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Gene Ontology resource: enriching a GOld mine

Carbon, Seth and Douglass, Eric and Good, Benjamin M. and Unni, Deepak R. and Harris, Nomi L. and Mungall, Christopher J. and Basu, Siddartha and Chisholm, Rex L. and Dodson, Robert J. and Hartline, Eric and Fey, Petra and Thomas, Paul D. and Albou, Laurent-Philippe and Ebert, Dustin and Kesling, Michael J. and Mi, Huaiyu and Muruganujan, Anushya and Huang, Xiaosong and Mushayahama, Tremayne and LaBonte, Sandra A. and Siegele, Deborah A. and Antonazzo, Giulia and Attrill, Helen and Brown, Nick H. and Garapati, Phani and Marygold, Steven J. and Trovisco, Vitor and dos Santos, Gil and Falls, Kathleen and Tabone, Christopher and Zhou, Pinglei and Goodman, Joshua L. and Strelets, Victor B. and Thurmond, Jim and Garmiri, Penelope and Ishtiaq, Rizwan and Rodríguez-López, Milagros and Acencio, Marcio L. and Kuiper, Martin and Lægreid, Astrid and Logie, Colin and Lovering, Ruth C. and Kramarz, Barbara and Saverimuttu, Shirin C. C. and Pinheiro, Sandra M. and Gunn, Heather and Su, Renzhi and Thurlow, Katherine E. and Chibucos, Marcus C. and Giglio, Michelle and Nadendla, Suvarna and Munro, James and Jackson, Rebecca and Duesbury, Margaret J. and Del-Toro, Noemi and Meldal, Birgit H. M. and Paneerselvam, Kalpana and Perfetto, Livia and Porras, Pablo and Orchard, Sandra and Shrivastava, Anjali and Chang, Hsin-Yu and Finn, Robert Daniel and Mitchell, Alexander Lawson and Rawlings, Neil David and Richardson, Lorna and Sangrador-Vegas, Amaia and Blake, Judith A. and Christie, Karen R. and Dolan, Mary E. and Drabkin, Harold J. and Hill, David P. and Ni, Li and Sitnikov, Dmitry M. and Harris, Midori A. and Oliver, Stephen G. and Rutherford, Kim M. and Wood, Valerie and Hayles, Jaqueline and Bähler, Jürg and Bolton, Elizabeth R. and De Pons, Jeffery L. and Dwinell, Melinda R. and Hayman, G. Thomas and Kaldunski, Mary L. and Kwitek, Anne E. and Laulederkind, Stanley J. F. and Plasterer, Cody and Tutaj, Marek A. and Vedi, Mahima and Wang, Shur-Jen and D’Eustachio, Peter and Matthews, Lisa and Balhoff, James P. and Aleksander, Suzi A. and Alexander, Michael J. and Cherry, J. Michael and Engel, Stacia R. and Gondwe, Felix and Karra, Kalpana and Miyasato, Stuart R. and Nash, Robert S. and Simison, Matt and Skrzypek, Marek S. and Weng, Shuai and Wong, Edith D. and Feuermann, Marc and Gaudet, Pascale and Morgat, Anne and Bakker, Erica and Berardini, Tanya Z. and Reiser, Leonore and Subramaniam, Shabari and Huala, Eva and Arighi, Cecilia N. and Auchincloss, Andrea and Axelsen, Kristian and Argoud-Puy, Ghislaine and Bateman, Alex and Blatter, Marie-Claude and Boutet, Emmanuel and Bowler, Emily and Breuza, Lionel and Bridge, Alan and Britto, Ramona and Bye-A-Jee, Hema and Casals Casas, Cristina and Coudert, Elisabeth and Denny, Paul and Estreicher, Anne and Famiglietti, Maria Livia and Georghiou, George and Gos, Arnaud and Gruaz-Gumowski, Nadine and Hatton-Ellis, Emma and Hulo, Chantal and Ignatchenko, Alexandr and Jungo, Florence and Laiho, Kati and Le Mercier, Philippe and Lieberherr, Damien and Lock, Antonia and Lussi, Yvonne and MacDougall, Alistair and Magrane, Michele and Martin, Maria J. and Masson, Patrick and Natale, Darren A. and Hyka-Nouspikel, Nevila and Orchard, Sandra and Pedruzzi, Ivo and Pourcel, Lucille and Poux, Sylvain and Pundir, Sangya and Rivoire, Catherine and Speretta, Elena and Sundaram, Shyamala and Tyagi, Nidhi and Warner, Kate and Zaru, Rossana and Wu, Cathy H. and Diehl, Alexander D. and Chan, Juancarlos N. and Grove, Christian and Lee, Raymond Y. N. and Müller, Hans-Michael and Raciti, Daniela and Van Auken, Kimberly and Sternberg, Paul W. and Berriman, Matthew and Paulini, Michael and Howe, Kevin and Gao, Sibyl and Wright, Adam and Stein, Lincoln and Howe, Douglas G. and Toro, Sabrina and Westerfield, Monte and Jaiswal, Pankaj and Cooper, Laurel and Elser, Justin (2021) Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research, 49 (D1). D325-D334. ISSN 0305-1048. PMCID PMC7779012. https://resolver.caltech.edu/CaltechAUTHORS:20210210-070215975

