The alliance of genome resources: transforming comparative genomics

Creators: Bult, Carol J.; Sternberg, Paul W.¹

1. California Institute of Technology

Abstract

Comparing genomic and biological characteristics across multiple species is essential to using model systems to investigate the molecular and cellular mechanisms underlying human biology and disease and to translate mechanistic insights from studies in model organisms for clinical applications. Building a scalable knowledge commons platform that supports cross-species comparison of rich, expertly curated knowledge regarding gene function, phenotype, and disease associations available for model organisms and humans is the primary mission of the Alliance of Genome Resources (the Alliance). The Alliance is a consortium of seven model organism knowledgebases (mouse, rat, yeast, nematode, zebrafish, frog, fruit fly) and the Gene Ontology resource. The Alliance uses a common set of gene ortholog assertions as the basis for comparing biological annotations across the organisms represented in the Alliance. The major types of knowledge associated with genes that are represented in the Alliance database currently include gene function, phenotypic alleles and variants, human disease associations, pathways, gene expression, and both protein–protein and genetic interactions. The Alliance has enhanced the ability of researchers to easily compare biological annotations for common data types across model organisms and human through the implementation of shared programmatic access mechanisms, data-specific web pages with a unified "look and feel", and interactive user interfaces specifically designed to support comparative biology. The modular infrastructure developed by the Alliance allows the resource to serve as an extensible "knowledge commons" capable of expanding to accommodate additional model organisms.

Copyright and License

© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Acknowledgement

The authors acknowledge and thank all of the software developers and biocuration scientists who make the Alliance of Genome Resources possible. We also thank the Alliance Central Scientific Advisory Board members (Gary Bader, Alex Bateman, Helen Berman, Titus Brown, Shawn Burgess, Andrew Chisholm, Phil Hieter, Calum MacRae, Brian Oliver, Abraham Palmer, and Michelle Southard-Smith) for their guidance and advice. Members of the Alliance of Genome Resources Executive Committee provide input and oversight for organizational and operational aspects of the Alliance (Brian Calvi, J. Michael Cherry, Anne Kwitek, Chris Mungall, Paul Thomas, Aaron Zorn, Monte Westerfield).

Contributions

CJB wrote the main manuscript and prepared the figures. PWS reviewed and edited the manuscript.

Funding

Alliance Central is funded by the National Human Genome Research Institute (NHGRI) HG0101859.

Data Availability

The annotations available from the Alliance of Genome Resources web portal (https://alliancegenome.org) are distributed under a CC BY 4.0 license.

Conflict of Interest

The authors declare no competing interests.

Additional Information

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