Harmonizing model organism data in the Alliance of Genome Resources

Agapite, Julie; Albou, Laurent-Philippe; Aleksander, Suzanne A.; Alexander, Micheal; Anagnostopoulos, Anna V.; Antonazzo, Giulia; Argasinska, Joanna; Arnaboldi, Valerio; Attrill, Helen; Becerra, Andrés; Bello, Susan M.; Blake, Judith A.; Blodgett, Olin; Bradford, Yvonne M.; Bult, Carol J.; Cain, Scott; Calvi, Brian R.; Carbon, Seth; Chan, Juancarlos; Chen, Wen J.; Michael Cherry, J.; Cho, Jaehyoung; Christie, Karen R.; Crosby, Madeline A.; Davis, Paul; da Veiga Beltrame, Eduardo; De Pons, Jeffrey L.; D’Eustachio, Peter; Diamantakis, Stavros; Dolan, Mary E.; dos Santos, Gilberto; Douglass, Eric; Dunn, Barbara; Eagle, Anne; Ebert, Dustin; Engel, Stacia R.; Fashena, David; Foley, Saoirse; Frazer, Ken; Gao, Sibyl; Gibson, Adam C.; Gondwe, Felix; Goodman, Josh; Sian Gramates, L.; Grove, Christian A.; Hale, Paul; Harris, Todd; Thomas Hayman, G.; Hill, David P.; Howe, Douglas G.; Howe, Kevin L.; Hu, Yanhui; Jha, Sagar; Kadin, James A.; Kaufman, Thomas C.; Kalita, Patrick; Karra, Kalpana; Kishore, Ranjana; Kwitek, Anne E.; Laulederkind, Stanley F.; Lee, Raymond; Longden, Ian; Luypaert, Manuel; MacPherson, Kevin A.; Martin, Ryan; Marygold, Steven J.; Matthews, Beverley; McAndrews, Monica S.; Millburn, Gillian; Miyasato, Stuart; Motenko, Howie; Moxon, Sierra; Muller, Hans-Michael; Mungall, Christopher J.; Muruganujan, Anushya; Mushayahama, Tremayne; Nalabolu, Harika S.; Nash, Robert S.; Ng, Patrick; Nuin, Paulo; Paddock, Holly; Paulini, Michael; Perrimon, Norbert; Pich, Christian; Quinton-Tulloch, Mark; Raciti, Daniela; Ramachandran, Sridhar; Richardson, Joel E.; Gelbart, Susan Russo; Ruzicka, Leyla; Schaper, Kevin; Schindelman, Gary; Shimoyama, Mary; Simison, Matt; Shaw, David R.; Shrivatsav, Ajay; Singer, Amy; Skrzypek, Marek; Smith, Constance M.; Smith, Cynthia L.; Smith, Jennifer R.; Stein, Lincoln; Sternberg, Paul W.; Tabone, Christopher J.; Thomas, Paul D.; Thorat, Ketaki; Thota, Jyothi; Toro, Sabrina; Tomczuk, Monika; Trovisco, Vitor; Tutaj, Marek A.; Tutaj, Monika; Urbano, Jose-Maria; Van Auken, Kimberly; Van Slyke, Ceri E.; Wang, Qinghua; Wang, Shur-Jen; Weng, Shuai; Westerfield, Monte; Williams, Gary; Wilming, Laurens G.; Wong, Edith D.; Wright, Adam; Yook, Karen; Zarowiecki, Magdalena; Zhou, Pinglei; Zytkovicz, Mark

doi:10.1093/genetics/iyac022

Title: Harmonizing model organism data in the Alliance of Genome Resources

Journal Article · Fri Feb 25 00:00:00 EST 2022 · Genetics (Online)

DOI:https://doi.org/10.1093/genetics/iyac022· OSTI ID:1894077

Agapite, Julie; Albou, Laurent-Philippe; Aleksander, Suzanne A.; Alexander, Micheal; Anagnostopoulos, Anna V.; Antonazzo, Giulia; Argasinska, Joanna; Arnaboldi, Valerio; Attrill, Helen; Becerra, Andrés; Bello, Susan M.; Blake, Judith A.; Blodgett, Olin; Bradford, Yvonne M.; Bult, Carol J.; Cain, Scott; Calvi, Brian R.; Carbon, Seth; Chan, Juancarlos; Chen, Wen J. more »

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Human Genome Research Institute; National Heart, Lung and Blood Institute; Eunice Kennedy Shriver National Institute of Child Health and Human Development; Medical Research Council-UK

Contributing Organization:: Alliance of Genome Resources Consortium

Grant/Contract Number:: AC02-05CH11231; U24HG010859; U24HG002659; U24HG002223; U41HG000739; U24HG001315; U24HG000330; U41HG002273; R01HL064541; P41HD062499; MR/L001020/1

OSTI ID:: 1894077

Alternate ID(s):: OSTI ID: 1846500

Journal Information:: Genetics (Online), Vol. 220, Issue 4; ISSN 1943-2631

Publisher:: Oxford University Press; Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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Title: Harmonizing model organism data in the Alliance of Genome Resources

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References (57)

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