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Results: 20

1.

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.

Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C.

Database (Oxford). 2013 Jan 17;2013:bas056. doi: 10.1093/database/bas056. Print 2013.

PMID:
23327936
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.

Lu Z, Hirschman L.

Database (Oxford). 2012 Nov 17;2012:bas043. doi: 10.1093/database/bas043. Print 2012.

PMID:
23160416
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

Kim S, Kim W, Wei CH, Lu Z, Wilbur WJ.

Database (Oxford). 2012 Nov 17;2012:bas042. doi: 10.1093/database/bas042. Print 2012.

PMID:
23160415
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

SR4GN: a species recognition software tool for gene normalization.

Wei CH, Kao HY, Lu Z.

PLoS One. 2012;7(6):e38460. doi: 10.1371/journal.pone.0038460. Epub 2012 Jun 5.

PMID:
22679507
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Text mining for the biocuration workflow.

Hirschman L, Burns GA, Krallinger M, Arighi C, Cohen KB, Valencia A, Wu CH, Chatr-Aryamontri A, Dowell KG, Huala E, Lourenço A, Nash R, Veuthey AL, Wiegers T, Winter AG.

Database (Oxford). 2012 Apr 18;2012:bas020. doi: 10.1093/database/bas020. Print 2012.

PMID:
22513129
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Cross-species gene normalization by species inference.

Wei CH, Kao HY.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S5. doi: 10.1186/1471-2105-12-S8-S5.

PMID:
22151999
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

BioCreative III interactive task: an overview.

Arighi CN, Roberts PM, Agarwal S, Bhattacharya S, Cesareni G, Chatr-Aryamontri A, Clematide S, Gaudet P, Giglio MG, Harrow I, Huala E, Krallinger M, Leser U, Li D, Liu F, Lu Z, Maltais LJ, Okazaki N, Perfetto L, Rinaldi F, Sætre R, Salgado D, Srinivasan P, Thomas PE, Toldo L, Hirschman L, Wu CH.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S4. doi: 10.1186/1471-2105-12-S8-S4.

PMID:
22151968
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.

Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M, Schneider G, Rinaldi F, Leaman R, Gonzalez G, Matos S, Kim S, Wilbur WJ, Rocha L, Shatkay H, Tendulkar AV, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Dogan RI, Fontaine JF, Andrade-Navarro MA, Valencia A.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S3. doi: 10.1186/1471-2105-12-S8-S3.

PMID:
22151929
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The gene normalization task in BioCreative III.

Lu Z, Kao HY, Wei CH, Huang M, Liu J, Kuo CJ, Hsu CN, Tsai RT, Dai HJ, Okazaki N, Cho HC, Gerner M, Solt I, Agarwal S, Liu F, Vishnyakova D, Ruch P, Romacker M, Rinaldi F, Bhattacharya S, Srinivasan P, Liu H, Torii M, Matos S, Campos D, Verspoor K, Livingston KM, Wilbur WJ.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S2. doi: 10.1186/1471-2105-12-S8-S2.

PMID:
22151901
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Overview of the BioCreative III Workshop.

Arighi CN, Lu Z, Krallinger M, Cohen KB, Wilbur WJ, Valencia A, Hirschman L, Wu CH.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S1. doi: 10.1186/1471-2105-12-S8-S1.

PMID:
22151647
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools.

Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10. doi: 10.1093/nar/gkr1090. Epub 2011 Dec 2.

PMID:
22140109
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications.

Fischer SE, Montgomery TA, Zhang C, Fahlgren N, Breen PC, Hwang A, Sullivan CM, Carrington JC, Ruvkun G.

PLoS Genet. 2011 Nov;7(11):e1002369. doi: 10.1371/journal.pgen.1002369. Epub 2011 Nov 10.

PMID:
22102828
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

WormBase 2012: more genomes, more data, new website.

Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R, Ganesan U, Grove C, Howe K, Kadam S, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Nash B, Ozersky P, Paulini M, Raciti D, Rangarajan A, Schindelman G, Shi X, Schwarz EM, Ann Tuli M, Van Auken K, Wang D, Wang X, Williams G, Hodgkin J, Berriman M, Durbin R, Kersey P, Spieth J, Stein L, Sternberg PW.

Nucleic Acids Res. 2012 Jan;40(Database issue):D735-41. doi: 10.1093/nar/gkr954. Epub 2011 Nov 8.

PMID:
22067452
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Is ABP1 an auxin receptor yet?

Shi JH, Yang ZB.

Mol Plant. 2011 Jul;4(4):635-40. doi: 10.1093/mp/ssr050. Epub 2011 Jun 29. Review.

PMID:
21715649
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

GeneTUKit: a software for document-level gene normalization.

Huang M, Liu J, Zhu X.

Bioinformatics. 2011 Apr 1;27(7):1032-3. doi: 10.1093/bioinformatics/btr042. Epub 2011 Feb 8.

PMID:
21303863
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction.

Névéol A, Islamaj Doğan R, Lu Z.

J Biomed Inform. 2011 Apr;44(2):310-8. doi: 10.1016/j.jbi.2010.11.001. Epub 2010 Nov 20.

PMID:
21094696
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Assisted curation: does text mining really help?

Alex B, Grover C, Haddow B, Kabadjov M, Klein E, Matthews M, Roebuck S, Tobin R, Wang X.

Pac Symp Biocomput. 2008:556-67.

PMID:
18229715
[PubMed - indexed for MEDLINE]
Free Article
18.

Integrating natural language processing with FlyBase curation.

Karamanis N, Lewin I, Seal R, Drysdale R, Briscoe E.

Pac Symp Biocomput. 2007:245-56.

PMID:
17990496
[PubMed - indexed for MEDLINE]
Free Article
19.

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
20.

PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine.

Donaldson I, Martin J, de Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CW.

BMC Bioinformatics. 2003 Mar 27;4:11. Epub 2003 Mar 27.

PMID:
12689350
[PubMed - indexed for MEDLINE]
Free PMC Article

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