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Results: 1 to 20 of 85

1.

Retro: Concept based clustering of biomedical topical sets.

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

Bioinformatics. 2014 Jul 29. pii: btu514. [Epub ahead of print]

PMID:
25075115
[PubMed - as supplied by publisher]
2.

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.

PMID:
25052701
[PubMed - in process]
Free PMC Article
3.

BioC interoperability track overview.

Comeau DC, Batista-Navarro RT, Dai HJ, Islamaj Doğan R, Jimeno Yepes A, 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.

PMID:
24980129
[PubMed - in process]
Free PMC Article
4.

A Study of the Morpho-Semantic Relationship in Medline.

Wilbur WJ, Smith L.

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

PMID:
24976874
[PubMed]
Free PMC Article
5.

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.

PMID:
24961236
[PubMed - in process]
Free PMC Article
6.

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.

PMID:
24935050
[PubMed - in process]
Free PMC Article
7.

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.

PMID:
24914232
[PubMed - in process]
Free PMC Article
8.

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.

PMID:
24048470
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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
10.

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
11.

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.

PMID:
23046816
[PubMed]
Free PMC Article
12.

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.

PMID:
23046528
[PubMed]
Free PMC Article
13.

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.

PMID:
22685160
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
22683889
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
22199390
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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
17.

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
18.

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
19.

Classifying protein-protein interaction articles using word and syntactic features.

Kim S, Wilbur WJ.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S9. doi: 10.1186/1471-2105-12-S8-S9.

PMID:
22151252
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Karsch-Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25. doi: 10.1093/nar/gkr1184. Epub 2011 Dec 2.

PMID:
22140104
[PubMed - indexed for MEDLINE]
Free PMC Article

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