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Abstract

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gkaa1113DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779012PubMed CentralArticle
ORCID:
AuthorORCID
Carbon, Seth0000-0001-8244-1536
Mungall, Christopher J.0000-0002-6601-2165
Thomas, Paul D.0000-0002-9074-3507
Albou, Laurent-Philippe0000-0001-5801-1974
Mi, Huaiyu0000-0001-8721-202X
Attrill, Helen0000-0003-3212-6364
Lovering, Ruth C.0000-0002-9791-0064
Chibucos, Marcus C.0000-0001-9586-0780
Giglio, Michelle0000-0001-7628-5565
Dolan, Mary E.0000-0001-7732-3295
Hill, David P.0000-0001-7476-6306
Harris, Midori A.0000-0003-4148-4606
Rutherford, Kim M.0000-0001-6277-726X
Wood, Valerie0000-0001-6330-7526
Balhoff, James P.0000-0002-8688-6599
Cherry, J. Michael0000-0001-9163-5180
Engel, Stacia R.0000-0001-5472-917X
Feuermann, Marc0000-0002-4187-2863
Gaudet, Pascale0000-0003-1813-6857
Reiser, Leonore0000-0003-0073-0858
Bateman, Alex0000-0002-6982-4660
Georghiou, George0000-0001-5067-3199
Lock, Antonia0000-0003-1179-5999
Poux, Sylvain0000-0001-7299-6685
Chan, Juancarlos N.0000-0002-7259-8107
Grove, Christian0000-0001-9076-6015
Lee, Raymond Y. N.0000-0002-8151-7479
Van Auken, Kimberly0000-0002-1706-4196
Sternberg, Paul W.0000-0002-7699-0173
Berriman, Matthew0000-0002-9581-0377
Howe, Kevin0000-0002-1751-9226
Stein, Lincoln0000-0002-1983-4588
Additional Information:© The Author(s) 2020. 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: 15 September 2020; Revision received: 22 October 2020; Accepted: 02 December 2020; Published: 08 December 2020. We want to thank all the contributors to the GO resource over the last 20 years (http://geneontology.org/page/acknowledgments-contributors), and all the authors of papers represented in the GO knowledgebase (https://pubmed.ncbi.nlm.nih.gov/?term=loprovGeneOntol[SB]). We would like to recognize the efforts of two members of the GO Consortium who passed away in early 2020, James C. Hu, professor at Texas A&M Department of Biochemistry and Biophysics, and Mary Ellen Shimoyama, associate professor of biomedical engineering at the Medical College of Wisconsin (MCW). We miss their participation in our meetings and discussions. Finally, we would like to acknowledge the immense contribution of Suzanna E. Lewis, one of the founders of the GO project, who retired in 2020. Her vision, creativity, enthusiasm and unshakable commitment to the project have been instrumental in creating one of the most useful projects to bioinformatics and keeping it relevant for over two decades. The GO resource is supported by grants from the National Human Genome Research Institute [U41 HG02273 to P.D.T., P.W.S., S.E.L., J.M.C., J.A.B., supplements to grant U41 HG001315 to J.M.C., U24 HG002223 to P.W.S.]; GO Consortium members are also supported by diverse funding sources: dictyBase is supported by the National Institute of General Medical Sciences [1R24GM137770-01 to R.L.C.]; The EcoliWiki group is supported by the National Institutes of Health [GM089636]; National Science Foundation [1565146]; EMBL-EBI is funded by EMBL core funds; FlyBase is supported by the UK Medical Research Council [MR/N030117/1]; National Human Genome Research Institute [U41HG000739]; InterPro is funded by the Wellcome Trust [108433/Z/15/Z]; Biotechnology and Biological Sciences Research Council [BB/N00521X/1, BB/N019172/1, BB/L024136/1 to R.D.F.]; The Institute for Genome Sciences GO-related work on ECO is supported by the National Science Foundation [1458400]; The Gene Regulation Consortium (GRECO) is supported by Gene Regulation; Ensemble Effort for the Knowledge Commons (GREEKC) COST Action [CA15205]; A.L. and M.L.A. are also supported by the Research Council of Norway [247727]; Functional Gene Annotation, University College London is supported by Alzheimer's Research UK [ARUK-NAS2017A-1 to R.C.L.]; National Institute for Health Research University College London Hospitals Biomedical Research