The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases

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 Dat...

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Veröffentlicht in:Genetics (Austin) 2019-12, Vol.213 (4), p.1189-1196
Hauptverfasser: Bult, Carol J, Blake, Judith A, Calvi, Brian R, Cherry, J Michael, DiFrancesco, Valentina, Fullem, Robert, Howe, Kevin L, Kaufman, Thom, Mungall, Chris, Perrimon, Norbert, Shimoyama, Mary, Sternberg, Paul W, Thomas, Paul, Westerfield, Monte
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container_end_page 1196
container_issue 4
container_start_page 1189
container_title Genetics (Austin)
container_volume 213
creator Bult, Carol J
Blake, Judith A
Calvi, Brian R
Cherry, J Michael
DiFrancesco, Valentina
Fullem, Robert
Howe, Kevin L
Kaufman, Thom
Mungall, Chris
Perrimon, Norbert
Shimoyama, Mary
Sternberg, Paul W
Thomas, Paul
Westerfield, Monte
description 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 [ (laboratory mouse), , , , , and ] 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.
doi_str_mv 10.1534/genetics.119.302523
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subjects Annotations
Archives & records
BASIC BIOLOGICAL SCIENCES
Bioinformatics
Biology
Biomedical research
Consortia
data stewardship
Databases, Genetic
Disease
Ecosystem
Environmental changes
Fruit flies
Functionals
Funding
Gene Ontology
Genetics
Genome
Genomes
Genomics
Infrastructure
Initiatives
Insects
Investments
Laboratories
model organism databases
Models, Biological
Nematodes
Ontology
Organisms
Researchers
sustainability
Websites
title The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases
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