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Results: 1 to 20 of 88

1.

Identifying named entities from PubMed for enriching semantic categories.

Kim S, Lu Z, Wilbur WJ.

BMC Bioinformatics. 2015 Feb 21;16:57. doi: 10.1186/s12859-015-0487-2.

2.

Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach.

Kim S, Liu H, Yeganova L, Wilbur WJ.

J Biomed Inform. 2015 Jun;55:23-30. doi: 10.1016/j.jbi.2015.03.002. Epub 2015 Mar 19.

3.

Retro: concept-based clustering of biomedical topical sets.

Yeganova L, Kim W, Kim S, Wilbur WJ.

Bioinformatics. 2014 Nov 15;30(22):3240-8. doi: 10.1093/bioinformatics/btu514. Epub 2014 Jul 29.

PMID:
25075115
4.

Assisting manual literature curation for protein-protein interactions using BioQRator.

Kwon D, Kim S, Shin SY, Chatr-aryamontri A, Wilbur WJ.

Database (Oxford). 2014 Jul 22;2014. pii: bau067. doi: 10.1093/database/bau067. Print 2014.

5.

BioC interoperability track overview.

Comeau DC, Batista-Navarro RT, Dai HJ, Doğan RI, Yepes AJ, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M, Peng Y, Rak R, Rinaldi F, Tsai RT, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.

Database (Oxford). 2014 Jun 30;2014. pii: bau053. doi: 10.1093/database/bau053. Print 2014. Review.

6.

A Study of the Morpho-Semantic Relationship in Medline.

Wilbur WJ, Smith L.

Open Inf Syst J. 2013 Nov 21;6:1-12.

7.

BioC implementations in Go, Perl, Python and Ruby.

Liu W, Islamaj Doğan R, Kwon D, Marques H, Rinaldi F, Wilbur WJ, Comeau DC.

Database (Oxford). 2014 Jun 23;2014. pii: bau059. doi: 10.1093/database/bau059. Print 2014.

8.

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus.

Comeau DC, Liu H, Islamaj Doğan R, Wilbur WJ.

Database (Oxford). 2014 Jun 16;2014. pii: bau056. doi: 10.1093/database/bau056. Print 2014. Erratum in: Database (Oxford). 2014;2014:bau072.

9.

Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora.

Islamaj Doğan R, Comeau DC, Yeganova L, Wilbur WJ.

Database (Oxford). 2014 Jun 9;2014. pii: bau044. doi: 10.1093/database/bau044. Print 2014.

10.

Stochastic Gradient Descent and the Prediction of MeSH for PubMed Records.

Wilbur WJ, Kim W.

AMIA Annu Symp Proc. 2014 Nov 14;2014:1198-207. eCollection 2014.

11.

BioC: a minimalist approach to interoperability for biomedical text processing.

Comeau DC, Islamaj Doğan R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.

Database (Oxford). 2013 Sep 18;2013:bat064. doi: 10.1093/database/bat064. Print 2013.

12.

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.

13.

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.

14.

Finding biomedical categories in Medline®.

Yeganova L, Kim W, Comeau DC, Wilbur WJ.

J Biomed Semantics. 2012 Oct 5;3 Suppl 3:S3. doi: 10.1186/2041-1480-3-S3-S3. Epub 2012 Oct 5.

15.

Thematic clustering of text documents using an EM-based approach.

Kim S, Wilbur WJ.

J Biomed Semantics. 2012 Oct 5;3 Suppl 3:S6. doi: 10.1186/2041-1480-3-S3-S6. Epub 2012 Oct 5.

16.

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

Névéol A, Wilbur WJ, Lu Z.

Database (Oxford). 2012 Jun 8;2012:bas026. doi: 10.1093/database/bas026. Print 2012.

17.

Identifying well-formed biomedical phrases in MEDLINE® text.

Kim W, Yeganova L, Comeau DC, Wilbur WJ.

J Biomed Inform. 2012 Dec;45(6):1035-41. doi: 10.1016/j.jbi.2012.05.005. Epub 2012 Jun 8.

18.

PIE the search: searching PubMed literature for protein interaction information.

Kim S, Kwon D, Shin SY, Wilbur WJ.

Bioinformatics. 2012 Feb 15;28(4):597-8. doi: 10.1093/bioinformatics/btr702. Epub 2011 Dec 22.

19.

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.

20.

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.

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