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Harmonizing model organism data in the Alliance of Genome Resources

Agapite, Julie and Albou, Laurent-Philippe and Aleksander, Suzanne A. and Alexander, Micheal and Anagnostopoulos, Anna V. and Antonazzo, Giulia and Argasinska, Joanna and Arnaboldi, Valerio and Attrill, Helen and Becerra, Andrés 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 Davis, Paul and da Veiga Beltrame, Eduardo and De Pons, Jeffrey L. and D’Eustachio, Peter and Diamantakis, Stavros and Dolan, Mary E. and dos Santos, Gilberto and Douglass, Eric and Dunn, Barbara and Eagle, Anne and Ebert, Dustin and Engel, Stacia R. and Fashena, David and Foley, Saoirse and Frazer, Ken and Gao, Sibyl and Gibson, Adam C. and Gondwe, Felix and Goodman, Josh and Gramates, L. Sian and Grove, Christian A. and Hale, Paul and Harris, Todd and Thomas Hayman, G. and Hill, David P. and Howe, Douglas G. and Howe, Kevin L. and Hu, Yanhui and Jha, Sagar and Kadin, James A. and Kaufman, Thomas C. and Kalita, Patrick and Karra, Kalpana and Kishore, Ranjana and Kwitek, Anne E. and Laulederkind, Stanley J. F. and Lee, Raymond and Longden, Ian and Luypaert, Manuel and MacPherson, Kevin A. and Martin, Ryan and Marygold, Steven J. and Matthews, Beverley and McAndrews, Monica S. and Millburn, Gillian and Miyasato, Stuart and Motenko, Howie and Moxon, Sierra and Müller, Hans-Michael and Mungall, Christopher J. and Muruganujan, Anushya and Mushayahama, Tremayne and Nalabolu, Harika S. and Nash, Robert S. and Ng, Patrick and Nuin, Paulo and Paddock, Holly and Paulini, Michael and Perrimon, Norbert and Pich, Christian and Quinton-Tulloch, Mark and Raciti, Daniela and Ramachandran, Sridhar and Richardson, Joel E. and Russo Gelbart, Susan and Ruzicka, Leyla and Schaper, Kevin and Schindelman, Gary and Shimoyama, Mary and Simison, Matt and Shaw, David R. and Shrivatsav, Ajay and Singer, Amy and Skrzypek, Marek and Smith, Constance M. and Smith, Cynthia L. and Smith, Jennifer R. and Stein, Lincoln and Sternberg, Paul W. and Tabone, Christopher J. and Thomas, Paul D. and Thorat, Ketaki and Thota, Jyothi and Toro, Sabrina and Tomczuk, Monika and Trovisco, Vitor and Tutaj, Marek A. and Tutaj, Monika and Urbano, Jose-Maria and Van Auken, Kimberly and Van Slyke, Ceri E. and Wang, Qinghua and Wang, Shur-Jen and Weng, Shuai and Westerfield, Monte and Williams, Gary and Wilming, Laurens G. and Wong, Edith D. and Wright, Adam and Yook, Karen and Zarowiecki, Magdalena and Zhou, Pinglei and Zytkovicz, Mark (2022) Harmonizing model organism data in the Alliance of Genome Resources. Genetics, 220 (4). Art. No. iyac022. ISSN 1943-2631. PMCID PMC8982023. doi:10.1093/genetics/iyac022. https://resolver.caltech.edu/CaltechAUTHORS:20220406-521823507

