PUBLICATION

Harmonizing model organism data in the Alliance of Genome Resources

Authors
Alliance of Genome Resources Consortium
ID
ZDB-PUB-220406-4
Date
2022
Source
Genetics   220(4): (Journal)
Registered Authors
Bradford, Yvonne, Eagle, Anne, Fashena, David, Frazer, K., Howe, Doug, Kalita, Patrick, Martin, Ryan, Moxon, Sierra (fka Taylor), Paddock, Holly, Pich, Christian, Ramachandran, Sridhar, Ruzicka, Leyla, Singer, Amy, Toro, Sabrina, Van Slyke, Ceri E., Westerfield, Monte
Keywords
biocuration, data mining, gene expression, gene function, gene interaction, genome, knowledgebase, phenotype, variants
MeSH Terms
  • Alleles
  • Animals
  • Databases, Genetic*
  • Gene Ontology
  • Humans
  • Internet
  • Mice
  • Molecular Sequence Annotation
  • Rats
  • Zebrafish*/genetics
PubMed
35380658 Full text @ Genetics
Abstract
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.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes