Xenbase: Facilitating the use of Xenopus to Model Human Disease
- 1Cincinnati Children's Hospital Medical Center, United States
- 2University of Calgary, Canada
- 3University of Oregon, United States
At a fundamental level most genes, signaling pathways, biological functions and organ systems are highly conserved between man and all vertebrate species. Leveraging this conservation, researchers are increasingly using the experimental advantages of the amphibian Xenopus to model human disease. The online Xenopus resource, Xenbase, enables human disease modeling by curating the Xenopus literature published in PubMed and integrating these Xenopus data with orthologous human genes, anatomy, and more recently with links to the Online Mendelian Inheritance in Man resource (OMIM) and the Human Disease Ontology (DO). Here we review how Xenbase supports disease modeling and report on a meta-analysis of the published Xenopus research providing an overview of the different types of diseases being modeled in Xenopus and the variety of experimental approaches being used. Text mining of over 50,000 Xenopus research articles imported into Xenbase from PubMed identified approximately 1,000 putative disease- modeling articles. These articles were manually assessed and annotated with disease ontologies, which were then used to classify papers based on disease type. We found that Xenopus is being used to study a diverse array of disease with three main experimental approaches: cell-free egg extracts to study fundamental aspects of cellular and molecular biology, oocytes to study ion transport and channel physiology and embryo experiments focused on congenital diseases. We integrated these data into Xenbase Disease Pages to allow easy navigation to disease information on external databases. Results of this analysis will equip Xenopus researchers with a suite of experimental approaches available to model or dissect a pathological process. Ideally clinicians and basic researchers will use this information to foster collaborations necessary to interrogate the development and treatment of human diseases.
Keywords: Xenopus, Xenbase, model organism database, ontologies, oocyte, cell-free egg extract, Human Disease
Received: 06 Nov 2018;
Accepted: 08 Feb 2019.
Edited by:John N. Griffin, Duke University, United States
Reviewed by:Anne H. Monsoro-Burq, Université Paris-Sud, France
Emily K. Mis, School of Medicine, Yale University, United States
Radek Sindelka, Institute of Biotechnology (ASCR), Czechia
Jose G. Abreu, Federal University of Rio de Janeiro, Brazil
Copyright: © 2019 Nenni, Fisher, James-Zorn, Pells, Ponferrada, Chu, Fortriede, Burns, Wang, Lotay, Wang, Segerdell, Chaturvedi, Karimi, Vize and Zorn. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
PhD. Mardi J. Nenni, Cincinnati Children's Hospital Medical Center, Cincinnati, United States, firstname.lastname@example.org
PhD. Malcolm E. Fisher, Cincinnati Children's Hospital Medical Center, Cincinnati, United States, Malcolm.Fisher@cchmc.org
PhD. Aaron M. Zorn, Cincinnati Children's Hospital Medical Center, Cincinnati, United States, email@example.com