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Items: 1 to 20 of 115


Automated annotation of chemical names in the literature with tunable accuracy.

Zhang JD, Geer LY, Bolton EE, Bryant SH.

J Cheminform. 2011 Nov 22;3(1):52. doi: 10.1186/1758-2946-3-52.


Detection of IUPAC and IUPAC-like chemical names.

Klinger R, Kolárik C, Fluck J, Hofmann-Apitius M, Friedrich CM.

Bioinformatics. 2008 Jul 1;24(13):i268-76. doi: 10.1093/bioinformatics/btn181.


Discovering gene annotations in biomedical text databases.

Cakmak A, Ozsoyoglu G.

BMC Bioinformatics. 2008 Mar 6;9:143. doi: 10.1186/1471-2105-9-143.


An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R.

BMC Bioinformatics. 2005;6 Suppl 1:S17. Epub 2005 May 24.


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.


Assessment of disease named entity recognition on a corpus of annotated sentences.

Jimeno A, Jimenez-Ruiz E, Lee V, Gaudan S, Berlanga R, Rebholz-Schuhmann D.

BMC Bioinformatics. 2008 Apr 11;9 Suppl 3:S3. doi: 10.1186/1471-2105-9-S3-S3.


Tunable machine vision-based strategy for automated annotation of chemical databases.

Park J, Rosania GR, Saitou K.

J Chem Inf Model. 2009 Aug;49(8):1993-2001. doi: 10.1021/ci900029v.


Recognizing names in biomedical texts: a machine learning approach.

Zhou G, Zhang J, Su J, Shen D, Tan C.

Bioinformatics. 2004 May 1;20(7):1178-90. Epub 2004 Feb 10.


CheNER: a tool for the identification of chemical entities and their classes in biomedical literature.

Usié A, Cruz J, Comas J, Solsona F, Alves R.

J Cheminform. 2015 Jan 19;7(Suppl 1 Text mining for chemistry and the CHEMDNER track):S15. doi: 10.1186/1758-2946-7-S1-S15. eCollection 2015.


Assessment of NER solutions against the first and second CALBC Silver Standard Corpus.

Rebholz-Schuhmann D, Jimeno Yepes A, Li C, Kafkas S, Lewin I, Kang N, Corbett P, Milward D, Buyko E, Beisswanger E, Hornbostel K, Kouznetsov A, Witte R, Laurila JB, Baker CJ, Kuo CJ, Clematide S, Rinaldi F, Farkas R, Móra G, Hara K, Furlong LI, Rautschka M, Neves ML, Pascual-Montano A, Wei Q, Collier N, Chowdhury MF, Lavelli A, Berlanga R, Morante R, Van Asch V, Daelemans W, Marina JL, van Mulligen E, Kors J, Hahn U.

J Biomed Semantics. 2011 Oct 6;2 Suppl 5:S11. doi: 10.1186/2041-1480-2-S5-S11.


NetiNeti: discovery of scientific names from text using machine learning methods.

Akella LM, Norton CN, Miller H.

BMC Bioinformatics. 2012 Aug 22;13:211. doi: 10.1186/1471-2105-13-211.


Evaluation of BioCreAtIvE assessment of task 2.

Blaschke C, Leon EA, Krallinger M, Valencia A.

BMC Bioinformatics. 2005;6 Suppl 1:S16. Epub 2005 May 24.


Integrating various resources for gene name normalization.

Hu Y, Li Y, Lin H, Yang Z, Cheng L.

PLoS One. 2012;7(9):e43558. doi: 10.1371/journal.pone.0043558. Epub 2012 Sep 12.


Tagging gene and protein names in biomedical text.

Tanabe L, Wilbur WJ.

Bioinformatics. 2002 Aug;18(8):1124-32.


Finding genomic ontology terms in text using evidence content.

Couto FM, Silva MJ, Coutinho PM.

BMC Bioinformatics. 2005;6 Suppl 1:S21. Epub 2005 May 24.


A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment.

Guo Y, Korhonen A, Liakata M, Silins I, Hogberg J, Stenius U.

BMC Bioinformatics. 2011 Mar 8;12:69. doi: 10.1186/1471-2105-12-69.


Search strategies to identify diagnostic accuracy studies in MEDLINE and EMBASE.

Beynon R, Leeflang MM, McDonald S, Eisinga A, Mitchell RL, Whiting P, Glanville JM.

Cochrane Database Syst Rev. 2013 Sep 11;(9):MR000022. doi: 10.1002/14651858.MR000022.pub3. Review.


Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets.

Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ.

J Biomed Inform. 2011 Dec;44 Suppl 1:S39-43. doi: 10.1016/j.jbi.2011.03.007. Epub 2011 Mar 21.


Protein function prediction using text-based features extracted from the biomedical literature: the CAFA challenge.

Wong A, Shatkay H.

BMC Bioinformatics. 2013;14 Suppl 3:S14. doi: 10.1186/1471-2105-14-S3-S14. Epub 2013 Feb 28.

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