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Title: 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 tomore » 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.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
Contributing Org.:
[The Alliance of Genome Resources Consortium]
OSTI Identifier:
1591843
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Accepted Manuscript
Journal Name:
Genetics
Additional Journal Information:
[ Journal Volume: 213; Journal Issue: 4]; Journal ID: ISSN 0016-6731
Publisher:
Genetics Society of America
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; model organism databases; bioinformatics; data stewardship; database; sustainability

Citation Formats

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, and Westerfield, Monte. The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. United States: N. p., 2019. Web. doi:10.1534/genetics.119.302523.
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. The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. United States. doi:10.1534/genetics.119.302523.
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, and Westerfield, Monte. Sun . "The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases". United States. doi:10.1534/genetics.119.302523. https://www.osti.gov/servlets/purl/1591843.
@article{osti_1591843,
title = {The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases},
author = {Bult, Carol J. and Blake, Judith A. and Calvi, Brian R. and Cherry, J. Michael and DiFrancesco, Valentina and Fullem, Robert and Howe, Kevin L. and Kaufman, Thom and Mungall, Chris and Perrimon, Norbert and Shimoyama, Mary and Sternberg, Paul W. and Thomas, Paul and Westerfield, Monte},
abstractNote = {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.},
doi = {10.1534/genetics.119.302523},
journal = {Genetics},
number = [4],
volume = [213],
place = {United States},
year = {2019},
month = {12}
}

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