 10 to NF stage 12.5). This allows the timing of anatomical development to be indicated by starts_during and ends_during relationships with NF stages.


Tips for using the Xenbase gene expression search tool

Common XAO/anatomy terms are available as check boxes, or you can type in a specific term. The term entry box autofills from available XAO terms and matches synonyms. For example, you can search for 'pronephric kidney' to find all images (ISH and IHC) in the Xenbase database with gene expression in the 'pronephric kidney'. Use the AND/OR buttons and the 'Exclude These Anatomy Terms' option to refine you search results (e.g., genes expressed in the 'pronephric kidney' AND the 'pronephric duct', but NOT expressed in the 'neural tube'). Further refine your gene expression search by limiting results by developmental stage.

View a comprehensive guide to the anatomy portion of the gene expression search here.


Download the XAO

The XAO is available to download from Xenbase in either OWL or OBO formats, and also from the Open Biomedical Ontologies (OBO Foundry)


Publications about the XAO

Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase Journal of Biomedical Semantics (2013) 4:31.Erik Segerdell, Virgilio G Ponferrada, Christina James-Zorn, Kevin A Burns, Joshua D Fortriede, Wasila M Dahdul, Peter D Vize and Aaron M Zorn.

An ontology for Xenopus anatomy and development. BMC Dev Biol (208) 8:92.Erik Segerdell, Bowes JB, Pollet N, and Peter D Vize


Other anatomical ontologies

My Xenbase: [ Log-in / Register ]
version: [3.2.3]


Major funding for Xenbase is provided by the National Institute of Child Health and Human Development, grant P41 HD064556