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

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 »

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.

View Accepted Manuscript (DOE)

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

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

Contributing Organization:: Alliance of Genome Resources Consortium

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1894077

Alternate ID(s):: OSTI ID: 1846500

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

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

Country of Publication:: United States

Language:: English

References (57)

Building a Cell and Anatomy Ontology of Caenorhabditis elegans Lee, Raymond Y. N.; Sternberg, Paul W. Comparative and Functional Genomics, Vol. 4, Issue 1 https://doi.org/10.1002/cfg.248	journal	January 2003
The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome: Tair: Making and Mining the “Gold Standard” Plant Genome Berardini, Tanya Z.; Reiser, Leonore; Li, Donghui genesis, Vol. 53, Issue 8 https://doi.org/10.1002/dvg.22877	journal	August 2015
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions Oughtred, Rose; Rust, Jennifer; Chang, Christie Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3978	journal	November 2020
The mammalian phenotype ontology: enabling robust annotation and comparative analysis Smith, Cynthia L.; Eppig, Janan T. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 1, Issue 3 https://doi.org/10.1002/wsbm.44	journal	November 2009
Gene expression and development databases forC. elegans Martinelli, Sylvia D.; Brown, Clive G.; Durbin, Richard Seminars in Cell & Developmental Biology, Vol. 8, Issue 5 https://doi.org/10.1006/scdb.1997.0171	journal	October 1997
Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data Hayamizu, Terry F.; Baldock, Richard A.; Ringwald, Martin Mammalian Genome, Vol. 26, Issue 9-10 https://doi.org/10.1007/s00335-015-9584-9	journal	July 2015
Sequence Ontology terminology for gene regulation Sant, David W.; Sinclair, Michael; Mungall, Christopher J. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1864, Issue 10 https://doi.org/10.1016/j.bbagrm.2021.194745	journal	October 2021
Molecular topography of an entire nervous system Taylor, Seth R.; Santpere, Gabriel; Weinreb, Alexis Cell, Vol. 184, Issue 16 https://doi.org/10.1016/j.cell.2021.06.023	journal	August 2021
Molecular evidence for a single origin of ultrafiltration-based excretory organs Gąsiorowski, Ludwik; Andrikou, Carmen; Janssen, Ralf Current Biology, Vol. 31, Issue 16 https://doi.org/10.1016/j.cub.2021.05.057	journal	August 2021
Evolution of the Sequence Ontology terms and relationships Mungall, Christopher J.; Batchelor, Colin; Eilbeck, Karen Journal of Biomedical Informatics, Vol. 44, Issue 1 https://doi.org/10.1016/j.jbi.2010.03.002	journal	February 2011
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
The PSI-MOD community standard for representation of protein modification data Montecchi-Palazzi, Luisa; Beavis, Ron; Binz, Pierre-Alain Nature Biotechnology, Vol. 26, Issue 8 https://doi.org/10.1038/nbt0808-864	journal	August 2008
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium Orchard, Sandra; Kerrien, Samuel; Abbani, Sara Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1931	journal	March 2012
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm Kumar, Prateek; Henikoff, Steven; Ng, Pauline C. Nature Protocols, Vol. 4, Issue 7 https://doi.org/10.1038/nprot.2009.86	journal	June 2009
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems Thomas, Paul D.; Hill, David P.; Mi, Huaiyu Nature Genetics, Vol. 51, Issue 10 https://doi.org/10.1038/s41588-019-0500-1	journal	September 2019
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium Gaudet, P.; Livstone, M. S.; Lewis, S. E. Briefings in Bioinformatics, Vol. 12, Issue 5 https://doi.org/10.1093/bib/bbr042	journal	August 2011
Reactome and the Gene Ontology: digital convergence of data resources Good, Benjamin M.; Van Auken, Kimberly; Hill, David P. Bioinformatics, Vol. 37, Issue 19 https://doi.org/10.1093/bioinformatics/btab325	journal	May 2021
Modeling sample variables with an Experimental Factor Ontology Malone, James; Holloway, Ele; Adamusiak, Tomasz Bioinformatics, Vol. 26, Issue 8 https://doi.org/10.1093/bioinformatics/btq099	journal	March 2010
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats Ison, J.; Kalas, M.; Jonassen, I. Bioinformatics, Vol. 29, Issue 10 https://doi.org/10.1093/bioinformatics/btt113	journal	March 2013
Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase Arnaboldi, Valerio; Raciti, Daniela; Van Auken, Kimberly Database, Vol. 2020 https://doi.org/10.1093/database/baaa006	journal	January 2020
Automated generation of gene summaries at the Alliance of Genome Resources Kishore, Ranjana; Arnaboldi, Valerio; Van Slyke, Ceri E. Database, Vol. 2020 https://doi.org/10.1093/database/baaa037	journal	January 2020
OntoMate: a text-mining tool aiding curation at the Rat Genome Database Liu, Weisong; Laulederkind, Stanley J. F.; Hayman, G. Thomas Database, Vol. 2015 https://doi.org/10.1093/database/bau129	journal	January 2015
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources Engel, Stacia R.; Wong, Edith D.; Nash, Robert S. Genetics https://doi.org/10.1093/genetics/iyab224	journal	December 2021
Ten Years of Collaborative Progress in the Quest for Orthologs Linard, Benjamin; Ebersberger, Ingo; McGlynn, Shawn E. Molecular Biology and Evolution, Vol. 38, Issue 8 https://doi.org/10.1093/molbev/msab098	journal	April 2021
The Human Phenotype Ontology in 2021 Köhler, Sebastian; Gargano, Michael; Matentzoglu, Nicolas Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1043	journal	December 2020
The Gene Ontology resource: enriching a GOld mine Carbon, Seth; Douglass, Eric; Good, Benjamin M. Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1113	journal	December 2020
Expression Atlas update: gene and protein expression in multiple species Moreno, Pablo; Fexova, Silvie; George, Nancy Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1030	journal	November 2021
The Human Disease Ontology 2022 update Schriml, Lynn M.; Munro, James B.; Schor, Mike Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1063	journal	November 2021
Saccharomyces Genome Database provides mutant phenotype data Engel, S. R.; Balakrishnan, R.; Binkley, G. Nucleic Acids Research, Vol. 38, Issue Database https://doi.org/10.1093/nar/gkp917	journal	November 2009
ChEBI in 2016: Improved services and an expanding collection of metabolites Hastings, Janna; Owen, Gareth; Dekker, Adriano Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1031	journal	October 2015
ECO, the Evidence & Conclusion Ontology: community standard for evidence information Giglio, Michelle; Tauber, Rebecca; Nadendla, Suvarna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1036	journal	November 2018
Alliance of Genome Resources Portal: unified model organism research platform Agapite, Julie; Albou, Laurent-Philippe; Aleksander, Suzi Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz813	journal	September 2019
Increased taxon sampling reveals thousands of hidden orthologs in flatworms Martín-Durán, José M.; Ryan, Joseph F.; Vellutini, Bruno C. Genome Research, Vol. 27, Issue 7 https://doi.org/10.1101/gr.216226.116	journal	April 2017
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution Musser, Jacob M.; Schippers, Klaske J.; Nickel, Michael Science, Vol. 374, Issue 6568 https://doi.org/10.1126/science.abj2949	journal	November 2021
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) cellular component curation Van Auken, Kimberly; Jaffery, Joshua; Chan, Juancarlos N. BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-228	journal	January 2009
Toward an interactive article: integrating journals and biological databases Rangarajan, Arun; Schedl, Tim; Yook, Karen BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-175	journal	May 2011
Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community Schindelman, Gary; Fernandes, Jolene S.; Bastiani, Carol A. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-32	journal	January 2011
An integrative approach to ortholog prediction for disease-focused and other functional studies Hu, Yanhui; Flockhart, Ian; Vinayagam, Arunachalam BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-357	journal	January 2011
