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.

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

“…These are used in two ways; to assign gene names consistent with human nomenclature according to HUGO Gene Nomenclature Committee (HGNC), and to map relationships between genomes in different echinoderm species. The purple sea urchin gene set from genome build 5 was run against all of the Alliance of Genome Resources ( 26 ) maintained genomes by DIOPT ( 27 ). This data processing is only partial, as DIOPT relies on external resources to perform some analyses, and these resources do not yet include the purple sea urchin gene set.…”

Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology

“…MGD is one of the founding members of the Alliance of Genome Resources, a new data resource integration effort among the major model organism (MOD) database groups and the Gene Ontology Consortium (GOC) ( 14 , 15 ). MGD contributes core data to the Alliance including, specifically, mouse genome and phenotype data, expression data, and variant data.…”

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

“…We completed the integration of all model organism databases forming the Alliance of Genome Resources ( 24 ) by importing ZFIN ( 25 ), a model organism database that hosts a wide array of expertly curated, organized and cross-referenced research data for zebrafish ( Danio rerio ). In order to provide genomic annotations for a broad range of organisms, we also imported ncRNAs from Ensembl Fungi, Metazoa and Protists ( 26 ).…”