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The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

Gaudet, Pascale and Chisholm, Rex and Berardini, Tanya and Dimmer, Emily and Engel, Stacia R. and Fey, Petra and Hill, David P. and Howe, Doug and Hu, James C. and Huntley, Rachael and Khodiyar, Varsha K. and Kishore, Ranjana and Li, Donghui and Lovering, Ruth C. and McCarthy, Fiona and Ni, Li and Petri, Victoria and Siegele, Deborah A. and Tweedie, Susan and Van Auken, Kimberly and Wood, Valerie and Basu, Siddhartha and Carbon, Seth and Dolan, Mary and Mungall, Christopher J. and Dolinski, Kara and Thomas, Paul and Ashburner, Michael and Blake, Judith A. and Cherry, J. Michael and Lewis, Suzanna E. (2009) The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Computational Biology, 5 (7). e1000431. ISSN 1553-734X. PMCID PMC2699109. http://resolver.caltech.edu/CaltechAUTHORS:20090911-153559023

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Abstract

The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms. Each contributing member of the GO Consortium independently associates GO terms to gene products from the organism(s) they are annotating. Here we introduce the Reference Genome project, which brings together those independent efforts into a unified framework based on the evolutionary relationships between genes in these different organisms. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO's logical structure and biological content.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.pcbi.1000431DOIArticle
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699109/PubMed CentralArticle
ORCID:
AuthorORCID
Van Auken, Kimberly0000-0002-1706-4196
Additional Information:© 2009 Gaudet et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: December 30, 2008; Accepted: June 3, 2009; Published: July 3, 2009. The Gene Ontology Consortium is supported by a NIH-NHGRI P41 grant, HG002273. Curation at the model organism databases is supported as follows: AgBase National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, grant number MISV-329140; dictyBase, NIH grants GM64426 and HG00022; EcoliWiki, NIGMS U24GM07790 to EcoliHub; FlyBase, Medical Research Council grant G0500293; GOA, core EMBL funding, British Heart Foundation grant SP/07/007/23671; MGI, NIH-NHGRI P41 grant HG000330 and NIH grant HD033745; RGD, National Heart, Lung, and Blood Institute grant HL64541; SGD, NIH-NHGRI P41 grant HG001315; TAIR, NSF grant DBI-0417062; WormBase, US NIH-NHGRI P41 grant HG02223; ZFIN, NIH-NCRR P41 grant HG002659-06; UCL-based human cardiovascular GO team, British Heart Foundation grant SP/07/007/23671. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist.
Funders:
Funding AgencyGrant Number
NIHP41 HG002273
Department of AgricultureMISV-329140
NIHGM64426
NIHHG00022
NIHU24GM07790
Medical Research Council (UK)G0500293
British Heart FoundationSP/07/007/23671
NIHP41 HG000330
NIHHD033745
NIHHL64541
NIHP41 HG001315
NSFDBI-0417062
NIHP41 HG02223
NIHP41 HG002659-06
British Heart FoundationSP/07/007/23671
Issue or Number:7
PubMed Central ID:PMC2699109
Record Number:CaltechAUTHORS:20090911-153559023
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20090911-153559023
Official Citation:The Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Comput Biol 5(7): e1000431. doi:10.1371/journal.pcbi.1000431
Usage Policy:This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The Reference Genome project is overseen by Pascale GaudetdictyBase, and Rex ChisholmdictyBase, Northwestern University, Chicago, IL, USA. It includes representatives from the curatorial staff: Tanya BerardiniTAIR, Carnegie Institution, Department of Plant Biology, Stanford, CA, USA; Emily DimmerGOA, UniProt, EBI, Hinxton, UK; Stacia R. EngelSGD, Department of Genetics, Stanford University, Stanford, CA, USA; Petra FeydictyBase, Northwestern University, Chicago, IL, USA; David P. HillMGI, The Jackson Laboratory, Bar Harbor, ME, USA; Doug HoweZFIN, University of Oregon, Eugene, OR, USA; James C. HuE.coliWiki, Texas A&M University, College Station, TX, USA; Rachael HuntleyGOA, UniProt, EBI, Hinxton, UK; Varsha K. KhodiyarUCL, Department of Medicine, University College London, London, UK; Ranjana KishoreWormBase, California Institute of Technology, Pasadena, CA, USA; Donghui LiTAIR, Carnegie Institution, Department of Plant Biology, Stanford, CA, USA; Ruth C. LoveringUCL, Department of Medicine, University College London, London, UK; Fiona McCarthyAgBase, Mississippi State University, Starkville, MS, USA; Li NiMGI, The Jackson Laboratory, Bar Harbor, ME, USA; Victoria PetriRGD, Medical College of Wisconsin, Milwaukee, WI, USA; Deborah A. SiegeleEcoliWiki, Texas A&M University, College Station, TX, USA; Susan TweedieFlyBase, Department of Genetics, University of Cambridge, Cambridge, UK; Kimberly Van AukenWormBase, California Institute of Technology, Pasadena, CA, USA; and Valerie WoodGeneDB, Wellcome Trust Sanger Institute, Hinxton, UK. It also includes the following computational staff representatives: Siddhartha BasudictyBase, Northwestern University, Chicago, IL, USA; Seth CarbonBBOP, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Mary DolanMGI, The Jackson Laboratory, Bar Harbor, ME, USA; and Christopher J. MungallBBOP, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. Those establishing the protein families to be annotated include: Kara DolinskiPPOD, Princeton University, Princeton, NJ, USA, and Paul ThomasPANTHER, SRI, Menlo Park, CA, USA. The Principal Investigators of the GO Consortium are Michael AshburnerFlyBase, Department of Genetics, University of Cambridge, Cambridge, UK; Judith A. BlakeMGI, The Jackson Laboratory, Bar Harbor, ME, USA; J. Michael CherrySGD, Department of Genetics, Stanford University, Stanford, CA, USA; and Suzanna E. LewisBBOP, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. The authors particularly wish to thank and recognize the invaluable contributions of their curator colleagues in the GO Consortium whose work ensures that the objectives of the Reference Genome project are fully realized: Rama BalakrishnanSGD, Karen R. ChristieSGD, Maria C. CostanzoSGD, Jennifer DeeganGOEO, Alexander D. DiehlMGI, Harold DrabkinMGI, Dianna G. FiskSGD, Midori HarrisGOEO, Jodi E. HirschmanSGD, Eurie L. HongSGD, Amelia IrelandGOEO, Jane LomaxGOEO, Robert S. NashSGD, Julie ParkSGD, Dmitry SitnikovMGI, and Marek S. SkrzypekSGD. We also thank these Principal Investigators for their enthusiastic support of this effort that is taking place within their research groups: Rolf ApweilerGOA, Carol BultMGI, Janan EppigMGI, Howard JacobRGD, Julian ParkhillGeneDB, Seung RheeTAIR, Martin RingwaldMGI, Paul SternbergWormBase, Philippa TalmudUCL, Simon TwiggerRGD, and Monte WesterfieldZFIN. We are very grateful to Richard Durbin and Erik Sonnhammer for stimulating discussions and help with resources.
ID Code:15793
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:07 Oct 2009 21:33
Last Modified:30 Oct 2017 20:27

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