Xenbase: 25 years of integrating molecular and biomedical data from Xenopus

Abstract

The Xenopus model organism knowledgebase, Xenbase (www.xenbase.org), bridges a wide variety of data types including genomes, anatomy, phenotypes, proteins, diseases and more. The goal of Xenbase is to support Xenopus molecular, cell and developmental biology research, to make these data available to the broader biomedical ecosystem, and accelerate the translation of Xenopus research into knowledge that will improve human health. Connections are made between data through relationships in our core data model and via a series of ontologies that serve as graph-based maps that can be traversed in various dimensions to find connections within our vast corpus of data. Data is input by a team of expert curators applying FAIR data management principles and also via automated pipelines and data processing routines. While our main focus is embryonic development and cell biology, these are often the underlying causes of compromised human health and are therefore invaluable for exploring the medical impacts of DNA sequence variants identified through patient exome or whole genome sequencing. One of the foundational elements in Xenbase with our gene-centric data structure is genomes, and we have recently vastly improved the quality of these core resources for both Xenopus laevis and Xenopus tropicalis. These and an extensive suite of other improvements are described, including updates and upgrades in content types, software and systems.