Xenopus Phenotype Ontology (XPO)
The highest priority at Xenbase is to transform the vast, valuable Xenopus data into human disease discovery. We utilize two key ontologies, the Xenopus Anatomy Ontology (XAO) and Xenopus Phenotype Ontology (XPO), to convert Xenopus anatomical, behavioral, and Gene Ontology (GO) phenotype data from the literature into easily accessible, computer searchable knowledge.
- The XPO is a controlled vocabulary of terms organized in a hierarchical graph structure.
- Each anatomical system (e.g., central nervous system, alimentary/biliary system), tissue and structure
(e.g., neural fold, optic vesicle, heart) and cell types (e.g., ciliated epidermal cell, migrating neural crest cell) have a range of phenotypes including:
- increased number
- decreased number
- abnormal morphology
- abnormal development
- Xenbase curators use the XPO to describe phenotypes of gross morphology and anatomy, at cellular and molecular levels, and aberrant behaviors.
- Phenotypes are curated from a wide range of experiments including gene knockout, knockdown and mutation, effects of toxins, reagents and drugs, and other experimental perturbations and stressors.
- The XPO is constantly being updated in response to the latest published Xenopus research.
- XPO terms also include changes to GO Biological Processes such as increased, decreased or absent cell proliferation or apoptosis in organs and tissues.
Publications about the XPO
- The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development, Fisher ME, Segerdell E, Matentzoglu N, Nenni MJ, Fortriede JD, Chu S, Pells TJ, Osumi-Sutherland D, Chaturvedi P, James-Zorn C, Sundararaj N, Lotay VS, Ponferrada V, Wang DZ, Kim E, Agalakov S, Arshinoff BI, Karimi K, Vize PD, Zorn AM. BMC Bioinformatics, 2022 Mar 22;23(1):99, doi:10.1186/s12859-022-04636-8
Use the XPO to describe your mutants/morphants
Search the XPO for terms you can use in your published research at the Ontology Lookup Service (OLS): https://www.ebi.ac.uk/ols/ontologies/xpo
Request a new XPO term
To request new XPO terms or to discuss appropriate use of XPO terms contact us on GitHub or via email: firstname.lastname@example.org
Download the XPO
The XPO is available to download from Xenbase in either OWL or OBO formats, and also from Open Biomedical Ontologies (OBO Foundry) website.
Other Phenotype Ontologies
- uPheno - Unified Phenotype Ontology (uPheno) is a multispecies phenotype ontology, including amphibians.
- Zebrafish - Zebrafish Phenotype Ontology (ZP)
- Mouse - Mammalian Phenotype Ontology (MP)
- Human - Human Phenotype Ontology (HPO)