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Annotation of gene product function from high-throughput studies using the Gene Ontology

Attrill, Helen and Gaudet, Pascale and Huntley, Rachael P. and Lovering, Ruth C. and Engel, Stacia R. and Poux, Sylvain and Van Auken, Kimberly M. and Georghiou, George and Chibucos, Marcus C. and Berardini, Tanya Z. and Wood, Valerie and Drabkin, Harold and Fey, Petra and Garmiri, Penelope and Harris, Midori A. and Sawford, Tony and Reiser, Leonore and Tauber, Rebecca and Toro, Sabrina (2019) Annotation of gene product function from high-throughput studies using the Gene Ontology. Database : The Journal of Biological Databases and Curation, 2019 . Art. No. baz007. ISSN 1758-0463. PMCID PMC6355445. https://resolver.caltech.edu/CaltechAUTHORS:20190211-083328204

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Abstract

High-throughput studies constitute an essential and valued source of information for researchers. However, high-throughput experimental workflows are often complex, with multiple data sets that may contain large numbers of false positives. The representation of high-throughput data in the Gene Ontology (GO) therefore presents a challenging annotation problem, when the overarching goal of GO curation is to provide the most precise view of a gene's role in biology. To address this, representatives from annotation teams within the GO Consortium reviewed high-throughput data annotation practices. We present an annotation framework for high-throughput studies that will facilitate good standards in GO curation and, through the use of new high-throughput evidence codes, increase the visibility of these annotations to the research community.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/database/baz007DOIArticle
http://geneontology.orgRelated ItemDatabase
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355445/PubMed CentralArticle
ORCID:
AuthorORCID
Attrill, Helen0000-0003-3212-6364
Gaudet, Pascale0000-0003-1813-6857
Engel, Stacia R.0000-0001-5472-917X
Van Auken, Kimberly M.0000-0002-1706-4196
Georghiou, George0000-0001-5067-3199
Chibucos, Marcus C.0000-0001-9586-0780
Reiser, Leonore0000-0003-0073-0858
Additional Information:© 2019 The Author(s). Published by Oxford University Press. 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: 30 October 2018; Revision Received: 21 December 2018; Accepted: 08 January 2019; Published: 01 February 2019. We would like to thank Robin Antrobus (Cambridge Institute for Medical Research, University of Cambridge, UK) and Stephanie Mohr (Drosophila RNAi Screening Center/Transgenic RNAi Project Functional Genomics Resources, Harvard Medical School, USA) for their invaluable advice on high-throughput technical standards. Funding: UK Medical Research Council (MR/N030117/1 funds H.A.); US National Institutes of Health, National Human Genome Research Institute (U41 HG000739 to FlyBase); State Secretariat for Education, Research and Innovation (Swiss-Prot group); British Heart Foundation (RG/13/5/30112 funds R.P.H. and R.C.L.); Parkinson's UK (G-1307 to R.C.L.); National Institute for Health Research, University College London Hospitals Biomedical Research Centre (R.P.H. and R.C.L.); National Human Genome Research Institute (U41 HG001315 to Saccharomyces Genome Database); National Eye Institute (UniProt Consortium); National Human Genome Research Institute (UniProt Consortium); National Heart, Lung, and Blood Institute (UniProt Consortium); National Institute of Allergy and Infectious Diseases (UniProt Consortium); National Institute of Diabetes and Digestive and Kidney Diseases (UniProt Consortium); National Institute of General Medical Sciences (UniProt Consortium); National Institute of Mental Health of the National Institutes of Health, National Human Genome Research Institute (U41 HG007822 and U41 HG002273 to UniProt Consortium); National Institute of General Medical Sciences (R01GM080646, P20GM103446 and U01GM120953 to UniProt Consortium); Biotechnology and Biological Sciences Research Council (BB/M011674/1); British Heart Foundation (RG/13/5/30112); State Secretariat for Education, Research and Innovation; European Molecular Biology Laboratory core funds; National Human Genome Research Institute (U41 HG002223 to WormBase); National Science Foundation Division of Biological Infrastructure (1458400 to Evidence and Conclusion Ontology); The Arabidopsis Information Resource (TAIR) is funded by academic institutional, corporate, and individual subscriptions. TAIR is administered by the 501(c)(3) non-profit Phoenix Bioinformatics. UK Wellcome Trust (104967/Z/14/Z to PomBase); National Human Genome Research Institute (U41 HG002273 and U41 HG000330 to H.D.); National Institute of General Medical Sciences (GM080646 funds H.D., ); National Institute of General Medical Sciences (GM064426 and GM087371 to dictyBase); National Human Genome Research Institute (U41 HG002659 to Zebrafish Information Network); NHGRI (U41 HG02273 to Gene Ontology resource). Conflict of interest. None declared.
Funders:
Funding AgencyGrant Number
Medical Research Council (UK)MR/N030117/1
NIHU41 HG000739
State Secretariat for Education, Research and Innovation (SER)UNSPECIFIED
British Heart FoundationRG/13/5/30112
Parkinson's UKG-1307
University College LondonUNSPECIFIED
NIHU41 HG001315
National Eye InstituteUNSPECIFIED
National Human Genome Research InstituteUNSPECIFIED
National Heart, Lung, and Blood InstituteUNSPECIFIED
National Institute of Allergy and Infectious DiseasesUNSPECIFIED
National Institute of Diabetes and Digestive and Kidney DiseasesUNSPECIFIED
National Institute of General Medical SciencesUNSPECIFIED
NIHU41 HG007822
NIHU41 HG002273
NIHR01GM080646
NIHP20GM103446
NIHU01GM120953
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011674/1
British Heart FoundationUNSPECIFIED
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
NIHU41 HG002223
NSFDBI-1458400
Arabidopsis Information Resource (TAIR)UNSPECIFIED
Wellcome Trust104967/Z/14/Z
NIHU41 HG000330
NIHGM080646
NIHGM064426
NIHGM087371
NIHU41 HG002659
PubMed Central ID:PMC6355445
Record Number:CaltechAUTHORS:20190211-083328204
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190211-083328204
Official Citation:Helen Attrill, Pascale Gaudet, Rachael P Huntley, Ruth C Lovering, Stacia R Engel, Sylvain Poux, Kimberly M Van Auken, George Georghiou, Marcus C Chibucos, Tanya Z Berardini, Valerie Wood, Harold Drabkin, Petra Fey, Penelope Garmiri, Midori A Harris, Tony Sawford, Leonore Reiser, Rebecca Tauber, Sabrina Toro, The Gene Ontology Consortium; Annotation of gene product function from high-throughput studies using the Gene Ontology, Database, Volume 2019, 1 January 2019, baz007, https://doi.org/10.1093/database/baz007
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:92819
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:12 Feb 2019 22:40
Last Modified:13 Apr 2020 16:16

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