Xenbase is taking an innovative approach to curate and display phenotypes in Xenopus. Our goal is to make a simple, easy to use interface for researchers to quickly find all relevant phenotypic data on Xenbase. We also want clinicians and non-model organism scientists to be able to find Xenopus phenotypes that relate to and/or phenocopy human disease conditions.
A bit of background on phenotypes:
Xenbase is collecting are 3 different types of phenotypic data:
1. Anatomical phenotypes- such as an abnormal tissue, organ or system.
2. GO phenotypes - abnormal molecular function, biological process or cellular component.
3. Gene expression phenotypes, known as 'Expression as Phenotype', or EaP, where the knock-down, knock-out or overexpression of one gene affects the observable expression of another gene.
For anatomical phenotypes and GO phenotypes, we are developing a Xenopus Phenotype Ontology, the XPO for short, to describe phenotypes arising from a wide range of experimental manipulations and disease modeling. The XPO uses easy to understand anatomy-based and GO term-based phrases (eg. abnormal eye development) as well as clinical terms (e.,g microphthalmia).
EaP statements describe whether expression of 'gene X' is seen in an increased or decreased amount in a tissue or embryo (e.g., pax6 increased amount [in the] retina). EaP phenotypes can be observed in WISH assays or captured from RNA-Seq assays (typically generating a long list of up and down-regulated genes in a tissue or whole embryo). EaP data is informative for pathway and gene regulatory network studies.
This survey will help us understand how you, the Xenopus researcher, would search for phenotypes on Xenbase, and how you might want that data displayed.