Gene Ontology Consortium: going forward

被引：1134

作者：

Blake, J. A. ^{[1
]}

Christie, K. R. ^{[1
]}

Dolan, M. E. ^{[1
]}

Drabkin, H. J. ^{[1
]}

Hill, D. P. ^{[1
]}

Ni, L. ^{[1
]}

Sitnikov, D. ^{[1
]}

Burgess, S. ^{[2
]}

Buza, T. ^{[2
]}

Gresham, C. ^{[2
]}

McCarthy, F. ^{[2
]}

Pillai, L. ^{[2
]}

Wang, H. ^{[2
]}

Carbon, S. ^{[3
]}

Dietze, H. ^{[3
]}

Lewis, S. E. ^{[3
]}

Mungall, C. J. ^{[3
]}

Munoz-Torres, M. C. ^{[3
]}

Feuermann, M. ^{[4
]}

Gaudet, P. ^{[4
]}

Basu, S. ^{[5
]}

Chisholm, R. L. ^{[5
]}

Dodson, R. J. ^{[5
]}

Fey, P. ^{[5
]}

Mi, H. ^{[6
]}

Thomas, P. D. ^{[6
]}

Muruganujan, A. ^{[6
]}

Poudel, S. ^{[6
]}

Hu, J. C. ^{[7
,8
]}

Aleksander, S. A. ^{[7
,8
]}

McIntosh, B. K. ^{[7
,8
]}

Renfro, D. P. ^{[7
,8
]}

Siegele, D. A. ^{[7
,8
]}

Attrill, H. ^{[9
,10
]}

Brown, N. H. ^{[9
,10
]}

Tweedie, S. ^{[9
,10
]}

Lomax, J. ^{[11
]}

Osumi-Sutherland, D. ^{[11
]}

Parkinson, H. ^{[11
]}

Roncaglia, P. ^{[11
]}

Lovering, R. C. ^{[12
]}

Talmud, P. J. ^{[12
]}

Humphries, S. E. ^{[12
]}

Denny, P. ^{[12
]}

Campbell, N. H. ^{[12
]}

Foulger, R. E. ^{[12
]}

Chibucos, M. C. ^{[13
]}

Giglio, M. Gwinn ^{[13
]}

Chang, H. Y. ^{[14
]}

Finn, R. ^{[14
]}

机构：

[1] Jackson Lab, MGI, Bar Harbor, ME 04609 USA

[2] Mississippi State Univ, AgBase, Starkville, MS USA

[3] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley Bioinformat Open Source Projects, Genom Div, Berkeley, CA 94720 USA

[4] SIB, CALIPHO Grp, Geneva, Switzerland

[5] Northwestern Univ, DictyBase, Chicago, IL 60611 USA

[6] Univ So Calif, Dept Prevent Med, Div Bioinformat, Los Angeles, CA 90089 USA

[7] Texas A&M Univ, Dept Biol, EcoliWiki, College Stn, TX 77843 USA

[8] Texas A&M Univ, Dept Biochem & Biophys, EcoliWiki, College Stn, TX 77843 USA

[9] Univ Cambridge, Gurdon Inst, FlyBase, Cambridge, England

[10] Univ Cambridge, Dept Genet, Cambridge, England

[11] GO EMBL EBI, Hinxton, England

[12] UCL, Inst Cardiovasc Sci, London, England

[13] Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA

[14] EMBL EBI, InterPro, Hinxton, England

[15] Collect & Refinement Physiol Data Mycobacterium, Berlin, Germany

[16] Univ Cambridge, PomBase, Cambridge, England

[17] UCL, PomBase, London, England

[18] EMBL EBI, PomBase, Hinxton, England

[19] Med Coll Wisconsin, RGD, Milwaukee, WI 53226 USA

[20] NYU, Sch Med, Reactome, Dept Biochem & Mol Pharmacol, New York, NY USA

[21] Stanford Univ, Dept Genet, SGD, Stanford, CA 94305 USA

[22] Phoenix Bioinformat, TAIR, Redwood City, CA USA

[23] UniProt EMBL EBI, Hinxton, England

[24] SIB, Geneva, Switzerland

[25] Prot Informat Resource, Washington, DC USA

[26] CALTECH, WormBase, Pasadena, CA 91125 USA

[27] Univ Oregon, ZFIN, Eugene, OR 97403 USA

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / D1期

基金：

美国国家卫生研究院; 英国生物技术与生命科学研究理事会;

关键词：

ANNOTATIONS; ANATOMY; DATABASE; TOOL;

D O I：

10.1093/nar/gku1179

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Gene Ontology (GO; ext-link-type="uri" xlink:href="http://www.geneontology.org" xlink:type="simple">http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology.