Automatic categorization of diverse experimental information in the bioscience literature Fang, Ruihua; Schindelman, Gary; Auken, Kimberly Van BMC Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2105-13-16	journal	January 2012
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions Kerrien, Samuel; Orchard, Sandra; Montecchi-Palazzi, Luisa BMC Biology, Vol. 5, Issue 1 https://doi.org/10.1186/1741-7007-5-44	journal	October 2007
The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications Smith, Jennifer R.; Park, Carissa A.; Nigam, Rajni Journal of Biomedical Semantics, Vol. 4, Issue 1 https://doi.org/10.1186/2041-1480-4-26	journal	January 2013
The Drosophila phenotype ontology Osumi-Sutherland, David; Marygold, Steven J.; Millburn, Gillian H. Journal of Biomedical Semantics, Vol. 4, Issue 1 https://doi.org/10.1186/2041-1480-4-30	journal	January 2013
The Drosophila anatomy ontology Costa, Marta; Reeve, Simon; Grumbling, Gary Journal of Biomedical Semantics, Vol. 4, Issue 1 https://doi.org/10.1186/2041-1480-4-32	journal	January 2013
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio Van Slyke, Ceri E.; Bradford, Yvonne M.; Westerfield, Monte Journal of Biomedical Semantics, Vol. 5, Issue 1 https://doi.org/10.1186/2041-1480-5-12	journal	January 2014
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon Haendel, Melissa A.; Balhoff, James P.; Bastian, Frederic B. Journal of Biomedical Semantics, Vol. 5, Issue 1 https://doi.org/10.1186/2041-1480-5-21	journal	January 2014
Relations in biomedical ontologies Smith, Barry; Ceusters, Werner; Klagges, Bert Genome Biology, Vol. 6, Issue 5, p. R46 https://doi.org/10.1186/gb-2005-6-5-r46	journal	January 2005
Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature Müller, H. -M.; Van Auken, K. M.; Li, Y. BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2103-8	journal	March 2018
JBrowse: a dynamic web platform for genome visualization and analysis Buels, Robert; Yao, Eric; Diesh, Colin M. Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-0924-1	journal	April 2016
The Ensembl Variant Effect Predictor McLaren, William; Gil, Laurent; Hunt, Sarah E. Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-0974-4	journal	June 2016
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability Diehl, Alexander D.; Meehan, Terrence F.; Bradford, Yvonne M. Journal of Biomedical Semantics, Vol. 7, Issue 1 https://doi.org/10.1186/s13326-016-0088-7	journal	July 2016
Automated data integration for developmental biological research Zhong, Weiwei; Sternberg, Paul W. Development, Vol. 134, Issue 18 https://doi.org/10.1242/dev.001073	journal	September 2007
Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature Müller, Hans-Michael; Kenny, Eimear E.; Sternberg, Paul W. PLoS Biology, Vol. 2, Issue 11 https://doi.org/10.1371/journal.pbio.0020309	journal	September 2004
Many, but not all, lineage-specific genes can be explained by homology detection failure Weisman, Caroline M.; Murray, Andrew W.; Eddy, Sean R. PLOS Biology, Vol. 18, Issue 11 https://doi.org/10.1371/journal.pbio.3000862	journal	November 2020
BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model Organisms Hu, Yanhui; Chung, Verena; Comjean, Aram G3 Genes\|Genomes\|Genetics, Vol. 10, Issue 12 https://doi.org/10.1534/g3.120.401775	journal	December 2020
Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression Walton, Sophie J.; Wang, Han; Quintero-Cadena, Porfirio Genetics, Vol. 215, Issue 4 https://doi.org/10.1534/genetics.120.302923	journal	August 2020
Mapping single-cell atlases throughout Metazoa unravels cell type evolution Tarashansky, Alexander J.; Musser, Jacob M.; Khariton, Margarita eLife, Vol. 10 https://doi.org/10.7554/eLife.66747	journal	May 2021

Similar Records

Updates to the Alliance of Genome Resources central infrastructure

Journal Article · Thu Mar 28 20:00:00 EDT 2024 · Genetics (Online) · OSTI ID:2345960

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
biocuration
data mining
gene expression
gene function
gene interaction
genome
knowledgebase
phenotype
variants

Harmonizing model organism data in the Alliance of Genome Resources

Citation Formats

References (57)

Similar Records

Related Subjects