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.
Highlights
The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms
As many forms of human disease are associated with defects in genes involved in the earliest steps of embryonic development, studying the orthologous genes in Xenopus laevis and X. tropicalis as model systems to elucidate the molecular and cellular pathways through which these genes function has grown in strength in recent decades
Upper-level nodes (e.g., ‘compound organ’, ‘organism subdivision’) comprise a structural axis of classification cross-referenced to the Common Anatomy Reference Ontology (CARO) [13], providing interoperability with other model organism anatomy ontologies that use CARO as well as a starting point for classifying Xenopus-specific features
Summary
The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Oocytes and synchronously developing embryos are obtained in large numbers allowing researchers to quickly gather large amounts of data Together these two Xenopus species accelerate our understanding of the mechanisms underlying human health and disease [5], yet a daunting challenge remains: to organize, integrate, and make accessible vast quantities of information as it emerges. Xenbase (http://www.xenbase.org), the Xenopus biology and genomics database [6,7], integrates diverse data from high-throughput screens, scientific literature, and other databases (such as NCBI) into a number of database modules, allowing researchers to investigate specific genes using well-defined terminologies that bridge different kinds of data To this end, the Xenopus Anatomy Ontology (XAO) was developed as a structured, controlled terminology that 1) unites anatomy and development of the vertebrate embryo with the molecular and cellular research findings, 2) enables powerful data searches, and 3) facilitates accurate annotation of research findings. We intended the XAO to be integral to the functionality of Xenbase, and as such the XAO acts as a platform to support automated and manual curation and to power the gene expression search feature
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