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The Gene Ontology Resource: 20 years and still GOing strong

Chan, J. and Cho, J. and Gao, S. and Grove, C. and Harrison, M. C. and Howe, K. and Lee, R. and Mendel, J. and Muller, H.-M. and Raciti, D. and Van Auken, K. and Berriman, M. and Stein, L. and Sternberg, P. W. (2019) The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Research, 47 (D1). D330-D338. ISSN 0305-1048. http://resolver.caltech.edu/CaltechAUTHORS:20190415-100854557

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Abstract

The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the ‘GO ribbon’ widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gky1055DOIArticle
ORCID:
AuthorORCID
Van Auken, K.0000-0002-1706-4196
Sternberg, P. W.0000-0002-7699-0173
Additional Information:© The Author(s) 2018. 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 September 22, 2018; Revised October 16, 2018; Editorial Decision October 17, 2018; Accepted October 17, 2018. Published: 05 November 2018. We would like to thank the domain experts Peter Yurchenco, Sylvie Ricard-Blum, Rachel Lennon, Geoff Meyer, David Sherwood and Jeff Miner for discussions leading to the refinement of the extracellular matrix area. We also 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://www.ncbi.nlm.nih.gov/pubmed/?term=loprovGeneOntol[SB]). The GO resource is supported by grant 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. and supplements to grant U41 HG001315 to J.M.C., U24 HG002223 to P.W.S.]. In addition, GO Consortium members are also supported by diverse funding sources: dictyBase is supported by the National Institute of General Medical Sciences [GM064426, GM087371 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 RDF]; 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 [grant CA15205]; A.L. and M.L.A. are also supported by the Research Council of Norway [project 247727]; The Institute of Cardiovascular Science, University College London (R. Lovering's group) is supported by British Heart Foundation [RG/13/5/30112]; Parkinson's UK [G-1307]; 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; 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 and by the National Heart, Lung, and Blood Institute [HL 64541]; 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, and National Institute of Mental Health of the National Institutes of Health under Award Number [U24HG007822], National Human Genome Research Institute under Award Numbers [U41HG007822 and U41HG002273]; National Institute of General Medical Sciences under Award Numbers [R01GM080646, P20GM103446 and U01GM120953]; Biotechnology and Biological Sciences Research Council [BB/M011674/1]; the British Heart Foundation [RG/13/5/30112]; Swiss Federal Government through the State Secretariat for Education, Research and Innovation (SERI); European Molecular Biology Laboratory core funds; The TAIR project is funded by academic institutional, corporate, and individual subscriptions. TAIR is administered by the 501(c)(3) non-profit Phoenix Bioinformatics; WormBase is supported by the US National Human Genome Research Institute [U24-HG002223]; UK Medical Research Council [MR/L001220]; UK Biotechnology and Biological Sciences Research Council [BB/K020080]; ZFIN also supported by the National Human Genome Research Institute [U41 HG002659 to M.W.]. 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
NIHGM064426
NIHGM087371
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
University College LondonUNSPECIFIED
British Heart FoundationRG/13/5/30112
Parkinson's UKG-1307
Wellcome Trust104967/Z/14/Z
NIHHG 000330
NIHHG 002273
NIHHL 64541
National Eye InstituteUNSPECIFIED
National Institute of Allergy and Infectious DiseasesUNSPECIFIED
National Institute of Diabetes and Digestive and Kidney DiseasesUNSPECIFIED
National Institute of General Medical SciencesUNSPECIFIED
NIHU24HG007822
NIHU41HG007822
NIHU41HG002273
NIHR01GM080646
NIHP20GM103446
NIHU01GM120953
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011674/1
Swiss Federal GovernmentUNSPECIFIED
State Secretariat for Education, Research and Innovation (SERI)UNSPECIFIED
Medical Research Council (UK)MR/L001220
Biotechnology and Biological Sciences Research Council (BBSRC)BB/K020080
NIHU41 HG002659
Record Number:CaltechAUTHORS:20190415-100854557
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20190415-100854557
Official Citation:The Gene Ontology Consortium, The Gene Ontology Resource: 20 years and still GOing strong, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D330–D338, https://doi.org/10.1093/nar/gky1055
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:94702
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:16 Apr 2019 21:57
Last Modified:16 Apr 2019 21:57

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