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An open-source framework for large-scale, flexible evaluation of biomedical text mining systems.

Baumgartner WA Jr, Cohen KB, Hunter L.

J Biomed Discov Collab. 2008 Jan 29;3:1.PMID: 18230184 [PubMed - in process]Related articlesFree article

Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge.

Krallinger M, Morgan A, Smith L, Leitner F, Tanabe L, Wilbur J, Hirschman L, Valencia A.

Genome Biol. 2008;9 Suppl 2:S1. Epub 2008 Sep 1.PMID: 18834487 [PubMed - indexed for MEDLINE]Related articlesFree article

LINNAEUS: A species name identification system for biomedical literature.

Gerner M, Nenadic G, Bergman CM.

BMC Bioinformatics. 2010 Feb 11;11:85.PMID: 20149233 [PubMed - in process]Related articlesFree article

OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.

Hunter L, Lu Z, Firby J, Baumgartner WA Jr, Johnson HL, Ogren PV, Cohen KB.

BMC Bioinformatics. 2008 Jan 31;9:78.PMID: 18237434 [PubMed - indexed for MEDLINE]Related articlesFree article

Automated de-identification of free-text medical records.

Neamatullah I, Douglass MM, Lehman LW, Reisner A, Villarroel M, Long WJ, Szolovits P, Moody GB, Mark RG, Clifford GD.

BMC Med Inform Decis Mak. 2008 Jul 24;8:32.PMID: 18652655 [PubMed - indexed for MEDLINE]Related articlesFree article

Inter-species normalization of gene mentions with GNAT.

Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G.

Bioinformatics. 2008 Aug 15;24(16):i126-132.PMID: 18689813 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene mention normalization and interaction extraction with context models and sentence motifs.

Hakenberg J, Plake C, Royer L, Strobelt H, Leser U, Schroeder M.

Genome Biol. 2008;9 Suppl 2:S14. Epub 2008 Sep 1.PMID: 18834492 [PubMed - indexed for MEDLINE]Related articlesFree article

Corpus refactoring: a feasibility study.

Johnson HL, Baumgartner WA Jr, Krallinger M, Cohen KB, Hunter L.

J Biomed Discov Collab. 2007 Sep 13;2:4.PMID: 17854502 [PubMed - in process]Related articlesFree article

Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension.

Yu H, Agarwal S, Johnston M, Cohen A.

J Biomed Discov Collab. 2009 Jan 6;4:1.PMID: 19126221 [PubMed - in process]Related articlesFree article

Extraction of semantic biomedical relations from text using conditional random fields.

Bundschus M, Dejori M, Stetter M, Tresp V, Kriegel HP.

BMC Bioinformatics. 2008 Apr 23;9:207.PMID: 18433469 [PubMed - indexed for MEDLINE]Related articlesFree article

Concept recognition for extracting protein interaction relations from biomedical text.

Baumgartner WA Jr, Lu Z, Johnson HL, Caporaso JG, Paquette J, Lindemann A, White EK, Medvedeva O, Cohen KB, Hunter L.

Genome Biol. 2008;9 Suppl 2:S9. Epub 2008 Sep 1.PMID: 18834500 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18426548 [PubMed - indexed for MEDLINE]Related articlesFree article

BioTagger-GM: a gene/protein name recognition system.

Torii M, Hu Z, Wu CH, Liu H.

J Am Med Inform Assoc. 2009 Mar-Apr;16(2):247-55. Epub 2008 Dec 11.PMID: 19074302 [PubMed - indexed for MEDLINE]Related articlesFree article

Text mining.

Clegg AB, Shepherd AJ.

Methods Mol Biol. 2008;453:471-91.PMID: 18712320 [PubMed - indexed for MEDLINE]Related articles

Beyond genes, proteins, and abstracts: Identifying scientific claims from full-text biomedical articles.

Blake C.

J Biomed Inform. 2009 Nov 10. [Epub ahead of print]PMID: 19900574 [PubMed - as supplied by publisher]Related articles

Large scale application of neural network based semantic role labeling for automated relation extraction from biomedical texts.

Barnickel T, Weston J, Collobert R, Mewes HW, Stümpflen V.

PLoS One. 2009 Jul 28;4(7):e6393.PMID: 19636432 [PubMed - indexed for MEDLINE]Related articlesFree article

MutationFinder: a high-performance system for extracting point mutation mentions from text.

Caporaso JG, Baumgartner WA Jr, Randolph DA, Cohen KB, Hunter L.

Bioinformatics. 2007 Jul 15;23(14):1862-5. Epub 2007 May 11.PMID: 17495998 [PubMed - indexed for MEDLINE]Related articlesFree article

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

Winnenburg R, Wächter T, Plake C, Doms A, Schroeder M.

Brief Bioinform. 2008 Nov;9(6):466-78. Epub 2008 Dec 6. Review.PMID: 19060303 [PubMed - indexed for MEDLINE]Related articles

Enhanced information retrieval from narrative German-language clinical text documents using automated document classification.

Spat S, Cadonna B, Rakovac I, Gütl C, Leitner H, Stark G, Beck P.

Stud Health Technol Inform. 2008;136:473-8.PMID: 18487776 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 19515247 [PubMed - indexed for MEDLINE]Related articlesFree article