Xenbase joins the Alliance of Genome Resources

Alliance of Genome Resources

The Alliance is pleased to announce the release of Xenopus data from Xenbase. These amphibians are an important tetrapod model, spanning the evolutionary gap between the mammalian (human, mouse, and rat) and zebrafish data already included in the Alliance. Xenopus have long been used in developmental and cell biology, and two species are widely studied. The African clawed frog, X. laevis (abbreviated Xla in the Alliance) is an allotetraploid (2n = 36) of hybrid origin. The resulting X. laevis genome has a set of ‘long’ and ‘short’ chromosomes and gene symbols are therefore appended with ‘.L’ or ‘.S’ denoting on which chromosome pair they reside. The second Xenopus species, the Western clawed frog X. tropicalis (Xtr), is a conventional diploid (2n=20), and is increasingly used in human disease modelling.

Data for both Xenopus species are organized on individual gene pages that feature data such as gene descriptions, orthology to human and other species, disease associations for orthologs, an expression ribbon view, and a Sequence Feature Viewer. In order to fully support Xenbase orthology, a subset of X. tropicalis orthology calls from DIOPT 8 have been merged into our current DIOPT 9 dataset. DIOPT 8 returns the TreeFam and RoundUp data sources, but only for X. tropicalis. Orthology calls by Xenbase curators are also included under the new algorithm category “Xenbase.”

Example: Xenoopus tropicalis pax6 data at the AGR - https://alliancegenome.org/gene/Xenbase:XB-GENE-484088

AGR Mission:

The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease. This understanding is fundamental for advancing genome biology research and for translating human genome data into clinical utility.

AGR Vision:

The unified Alliance information system will represent the union of the data and information represented in the current individual MODs rather than the intersection, and thus provide the best of each in one place while maintaining community integrity and preserving the unique aspects of each model organism. By working together we can be more comprehensive and efficient, and hence more sustainable. Through the implementation of a shared, modular information system architecture, the Alliance seeks to serve diverse user communities including:

• human geneticists who want access to all model organism data for orthologous human genes
• basic science researchers who use specific model organisms to understand fundamental biology
• computational biologists and data scientists who need access to standardized, well-structured data, both big and small
• educators and students

AGR History:

Community genome resources such as the Model Organism Databases and the Gene Ontology Consortium have developed high quality resources enabling cost and time effective information retrieval and aggregation that would otherwise require countless hours to achieve. Regardless of their success and utility, there remain challenges to using and sustaining MODs. Searching across multiple model organism database resources remains a barrier to realizing the full impact of these resources in advancing genome biology and genomic medicine. In addition, despite a growing need for MODs by the biomedical research community as well as the increasing volumes of data and publications, the financial resources available to sustain MODs and related information resources are being reduced. We believe that one contribution to solving these challenges while continuing to serve our diverse user communities is to unify our efforts. To this end, in the fall of 2016, the Gene Ontology (GO) project joined six MODs to form the Alliance of Genome Resources (the Alliance) consortium, and a seventh, Xenbase, joined in 2022:

• FlyBase
• Mouse Genome Database (MGI)
• Rat Genome Database (RGD)
• Saccharomyces Genome Database (SGD)
• WormBase
• Xenbase
• Zebrafish Information Network (ZFIN)
• GO Consortium