Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase

Abstract

BackgroundThe African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying human disease. The Xenopus Anatomy Ontology (XAO) reflects the anatomy and embryological development of Xenopus. The XAO provides consistent terminology that can be applied to anatomical feature descriptions along with a set of relationships that indicate how each anatomical entity is related to others in the embryo, tadpole, or adult frog. The XAO is integral to the functionality of Xenbase (http://www.xenbase.org), the Xenopus model organism database.ResultsWe significantly expanded the XAO in the last five years by adding 612 anatomical terms, 2934 relationships between them, 640 synonyms, and 547 ontology cross-references. Each term now has a definition, so database users and curators can be certain they are selecting the correct term when specifying an anatomical entity. With developmental timing information now asserted for every anatomical term, the ontology provides internal checks that ensure high-quality gene expression and phenotype data annotation. The XAO, now with 1313 defined anatomical and developmental stage terms, has been integrated with Xenbase expression and anatomy term searches and it enables links between various data types including images, clones, and publications. Improvements to the XAO structure and anatomical definitions have also enhanced cross-references to anatomy ontologies of other model organisms and humans, providing a bridge between Xenopus data and other vertebrates. The ontology is free and open to all users.ConclusionsThe expanded and improved XAO allows enhanced capture of Xenopus research data and aids mechanisms for performing complex retrieval and analysis of gene expression, phenotypes, and antibodies through text-matching and manual curation. Its comprehensive references to ontologies across taxa help integrate these data for human disease modeling.

Sequence and timing of early cranial skeletal development in Xenopus laevis

“…The sequence of skeletal development does not vary between tadpoles raised at different temperatures. Naming of cartilaginous structures and corresponding abbreviations follow the guidelines of Xenopus Anatomical Ontology (Segerdell, Bowes, Pollet, & Vize, ; Segerdell et al, ) (see als Supporting Information for terminological concordance with earlier publications).…”

“…All tadpoles were initially staged after fixation according to the staging table of Nieuwkoop and Faber (1994 (Segerdell, Bowes, Pollet, & Vize, 2008;Segerdell et al, 2013) (see als Supporting Information for terminological concordance with earlier publications).…”

The gene expression database for mouse development (GXD): Putting developmental expression information at your fingertips

“…Terms from the mouse developmental ontology are also being used to label the EMAP 3D atlas and to describe expression patterns in EMAGE (Armit et al, ). Efforts to establish cross‐references to anatomical ontologies from other model organism and human databases are underway (Mungall et al, ; Dahdul et al, ; Hayamizu et al, ; Segerdell et al, , Costa et al, ; Van Slyke et al, ). This will foster the comparative analysis of expression patterns between model organisms used in developmental research.…”

Flow sensing in developing Xenopus laevis is disrupted by visual cues and ototoxin exposure

“…The colony room was maintained on a 12:12 light/dark cycle at room temperatures of 22-24 °C. We used Nieuwkoop and Faber's (1994) staging system and the labels suggested by Segerdell et al (2013) to classify animals into four developmental groups: premetamorphic , periods of limb bud growth; mean snout-vent length (SVL) 3.7 cm, range 2-5.4 cm]; prometamorphic (stages 55-59, characterized by toe differentiation and rapid hind limb growth; mean SVL 5.5 cm, range 3.2-8 cm); metamorphic climax (stages 60-65, characterized by forelimb growth, resorption of the tail, and narrowing of the 1 3 head; mean SVL 4.4 cm, range 1.5-8 cm); and froglets (1-22 days after completion of metamorphic climax; mean SVL 2.1 cm, range 1.5-3 cm). In Xenopus tadpoles, SVL first increases as the animal progresses toward metamorphosis, but then begins to decrease during metamorphic climax as the tail resorbs.…”