Harmonizing model organism data in the Alliance of Genome Resources
- Creators
- Agapite, Julie
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Albou, Laurent-Philippe
- Aleksander, Suzanne A.
- Alexander, Micheal
- Anagnostopoulos, Anna V.
- Antonazzo, Giulia
- Argasinska, Joanna
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Arnaboldi, Valerio
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Attrill, Helen
- Becerra, Andrés
- Bello, Susan M.
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Blake, Judith A.
- Blodgett, Olin
- Bradford, Yvonne M.
- Bult, Carol J.
- Cain, Scott
- Calvi, Brian R.
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Carbon, Seth
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Chan, Juancarlos
- Chen, Wen J.
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Cherry, J. Michael
- Cho, Jaehyoung
- Christie, Karen R.
- Crosby, Madeline A.
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Davis, Paul
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da Veiga Beltrame, Eduardo
- De Pons, Jeffrey L.
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D'Eustachio, Peter
- Diamantakis, Stavros
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Dolan, Mary E.
- dos Santos, Gilberto
- Douglass, Eric
- Dunn, Barbara
- Eagle, Anne
- Ebert, Dustin
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Engel, Stacia R.
- Fashena, David
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Foley, Saoirse
- Frazer, Ken
- Gao, Sibyl
- Gibson, Adam C.
- Gondwe, Felix
- Goodman, Josh
- Gramates, L. Sian
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Grove, Christian A.
- Hale, Paul
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Harris, Todd
- Thomas Hayman, G.
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Hill, David P.
- Howe, Douglas G.
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Howe, Kevin L.
- Hu, Yanhui
- Jha, Sagar
- Kadin, James A.
- Kaufman, Thomas C.
- Kalita, Patrick
- Karra, Kalpana
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Kishore, Ranjana
- Kwitek, Anne E.
- Laulederkind, Stanley J. F.
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Lee, Raymond
- Longden, Ian
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Luypaert, Manuel
- MacPherson, Kevin A.
- Martin, Ryan
- Marygold, Steven J.
- Matthews, Beverley
- McAndrews, Monica S.
- Millburn, Gillian
- Miyasato, Stuart
- Motenko, Howie
- Moxon, Sierra
- Müller, Hans-Michael
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Mungall, Christopher J.
- Muruganujan, Anushya
- Mushayahama, Tremayne
- Nalabolu, Harika S.
- Nash, Robert S.
- Ng, Patrick
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Nuin, Paulo
- Paddock, Holly
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Paulini, Michael
- Perrimon, Norbert
- Pich, Christian
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Quinton-Tulloch, Mark
- Raciti, Daniela
- Ramachandran, Sridhar
- Richardson, Joel E.
- Russo Gelbart, Susan
- 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
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Sternberg, Paul W.
- Tabone, Christopher J.
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Thomas, Paul D.
- Thorat, Ketaki
- Thota, Jyothi
- Toro, Sabrina
- Tomczuk, Monika
- Trovisco, Vitor
- Tutaj, Marek A.
- Tutaj, Monika
- Urbano, Jose-Maria
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Van Auken, Kimberly
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Van Slyke, Ceri E.
- Wang, Qinghua
- Wang, Shur-Jen
- Weng, Shuai
- Westerfield, Monte
- Williams, Gary
- Wilming, Laurens G.
- Wong, Edith D.
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Wright, Adam
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Yook, Karen
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Zarowiecki, Magdalena
- Zhou, Pinglei
- Zytkovicz, Mark
- Alliance of Genome Resources Consortium
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.
Additional Information
© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 12 December 2021. Accepted: 26 January 2022. Published: 25 February 2022. The authors thank our user communities for their patience as we transition our heavily used resources to shared infrastructure, as well as for contributing data and suggestions. They also thank the members of our Scientific Advisory Board (Gary Bader, Alex Bateman, Helen Berman, Shawn Burgess, Andrew Chisholm, Phil Hieter, Brian Oliver, Calum Macrae, Titus Brown, Abraham Palmer and Michelle Southard-Smith) for cogent advice, and NGHRI Program Staff (Valentina di Francesco, Ajay Pillai, Sean Garin, and Helen Thompson) for advice. The core funding for the Alliance is from the National Human Genome Research Institute and the National Heart, Lung and Blood Institute (U24HG010859). The curation of data and its harmonization is supported by National Human Genome Research Institute grants U24HG002659 (ZFIN), U24HG002223 (WormBase), U41HG000739 (FlyBase), U24HG001315 (SGD), U24HG000330 (MGD), and U41HG002273 (GO Consortium), as well as grant R01HL064541 from the National Heart, Lung and Blood Institute (RGD), P41HD062499 from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (GXD), and the Medical Research Council-UK grant MR/L001020/1 (WormBase). Additional effort was supported by DOE DE-AC02-05CH11231. Data availability. Data are available by browsing, displays analytical tools, downloads, and APIs via the Portal at alliancegenome.org. Conflicts of interest: None declared.Additional details
- PMCID
- PMC8982023
- Eprint ID
- 114173
- Resolver ID
- CaltechAUTHORS:20220406-521823507
- NIH
- U24HG010859
- NIH
- U24HG002659
- NIH
- U24HG002223
- NIH
- U41HG000739
- NIH
- U24HG001315
- NIH
- U24HG000330
- NIH
- U41HG002273
- NIH
- R01HL064541
- NIH
- P41HD062499
- Medical Research Council (UK)
- MR/L001020/1
- Department of Energy (DOE)
- DE-AC02-05CH11231
- Created
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2022-04-06Created from EPrint's datestamp field
- Updated
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2022-04-20Created from EPrint's last_modified field
- Caltech groups
- Division of Biology and Biological Engineering (BBE)