Cloud implementation of Xenbase the Xenopus model organism knowledgebase

Cincinnati Childrens Hosp Med Ctr, Cincinnati OH

Investigators

Linked publications & trials

Abstract

PROJECT SUMMARY Xenbase.org, the Xenopus model organism knowledgebase, is a web accessible resource that integrates the vast and diverse genomic and biological data from Xenopus research. The parent award to this supplement application is 2P41HD064556, 5/13/2021-04/30/2026 (PIs AM Zorn and PD Vize). Our mission is to accelerate the translation of Xenopus research into knowledge that will improve human health. We aim to empower Xenopus research and enhance the impact of Xenopus data in the broader biomedical community. Animal models such as Xenopus are essential for biomedical research and have led to a wealth of discoveries. In this post genomic era with thousands of scientific publications annually and the exponential growth of “omic” datasets, resources such as Xenbase are essential to translate this vast body of data into meaningful biological syntheses. Xenbase is the only central repository for the enormous amount of data generated from research using Xenopus. Our relational database and user-friendly interface allow investigators to quickly interrogate and link different data types in ways that would otherwise be difficult, time consuming, or impossible. Xenbase implements the FAIR data management principles that aim to make data findable, accessible, interoperable and reusable. Xenbase enhances the value of Xenopus data through high quality curation, ontology development, data integration, bioinformatics tools optimized for Xenopus experiments, and by linking Xenopus data to humans and other model organisms. Xenbase plays an indispensable role in making Xenopus data accessible to the broader biomedical community by continually providing annotated data updates to many organizations such as NCBI, UniProt, Ensembl the Alliance of Genome Resources (AGR) and other model organism knowledgebases (MOKs). Xenbase has over 1,800 registered users with ~1 million pageviews a year and ~50 unique visitors per weekday. The goals of the parent grant are to: Aim1 Maintain Xenbase, Curate and Disseminate Xenopus research data Aim 2 Enhance support for Xenopus models of human diseases Aim 3 Enhance Integrated Omics support The goal of this administrative supplement is to migrate Xenbase from a suite of physical virtual machines to a public AWS cloud. We will then perform a series of reiterative tests and improvements to enhance system reliability, performance, security and enhance large-scale data tools.