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, J., 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
Citation
Alliance of Genome Resources Consortium (2022) Harmonizing model organism data in the Alliance of Genome Resources. Genetics. 220(4):.
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
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping