BMC Bioinformatics

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Corpus annotation for mining biomedical events from literature

Jin-Dong Kim*, Tomoko Ohta and Jun'ichi Tsujii

BMC Bioinformatics 2008, 9:10 doi:10.1186/1471-2105-9-10

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BioMed Central: 22 citations

Proceedings   Open Access

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011

Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun'ichi Tsujii, Sophia Ananiadou BMC Bioinformatics 2012, 13(Suppl 11):S2 (26 June 2012)

Research article   Open Access Highly Accessed

Constructing a semantic predication gold standard from the biomedical literature

Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C Rindflesch BMC Bioinformatics 2011, 12:486 (20 December 2011)

Research article   Open Access

U-Compare bio-event meta-service: compatible BioNLP event extraction services

Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana Neves, Alberto Pascual-Montano, Arzucan Özgür, Dragomir R Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii BMC Bioinformatics 2011, 12:481 (18 December 2011)

Research article   Open Access

Survival models with preclustered gene groups as covariates

Kai Kammers, Michel Lang, Jan G Hengstler, Marcus Schmidt, Jörg Rahnenführer BMC Bioinformatics 2011, 12:478 (16 December 2011)

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Enriching a biomedical event corpus with meta-knowledge annotation

Paul Thompson, Raheel Nawaz, John McNaught, Sophia Ananiadou BMC Bioinformatics 2011, 12:393 (10 October 2011)

An annotation scheme for meta-knowledge enrichment of biomedical event corpora achieves high levels of inter-annotator agreement when applied to the GENIA event corpus, and facilitates more sophisticated training of information extraction systems.

Research   Open Access

Linguistic scope-based and biological event-based speculation and negation annotations in the BioScope and Genia Event corpora

Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta, Richárd Farkas Journal of Biomedical Semantics 2011, 2(Suppl 5):S8 (6 October 2011)

Research   Open Access

Coreference based event-argument relation extraction on biomedical text

Katsumasa Yoshikawa, Sebastian Riedel, Tsutomu Hirao, Masayuki Asahara, Yuji Matsumoto Journal of Biomedical Semantics 2011, 2(Suppl 5):S6 (6 October 2011)

Research   Open Access

An analysis of gene/protein associations at PubMed scale

Sampo Pyysalo, Tomoko Ohta, Jun’ichi Tsujii Journal of Biomedical Semantics 2011, 2(Suppl 5):S5 (6 October 2011)

Poster presentation   Open Access

Medie and Info-pubmed: 2010 update

Tomoko Ohta, Takuya Matsuzaki, Naoaki Okazaki, Makoto Miwa, Rune Sætre, Sampo Pyysalo, Jun’ichi Tsujii BMC Bioinformatics 2010, 11(Suppl 5):P7 (6 October 2010)

Technical Note   Open Access

ISDB: Interaction Sentence Database

Michael A Bauer, Robert E Belford, Jing Ding, Daniel Berleant BMC Research Notes 2010, 3:122 (3 May 2010)

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Research article   Open Access

Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations

Aurélie Bonin, Margot Paris, Guillaume Tetreau, Jean-Philippe David, Laurence Després BMC Genomics 2009, 10:551 (21 November 2009)

Research   Open Access

BioDEAL: community generation of biological annotations

Paul Breimyer, Nathan Green, Vinay Kumar, Nagiza F Samatova BMC Medical Informatics and Decision Making 2009, 9(Suppl 1):S5 (3 November 2009)

Research article   Open Access

Construction of an annotated corpus to support biomedical information extraction

Paul Thompson, Syed A Iqbal, John McNaught, Sophia Ananiadou BMC Bioinformatics 2009, 10:349 (23 October 2009)

Research article   Open Access Highly Accessed

Challenges for automatically extracting molecular interactions from full-text articles

Tara McIntosh, James R Curran BMC Bioinformatics 2009, 10:311 (24 September 2009)

Research   Open Access

From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways

Anna Bauer-Mehren, Laura I Furlong, Michael Rautschka, Ferran Sanz BMC Bioinformatics 2009, 10(Suppl 8):S6 (27 August 2009)

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A realistic assessment of methods for extracting gene/protein interactions from free text

Renata Kabiljo, Andrew B Clegg, Adrian J Shepherd BMC Bioinformatics 2009, 10:233 (28 July 2009)

Proceedings   Open Access

Open Biomedical Ontology-based Medline exploration

Weijian Xuan, Manhong Dai, Barbara Mirel, Jean Song, Brian Athey, Stanley J Watson, Fan Meng BMC Bioinformatics 2009, 10(Suppl 5):S6 (6 May 2009)

Research   Open Access

The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes

Veronika Vincze, György Szarvas, Richárd Farkas, György Móra, János Csirik BMC Bioinformatics 2008, 9(Suppl 11):S9 (19 November 2008)

Research   Open Access

All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning

Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski BMC Bioinformatics 2008, 9(Suppl 11):S2 (19 November 2008)

Software   Open Access

BibGlimpse: The case for a light-weight reprint manager in distributed literature research

Thomas Tüchler, Golda Velez, Alexandra Graf, David P Kreil BMC Bioinformatics 2008, 9:406 (1 October 2008)

Proceedings   Open Access

Large-scale directional relationship extraction and resolution

Cory B Giles, Jonathan D Wren BMC Bioinformatics 2008, 9(Suppl 9):S11 (12 August 2008)

Proceedings   Open Access

New challenges for text mining: mapping between text and manually curated pathways

Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi, Jun'ichi Tsujii BMC Bioinformatics 2008, 9(Suppl 3):S5 (11 April 2008)