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/genetics/iyac022DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982023/PubMed CentralArticle
ORCID:
AuthorORCID
Albou, Laurent-Philippe0000-0001-5801-1974
Arnaboldi, Valerio0000-0002-2563-5374
Attrill, Helen0000-0003-3212-6364
Blake, Judith A.0000-0001-8522-334X
Carbon, Seth0000-0001-8244-1536
Chan, Juancarlos0000-0002-7259-8107
Cherry, J. Michael0000-0001-9163-5180
Davis, Paul0000-0001-5545-0824
da Veiga Beltrame, Eduardo0000-0002-1529-9207
D’Eustachio, Peter0000-0002-5494-626X
Dolan, Mary E.0000-0001-7732-3295
Engel, Stacia R.0000-0001-5472-917X
Foley, Saoirse0000-0002-1791-2837
Grove, Christian A.0000-0001-9076-6015
Harris, Todd0000-0003-3406-163X
Hill, David P.0000-0001-7476-6306
Howe, Kevin L.0000-0002-1751-9226
Kishore, Ranjana0000-0002-1478-7671
Lee, Raymond0000-0002-8151-7479
Luypaert, Manuel0000-0003-3966-849X
Mungall, Christopher J.0000-0002-6601-2165
Nuin, Paulo0000-0003-4915-664X
Paulini, Michael0000-0002-6968-2340
Quinton-Tulloch, Mark0000-0001-5713-0736
Sternberg, Paul W.0000-0002-7699-0173
Thomas, Paul D.0000-0002-9074-3507
Van Auken, Kimberly0000-0002-1706-4196
Van Slyke, Ceri E.0000-0002-2244-7917
Wright, Adam0000-0002-5719-4024
Yook, Karen0000-0002-4457-6787
Zarowiecki, Magdalena0000-0001-6102-7731
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.
Funders:
Funding AgencyGrant Number
NIHU24HG010859
NIHU24HG002659
NIHU24HG002223
NIHU41HG000739
NIHU24HG001315
NIHU24HG000330
NIHU41HG002273
NIHR01HL064541
NIHP41HD062499
Medical Research Council (UK)MR/L001020/1
Department of Energy (DOE)DE-AC02-05CH11231
Subject Keywords:genome, knowledgebase, phenotype, data mining, biocuration, gene function, gene expression, gene interaction, variants
Issue or Number:4
PubMed Central ID:PMC8982023
DOI:10.1093/genetics/iyac022
Record Number:CaltechAUTHORS:20220406-521823507
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220406-521823507
Official Citation:Alliance of Genome Resources Consortium, Harmonizing model organism data in the Alliance of Genome Resources, Genetics, Volume 220, Issue 4, April 2022, iyac022, https://doi.org/10.1093/genetics/iyac022
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:114173
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Apr 2022 13:36
Last Modified:20 Apr 2022 21:22

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  • Agapite, Julie and Albou, Laurent-Philippe and Aleksander, Suzanne A. and Alexander, Micheal and Anagnostopoulos, Anna V. and Antonazzo, Giulia and Argasinska, Joanna and Arnaboldi, Valerio and Attrill, Helen and Becerra, Andrés 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 Davis, Paul and da Veiga Beltrame, Eduardo and De Pons, Jeffrey L. and D’Eustachio, Peter and Diamantakis, Stavros and Dolan, Mary E. and dos Santos, Gilberto and Douglass, Eric and Dunn, Barbara and Eagle, Anne and Ebert, Dustin and Engel, Stacia R. and Fashena, David and Foley, Saoirse and Frazer, Ken and Gao, Sibyl and Gibson, Adam C. and Gondwe, Felix and Goodman, Josh and Gramates, L. Sian and Grove, Christian A. and Hale, Paul and Harris, Todd and Thomas Hayman, G. and Hill, David P. and Howe, Douglas G. and Howe, Kevin L. and Hu, Yanhui and Jha, Sagar and Kadin, James A. and Kaufman, Thomas C. and Kalita, Patrick and Karra, Kalpana and Kishore, Ranjana and Kwitek, Anne E. and Laulederkind, Stanley J. F. and Lee, Raymond and Longden, Ian and Luypaert, Manuel and MacPherson, Kevin A. and Martin, Ryan and Marygold, Steven J. and Matthews, Beverley and McAndrews, Monica S. and Millburn, Gillian and Miyasato, Stuart and Motenko, Howie and Moxon, Sierra and Müller, Hans-Michael and Mungall, Christopher J. and Muruganujan, Anushya and Mushayahama, Tremayne and Nalabolu, Harika S. and Nash, Robert S. and Ng, Patrick and Nuin, Paulo and Paddock, Holly and Paulini, Michael and Perrimon, Norbert and Pich, Christian and Quinton-Tulloch, Mark and Raciti, Daniela and Ramachandran, Sridhar and Richardson, Joel E. and Russo Gelbart, Susan and Ruzicka, Leyla and Schaper, Kevin and Schindelman, Gary and Shimoyama, Mary and Simison, Matt and Shaw, David R. and Shrivatsav, Ajay and Singer, Amy and Skrzypek, Marek and Smith, Constance M. and Smith, Cynthia L. and Smith, Jennifer R. and Stein, Lincoln and Sternberg, Paul W. and Tabone, Christopher J. and Thomas, Paul D. and Thorat, Ketaki and Thota, Jyothi and Toro, Sabrina and Tomczuk, Monika and Trovisco, Vitor and Tutaj, Marek A. and Tutaj, Monika and Urbano, Jose-Maria and Van Auken, Kimberly and Van Slyke, Ceri E. and Wang, Qinghua and Wang, Shur-Jen and Weng, Shuai and Westerfield, Monte and Williams, Gary and Wilming, Laurens G. and Wong, Edith D. and Wright, Adam and Yook, Karen and Zarowiecki, Magdalena and Zhou, Pinglei and Zytkovicz, Mark Harmonizing model organism data in the Alliance of Genome Resources. (deposited 06 Apr 2022 13:36) [Currently Displayed]

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