BMC Bioinformatics

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This article is part of the supplement: A critical assessment of text mining methods in molecular biology

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ProMiner: rule-based protein and gene entity recognition

Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer and Juliane Fluck*

BMC Bioinformatics 2005, 6(Suppl 1):S14 doi:10.1186/1471-2105-6-S1-S14

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Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)

Elina Tjioe, Michael W Berry, Ramin Homayouni BMC Bioinformatics 2010, 11(Suppl 6):S14 (7 October 2010)

Research article   Open Access

Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model

Xin He, Moushumi Sarma, Xu Ling, Brant Chee, Chengxiang Zhai, Bruce Schatz BMC Bioinformatics 2010, 11:272 (20 May 2010)

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LINNAEUS: A species name identification system for biomedical literature

Martin Gerner, Goran Nenadic, Casey M Bergman BMC Bioinformatics 2010, 11:85 (11 February 2010)

Research article   Open Access

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)

Thomas C Wiegers, Allan Davis, K Bretonnel Cohen, Lynette Hirschman, Carolyn J Mattingly BMC Bioinformatics 2009, 10:326 (8 October 2009)

Research   Open Access

EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts

Süveyda Yeniterzi, Uğur Sezerman BMC Bioinformatics 2009, 10(Suppl 8):S2 (27 August 2009)

Research   Open Access

Identification of histone modifications in biomedical text for supporting epigenomic research

Corinna Kolářik, Roman Klinger, Martin Hofmann-Apitius BMC Bioinformatics 2009, 10(Suppl 1):S28 (30 January 2009)

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Distinguishing the species of biomedical named entities for term identification

Xinglong Wang, Michael Matthews BMC Bioinformatics 2008, 9(Suppl 11):S6 (19 November 2008)

Oral presentation   Open Access

Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation

David Ruau, Corinna Kolárik, Heinz-Theodor Mevissen, Emmanuel Müller, Ira Assent, Ralph Krieger, Thomas Seidl, Martin Hofmann-Apitius, Martin Zenke BMC Bioinformatics 2008, 9(Suppl 10):O5 (30 October 2008)

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Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Martin Krallinger, Alfonso Valencia, Lynette Hirschman Genome Biology 2008, 9(Suppl 2):S8 (1 September 2008)

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Overview of BioCreative II gene normalization

Alexander A Morgan, Zhiyong Lu, Xinglong Wang, Aaron M Cohen, Juliane Fluck, Patrick Ruch, Anna Divoli, Katrin Fundel, Robert Leaman, Jörg Hakenberg, Chengjie Sun, Heng-hui Liu, Rafael Torres, Michael Krauthammer, William W Lau, Hongfang Liu, Chun-Nan Hsu, Martijn Schuemie, K Bretonnel Cohen, Lynette Hirschman Genome Biology 2008, 9(Suppl 2):S3 (1 September 2008)

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Normalizing biomedical terms by minimizing ambiguity and variability

Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou BMC Bioinformatics 2008, 9(Suppl 3):S2 (11 April 2008)

Methodology article   Open Access

OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

Laura I Furlong, Holger Dach, Martin Hofmann-Apitius, Ferran Sanz BMC Bioinformatics 2008, 9:84 (5 February 2008)

Methodology article   Open Access

The strength of co-authorship in gene name disambiguation

Richárd Farkas BMC Bioinformatics 2008, 9:69 (29 January 2008)

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A graph-search framework for associating gene identifiers with documents

William W Cohen, Einat Minkov BMC Bioinformatics 2006, 7:440 (10 October 2006)

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Gene and protein nomenclature in public databases

Katrin Fundel, Ralf Zimmer BMC Bioinformatics 2006, 7:372 (9 August 2006)

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The Autoimmune Disease Database: a dynamically compiled literature-derived database

Thomas Karopka, Juliane Fluck, Heinz-Theodor Mevissen, Änne Glass BMC Bioinformatics 2006, 7:325 (27 June 2006)

Report   Open Access

Overview of BioCreAtIvE task 1B: normalized gene lists

Lynette Hirschman, Marc Colosimo, Alexander Morgan, Alexander Yeh BMC Bioinformatics 2005, 6(Suppl 1):S11 (24 May 2005)

Introduction   Open Access Highly Accessed

Overview of BioCreAtIvE: critical assessment of information extraction for biology

Lynette Hirschman, Alexander Yeh, Christian Blaschke, Alfonso Valencia BMC Bioinformatics 2005, 6(Suppl 1):S1 (24 May 2005)