引用

页码：D1049 / D1056

页数：8

共 24 条

[1] Gene Ontology: tool for the unification of biology
Ashburner, M
Ball, CA
Blake, JA
Botstein, D
Butler, H
Cherry, JM
Davis, AP
Dolinski, K
Dwight, SS
Eppig, JT
Harris, MA
Hill, DP
Issel-Tarver, L
Kasarskis, A
Lewis, S
Matese, JC
Richardson, JE
Ringwald, M
Rubin, GM
Sherlock, G
[J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
[2] An ontology for cell types
Bard, J
Rhee, SY
Ashburner, M
[J]. GENOME BIOLOGY, 2005, 6 (02)
[3] Gene Ontology Annotations and Resources
Blake, J. A.
Dolan, M.
Drabkin, H.
Hill, D. P.
Ni, Li
Sitnikov, D.
Bridges, S.
Burgess, S.
Buza, T.
McCarthy, F.
Peddinti, D.
Pillai, L.
Carbon, S.
Dietze, H.
Ireland, A.
Lewis, S. E.
Mungall, C. J.
Gaudet, P.
Chisholm, R. L.
Fey, P.
Kibbe, W. A.
Basu, S.
Siegele, D. A.
McIntosh, B. K.
Renfro, D. P.
Zweifel, A. E.
Hu, J. C.
Brown, N. H.
Tweedie, S.
Alam-Faruque, Y.
Apweiler, R.
Auchinchloss, A.
Axelsen, K.
Bely, B.
Blatter, M-C.
Bonilla, C.
Bougueleret, L.
Boutet, E.
Breuza, L.
Bridge, A.
Chan, W. M.
Chavali, G.
Coudert, E.
Dimmer, E.
Estreicher, A.
Famiglietti, L.
Feuermann, M.
Gos, A.
Gruaz-Gumowski, N.
Hieta, R.
[J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D530 - D535
[4] The Gene Ontology: enhancements for 2011
Blake, J. A.
Dolan, M.
Drabkin, H.
Hill, D. P.
Ni, L.
Sitnikov, D.
Burgess, S.
Buza, T.
Gresham, C.
McCarthy, F.
Pillai, L.
Wang, H.
Carbon, S.
Lewis, S. E.
Mungall, C. J.
Gaudet, P.
Chisholm, R. L.
Fey, P.
Kibbe, W. A.
Basu, S.
Siegele, D. A.
McIntosh, B. K.
Renfro, D. P.
Zweifel, A. E.
Hu, J. C.
Brown, N. H.
Tweedie, S.
Alam-Faruque, Y.
Apweiler, R.
Auchinchloss, A.
Axelsen, K.
Argoud-Puy, G.
Bely, B.
Blatter, M. -C.
Bougueleret, L.
Boutet, E.
Branconi-Quintaje, S.
Breuza, L.
Bridge, A.
Browne, P.
Chan, W. M.
Coudert, E.
Cusin, I.
Dimmer, E.
Duek-Roggli, P.
Eberhardt, R.
Estreicher, A.
Famiglietti, L.
Ferro-Rojas, S.
Feuermann, M.
[J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) : D559 - D564
[5] The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
Cooper, Laurel
Walls, Ramona L.
Elser, Justin
Gandolfo, Maria A.
Stevenson, Dennis W.
Smith, Barry
Preece, Justin
Athreya, Balaji
Mungall, Christopher J.
Rensing, Stefan
Hiss, Manuel
Lang, Daniel
Reski, Ralf
Berardini, Tanya Z.
Li, Donghui
Huala, Eva
Schaeffer, Mary
Menda, Naama
Arnaud, Elizabeth
Shrestha, Rosemary
Yamazaki, Yukiko
Jaiswal, Pankaj
[J]. PLANT AND CELL PHYSIOLOGY, 2013, 54 (02) : E1 - +
[6] Dietze H., 2014, J BIOMED SE IN PRESS
[7] The UniProt-GO Annotation database in 2011
Dimmer, Emily C.
Huntley, Rachael P.
Alam-Faruque, Yasmin
Sawford, Tony
O'Donovan, Claire
Martin, Maria J.
Bely, Benoit
Browne, Paul
Chan, Wei Mun
Eberhardt, Ruth
Gardner, Michael
Laiho, Kati
Legge, Duncan
Magrane, Michele
Pichler, Klemens
Poggioli, Diego
Sehra, Harminder
Auchincloss, Andrea
Axelsen, Kristian
Blatter, Marie-Claude
Boutet, Emmanuel
Braconi-Quintaje, Silvia
Breuza, Lionel
Bridge, Alan
Coudert, Elizabeth
Estreicher, Anne
Famiglietti, Livia
Ferro-Rojas, Serenella
Feuermann, Marc
Gos, Arnaud
Gruaz-Gumowski, Nadine
Hinz, Ursula
Hulo, Chantal
James, Janet
Jimenez, Silvia
Jungo, Florence
Keller, Guillaume
Lemercier, Phillippe
Lieberherr, Damien
Masson, Patrick
Moinat, Madelaine
Pedruzzi, Ivo
Poux, Sylvain
Rivoire, Catherine
Roechert, Bernd
Schneider, Michael
Stutz, Andre
Sundaram, Shyamala
Tognolli, Michael
Bougueleret, Lydie
[J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) : D565 - D570
[8] Doenitz Juergen, 2012, Frontiers in Genetics, V3, P197, DOI 10.3389/fgene.2012.00197
[9] The Sequence Ontology: a tool for the unification of genome annotations
Eilbeck, K
Lewis, SE
Mungall, CJ
Yandell, M
Stein, L
Durbin, R
Ashburner, M
[J]. GENOME BIOLOGY, 2005, 6 (05)
[10] Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium
Gaudet, Pascale
Livstone, Michael S.
Lewis, Suzanna E.
Thomas, Paul D.
[J]. BRIEFINGS IN BIOINFORMATICS, 2011, 12 (05) : 449 - 462

← 1 2 3 →