Centre; IntAct and the Complex Portal are supported by the European Molecular Biology Laboratory core funds, Open Targets [OTAR-044, OTAR02-048]; Wellcome Trust grant INVAR [212925/Z/18/Z]; PomBase is supported by the Wellcome Trust [104967/Z/14/Z to S.G.O.]; MGI is supported by the National Human Genome Research Institute [HG 000330, HG 002273]; RGD is supported by the National Heart, Lung, and Blood Institute [HL 64541]; Reactome is supported by the National Human Genome Research Institute [HG 003751]; the TAIR project is funded by academic institutional, corporate and individual subscriptions; TAIR is administered by the 501(c)(3) non-profit Phoenix Bioinformatics; the UniProt Consortium is supported by the National Eye Institute, National Human Genome Research Institute, National Heart, Lung and Blood Institute, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of General Medical Sciences; National Institute of Mental Health of the National Institutes of Health [U24HG007822]; National Human Genome Research Institute [U41HG007822, U41HG002273]; National Institute of General Medical Sciences [R01GM080646, P20GM103446, U01GM120953]; Swiss Federal Government through the State Secretariat for Education, Research and Innovation SERI; European Molecular Biology Laboratory core funds; Biotechnology and Biological Sciences Research Council [BB/M011674/1]; the Alzheimer's Research UK [ARUK-NAS2017A-1]; WormBase is supported by the US National Human Genome Research Institute [U24-HG002223]; UK Medical Research Council [MR/S000453/1]; UK Biotechnology and Biological Sciences Research Council [BB/P024610, BB/P024602]; ZFIN is supported by the National Human Genome Research Institute [HG002659 to M.W. and HG010859 to P.W.S]. Gramene contributions are supported by the National Science Foundation award [IOS #1127112] and Planteome contributions are supported by National Science Foundation award [IOS #1340112]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. Funding for open access charges: National Human Genome Research Institute [U41 HG02273]. Conflict of interest statement: None declared.
Funders:
Funding AgencyGrant Number
NIHU41 HG02273
NIHU41 HG001315
NIHU24 HG002223
NIH1R24GM137770-01
NIHGM089636
NSFDBI-1565146
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
Medical Research Council (UK)MR/N030117/1
NIHU41HG000739
Wellcome Trust108433/Z/15/Z
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N00521X/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N019172/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L024136/1
NSFDBI-1458400
Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC)CA15205
Research Council of Norway247727
Alzheimer’s Research UKARUK-NAS2017A-1
National Institute for Health ResearchUNSPECIFIED
University College LondonUNSPECIFIED
Open TargetsOTAR-044
Open TargetsOTAR02-048
Wellcome Trust212925/Z/18/Z
Wellcome Trust104967/Z/14/Z
NIHHG 000330
NIHHG 002273
NIHHL 64541
NIHHG 003751
Phoenix BioinformaticsUNSPECIFIED
NIHU24HG007822
NIHU41HG007822
NIHU41HG002273
NIHR01GM080646
NIHP20GM103446
NIHU01GM120953
State Secretariat for Education, Research and Innovation (SERI)UNSPECIFIED
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011674/1
NIHU24-HG002223
Medical Research Council (UK)MR/S000453/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P024610
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P024602/1
NIHHG002659
NIHHG010859
NSFIOS-1127112
NSFIOS-1340112
NIHU41 HG02273
Issue or Number:D1
PubMed Central ID:PMC7779012
Record Number:CaltechAUTHORS:20210210-070215975
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210210-070215975
Official Citation:The Gene Ontology Consortium, The Gene Ontology resource: enriching a GOld mine, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D325–D334, https://doi.org/10.1093/nar/gkaa1113
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:107976
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Feb 2021 18:06
Last Modified:10 Feb 2021 18:06

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