Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published December 2019 | Published
Journal Article Open

The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases

Abstract

Model organisms are essential experimental platforms for discovering gene functions, defining protein and genetic networks, uncovering functional consequences of human genome variation, and for modeling human disease. For decades, researchers who use model organisms have relied on Model Organism Databases (MODs) and the Gene Ontology Consortium (GOC) for expertly curated annotations, and for access to integrated genomic and biological information obtained from the scientific literature and public data archives. Through the development and enforcement of data and semantic standards, these genome resources provide rapid access to the collected knowledge of model organisms in human readable and computation-ready formats that would otherwise require countless hours for individual researchers to assemble on their own. Since their inception, the MODs for the predominant biomedical model organisms [Mus sp. (laboratory mouse), Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, and Rattus norvegicus] along with the GOC have operated as a network of independent, highly collaborative genome resources. In 2016, these six MODs and the GOC joined forces as the Alliance of Genome Resources (the Alliance). By implementing shared programmatic access methods and data-specific web pages with a unified "look and feel," the Alliance is tackling barriers that have limited the ability of researchers to easily compare common data types and annotations across model organisms. To adapt to the rapidly changing landscape for evaluating and funding core data resources, the Alliance is building a modern, extensible, and operationally efficient "knowledge commons" for model organisms using shared, modular infrastructure.

Additional Information

© 2019 Bult et al. Available freely online through the author-supported open access option. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Manuscript received July 15, 2019; accepted for publication October 11, 2019; published Early Online October 17, 2019. We thank all members of the Alliance of Genome Resources, the staff of the MODs and GOC, and the Alliance Scientific Advisory Board for their contributions to developing the vision and approach for the Alliance. V.D.F. and R.F. contributed to this manuscript in their official roles as program coordinators for the National Institutes of Health National Human Genome Research Institute.

Attached Files

Published - 1189.full.pdf

Files

1189.full.pdf
Files (794.3 kB)
Name Size Download all
md5:6671c892c0695cd8fb78ed47c56b1cde
794.3 kB Preview Download

Additional details

Created:
August 22, 2023
Modified:
October 18, 2023