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Results: 1 to 20 of 139

1.

Assessment of community-submitted ontology annotations from a novel database-journal partnership.

Berardini TZ, Li D, Muller R, Chetty R, Ploetz L, Singh S, Wensel A, Huala E.

Database (Oxford). 2012 Aug 1;2012:bas030. doi: 10.1093/database/bas030. Print 2012.

PMID:
22859749
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Quality of computationally inferred gene ontology annotations.

Skunca N, Altenhoff A, Dessimoz C.

PLoS Comput Biol. 2012 May;8(5):e1002533. doi: 10.1371/journal.pcbi.1002533. Epub 2012 May 31.

PMID:
22693439
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations.

Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL.

Database (Oxford). 2012 Mar 20;2012:bas001. doi: 10.1093/database/bas001. Print 2012.

PMID:
22434836
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Building an efficient curation workflow for the Arabidopsis literature corpus.

Li D, Berardini TZ, Muller RJ, Huala E.

Database (Oxford). 2012 Dec 6;2012:bas047. doi: 10.1093/database/bas047. Print 2012.

PMID:
23221298
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Gene Ontology annotations at SGD: new data sources and annotation methods.

Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. Epub 2007 Nov 3.

PMID:
17982175
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.

Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL.

Database (Oxford). 2011 Mar 15;2011:bar004. doi: 10.1093/database/bar004. Print 2011.

PMID:
21411447
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations.

Liu H, Jin T, Liao R, Wan L, Xu B, Zhou S, Guan J.

BMC Plant Biol. 2012 May 14;12:68. doi: 10.1186/1471-2229-12-68.

PMID:
22583976
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Gene Ontology annotations and resources.

Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.

Nucleic Acids Res. 2013 Jan;41(Database issue):D530-5. doi: 10.1093/nar/gks1050. Epub 2012 Nov 17.

PMID:
23161678
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6.

PMID:
14681408
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature.

Yoo D, Xu I, Berardini TZ, Rhee SY, Narayanasamy V, Twigger S.

Curr Protoc Bioinformatics. 2006 Mar;Chapter 9:Unit9.7. doi: 10.1002/0471250953.bi0907s13.

PMID:
18428773
[PubMed - indexed for MEDLINE]
11.

Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens.

Zaremba S, Ramos-Santacruz M, Hampton T, Shetty P, Fedorko J, Whitmore J, Greene JM, Perna NT, Glasner JD, Plunkett G 3rd, Shaker M, Pot D.

BMC Bioinformatics. 2009 Jun 10;10:177. doi: 10.1186/1471-2105-10-177.

PMID:
19515247
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.

Drabkin HJ, Blake JA; Mouse Genome Informatics Database.

Database (Oxford). 2012 Oct 29;2012:bas045. doi: 10.1093/database/bas045. Print 2012.

PMID:
23110975
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Textpresso: an ontology-based information retrieval and extraction system for biological literature.

Müller HM, Kenny EE, Sternberg PW.

PLoS Biol. 2004 Nov;2(11):e309. Epub 2004 Sep 21.

PMID:
15383839
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Creating the gene ontology resource: design and implementation.

Gene Ontology Consortium.

Genome Res. 2001 Aug;11(8):1425-33.

PMID:
11483584
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.

Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Zapata F, Ware D.

Nucleic Acids Res. 2008 Jan;36(Database issue):D449-54. doi: 10.1093/nar/gkm908.

PMID:
18194960
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

The UniProt-GO Annotation database in 2011.

Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R.

Nucleic Acids Res. 2012 Jan;40(Database issue):D565-70. doi: 10.1093/nar/gkr1048. Epub 2011 Nov 28.

PMID:
22123736
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

MILANO--custom annotation of microarray results using automatic literature searches.

Rubinstein R, Simon I.

BMC Bioinformatics. 2005 Jan 20;6:12.

PMID:
15661078
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

FuncBase: a resource for quantitative gene function annotation.

Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP.

Bioinformatics. 2010 Jul 15;26(14):1806-7. doi: 10.1093/bioinformatics/btq265. Epub 2010 May 21.

PMID:
20495000
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Functional annotation of the Arabidopsis genome using controlled vocabularies.

Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, Rhee SY.

Plant Physiol. 2004 Jun;135(2):745-55. Epub 2004 Jun 1.

PMID:
15173566
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

OnEX: Exploring changes in life science ontologies.

Hartung M, Kirsten T, Gross A, Rahm E.

BMC Bioinformatics. 2009 Aug 13;10:250. doi: 10.1186/1471-2105-10-250.

PMID:
19678926
[PubMed - indexed for MEDLINE]
Free PMC Article

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