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Alliance of Genome Resources Portal: unified model organism research platform

Agapite, Julie and Albou, Laurent-Philippe and Aleksander, Suzi and Argasinska, Joanna and Arnaboldi, Valerio and Attrill, Helen and Bello, Susan M. and Blake, Judith A. and Blodgett, Olin and Bradford, Yvonne M. and Bult, Carol J. and Cain, Scott and Calvi, Brian R. and Carbon, Seth and Chan, Juancarlos and Chen, Wen J. and Cherry, J. Michael and Cho, Jaehyoung and Christie, Karen R. and Crosby, Madeline A. and De Pons, Jeff and Dolan, Mary E and dos Santos, Gilberto and Dunn, Barbara and Dunn, Nathan and Eagle, Anne and Ebert, Dustin and Engel, Stacia R. and Fashena, David and Frazer, Ken and Gao, Sibyl and Gondwe, Felix and Goodman, Josh and Gramates, L. Sian and Grove, Christian A. and Harris, Todd and Harrison, Marie-Claire and Howe, Douglas G. and Howe, Kevin L. and Jha, Sagar and Kadin, James A. and Kaufman, Thomas C. and Kalita, Patrick and Karra, Kalpana and Kishore, Ranjana and Laulederkind, Stan and Lee, Raymond and MacPherson, Kevin A. and Marygold, Steven J. and Matthews, Beverley and Millburn, Gillian and Miyasato, Stuart and Moxon, Sierra and Mueller, Hans-Michael and Mungall, Christopher and Muruganujan, Anushya and Mushayahama, Tremayne and Nash, Robert S. and Ng, Patrick and Paulini, Michael and Perrimon, Norbert and Pich, Christian and Raciti, Daniela and Richardson, Joel E. and Russell, Matthew and Russo Gelbart, Susan and Ruzicka, Leyla and Schaper, Kevin and Shimoyama, Mary and Simison, Matt and Smith, Cynthia and Shaw, David R. and Shrivatsav, Ajay and Skrzypek, Marek and Smith, Jennifer R. and Sternberg, Paul W. and Tabone, Christopher J. and Thomas, Paul D. and Thota, Jyothi and Toro, Sabrina and Tomczuk, Monika and Tutaj, Marek and Tutaj, Monika and Urbano, Jose-Maria and Van Auken, Kimberly and Van Slyke, Ceri E. and Wang, Shur-Jen and Weng, Shuai and Westerfield, Monte and Williams, Gary and Wong, Edith D. and Wright, Adam and Yook, Karen (2020) Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Research, 48 (D1). D650-D658. ISSN 0305-1048. PMCID PMC6943066. https://resolver.caltech.edu/CaltechAUTHORS:20200413-081503928

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Abstract

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gkz813DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943066PubMed CentralArticle
ORCID:
AuthorORCID
Engel, Stacia R.0000-0001-5472-917X
Grove, Christian A.0000-0001-9076-6015
Sternberg, Paul W.0000-0002-7699-0173
Thomas, Paul D.0000-0002-9074-3507
Van Auken, Kimberly0000-0002-1706-4196
Additional Information:© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 31 July 2019; Revision received: 03 September 2019; Accepted: 19 September 2019; Published: 25 September 2019. The Alliance platform is designed and implemented by a core group of developers and curators at SGD, WormBase, ZFIN, RGD, MGD, FlyBase and the GOC. We would particularly like to acknowledge other staff at those projects who continue to provide gold-standard curation of model organism data without which the work described here would not be possible. Funding: National Institutes of Health/National Human Genome Research Institute grant [U24HG002223-19S1]; National Institutes of Health/National Human Genome Research Institute grants [P41HG002659 (ZFIN), U24HG002223 (WormBase), U41HG000739 (FlyBase), U41HG001315 (SGD), HG000330 (MGD), U41HG002273] (GOC, which also provides funding to W.B., M.G.D., S.G.D.); National Institutes of Health/National Heart, Lung and Blood Institute [HL64541 to R.G.D.]; Medical Research Council-UK [MR/L001020/1 (WormBase)]. Funding for open access charge: National Institutes of Health/National Human Genome Research Institute grant [1U24HG010859-01]. Conflict of interest statement. None declared.
Funders:
Funding AgencyGrant Number
NIHU24HG002223-19S1
NIHP41HG002659
NIHU24HG002223
NIHU41HG000739
NIHU41HG001315
NIHHG000330
NIHU41HG002273
NIHHL64541
Medical Research Council (UK)MR/L001020/1
NIH1U24HG010859-01
Issue or Number:D1
PubMed Central ID:PMC6943066
Record Number:CaltechAUTHORS:20200413-081503928
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200413-081503928
Official Citation:The Alliance of Genome Resources Consortium, Alliance of Genome Resources Portal: unified model organism research platform, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D650–D658, https://doi.org/10.1093/nar/gkz813
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:102491
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:13 Apr 2020 16:16
Last Modified:13 Apr 2020 16:16

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