Harmonizing model organism data in the Alliance of Genome Resources. Genetics 2022 Apr 04;220(4)
Date
04/06/2022Pubmed ID
35380658Pubmed Central ID
PMC8982023DOI
10.1093/genetics/iyac022Scopus ID
2-s2.0-85128598390 (requires institutional sign-in at Scopus site) 23 CitationsAbstract
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.
Author List
Alliance of Genome Resources ConsortiumAuthors
Anne E. Kwitek PhD Professor in the Physiology department at Medical College of WisconsinMonika Tutaj Research Scientist II in the Physiology department at Medical College of Wisconsin
Shur-Jen Wang Research Scientist II in the Physiology department at Medical College of Wisconsin
MESH terms used to index this publication - Major topics in bold
AllelesAnimals
Caenorhabditis elegans
Databases, Genetic
Drosophila
Gene Ontology
Humans
Internet
Mice
Molecular Sequence Annotation
Rats
Saccharomycetales
Zebrafish
