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Overview of the protein-protein interaction annotation extraction task of BioCreative II
Martin Krallinger, Florian Leitner, Carlos Rodriguez-Penagos, Alfonso Valencia
Genome Biol. 2008; 9(Suppl 2): S4. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s4
PMCID:
PMC2559988
Abstract Full Text PDF–2.2M

Is Cited by the Following 31 Articles in this Archive:

Using ODIN for a PharmGKB revalidation experiment
Fabio Rinaldi, Simon Clematide, Yael Garten, Michelle Whirl-Carrillo, Li Gong, Joan M. Hebert, Katrin Sangkuhl, Caroline F. Thorn, Teri E. Klein, Russ B. Altman
Database (Oxford) 2012; 2012: bas021. Published online 2012 April 23. doi: 10.1093/database/bas021
PMCID:
PMC3332569
Abstract Full Text PDF–1.3M
Text mining for the biocuration workflow
Lynette Hirschman, Gully A. P. C Burns, Martin Krallinger, Cecilia Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-Aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert Nash, Anne-Lise Veuthey, Thomas Wiegers, Andrew G. Winter
Database (Oxford) 2012; 2012: bas020. Published online 2012 April 18. doi: 10.1093/database/bas020
PMCID:
PMC3328793
Abstract Full Text PDF–306K
How to link ontologies and protein–protein interactions to literature: text-mining approaches and the BioCreative experience
Martin Krallinger, Florian Leitner, Miguel Vazquez, David Salgado, Christophe Marcelle, Mike Tyers, Alfonso Valencia, Andrew Chatr-aryamontri
Database (Oxford) 2012; 2012: bas017. Published online 2012 March 21. doi: 10.1093/database/bas017
PMCID:
PMC3309177
Abstract Full Text PDF–1.7M
IMID: integrated molecular interaction database
Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S. Liu, Jinfeng Zhang
Bioinformatics. 2012 March 1; 28(5): 747–749. Published online 2012 January 11. doi: 10.1093/bioinformatics/bts010
PMCID:
PMC3289914
Free in PMC on 2013/03/01
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. Published online 2011 December 18. doi: 10.1186/1471-2105-12-481
PMCID:
PMC3299809
Full Text PDF–374K
Extraction of data deposition statements from the literature: a method for automatically tracking research results
Aurélie Névéol, W. John Wilbur, Zhiyong Lu
Bioinformatics. 2011 December 1; 27(23): 3306–3312. Published online 2011 October 13. doi: 10.1093/bioinformatics/btr573
PMCID:
PMC3223368
Abstract Full Text PDF–300K Supplementary Material
The BioLexicon: a large-scale terminological resource for biomedical text mining
Paul Thompson, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, Valeria Quochi, CJ Rupp, Yutaka Sasaki, Giulia Venturi, Dietrich Rebholz-Schuhmann, Sophia Ananiadou
BMC Bioinformatics. 2011; 12: 397. Published online 2011 October 12. doi: 10.1186/1471-2105-12-397
PMCID:
PMC3228855
Abstract Full Text PDF–3.2M
Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature
Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, CJ Rupp, Riza Theresa B Batista-Navarro, Raheel Nawaz, Sophia Ananiadou
BMC Bioinformatics. 2011; 12(Suppl 8): S11. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S11
PMCID:
PMC3269934
Abstract Full Text PDF–524K
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sergio Matos, Sun Kim, W John Wilbur, Luis Rocha, Hagit Shatkay, Ashish V Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu, Rezarta Islamaj Dogan, Jean-Fred Fontaine, Miguel A Andrade-Navarro, Alfonso Valencia
BMC Bioinformatics. 2011; 12(Suppl 8): S3. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S3
PMCID:
PMC3269938
Abstract Full Text PDF–948K Supplementary Material
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases
Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers
BMC Bioinformatics. 2011; 12(Suppl 8): S8. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S8
PMCID:
PMC3269943
Abstract Full Text PDF–480K
Automatic extraction of angiogenesis bioprocess from text
Xinglong Wang, Iain McKendrick, Ian Barrett, Ian Dix, Tim French, Jun'ichi Tsujii, Sophia Ananiadou
Bioinformatics. 2011 October 1; 27(19): 2730–2737. Published online 2011 August 5. doi: 10.1093/bioinformatics/btr460
PMCID:
PMC3179660
Abstract Full Text PDF–257K
Integrated Bio-Entity Network: A System for Biological Knowledge Discovery
Lindsey Bell, Rajesh Chowdhary, Jun S. Liu, Xufeng Niu, Jinfeng Zhang
PLoS One. 2011; 6(6): e21474. Published online 2011 June 27. doi: 10.1371/journal.pone.0021474
PMCID:
PMC3124513
Abstract Full Text PDF–472K Supplementary Material
A context-blocks model for identifying clinical relationships in patient records
Rezarta Islamaj Doğan, Aurélie Névéol, Zhiyong Lu
BMC Bioinformatics. 2011; 12(Suppl 3): S3. Published online 2011 June 9. doi: 10.1186/1471-2105-12-S3-S3
PMCID:
PMC3111589
Abstract Full Text PDF–690K
A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents
Isabel Segura-Bedmar, Paloma Martínez, César de Pablo-Sánchez
BMC Bioinformatics. 2011; 12(Suppl 2): S1. Published online 2011 March 29. doi: 10.1186/1471-2105-12-S2-S1
PMCID:
PMC3073181
Abstract Full Text PDF–401K
PubMed and beyond: a survey of web tools for searching biomedical literature
Zhiyong Lu
Database (Oxford) 2011; 2011: baq036. Published online 2011 January 17. doi: 10.1093/database/baq036
PMCID:
PMC3025693
Abstract Full Text PDF–573K
The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions
Martin Krallinger, Ashish V Tendulkar, Florian Leitner, Andrew Chatr-aryamontri, Alfonso Valencia
BMC Bioinformatics. 2010; 11(Suppl 5): O1. Published online 2010 October 6. doi: 10.1186/1471-2105-11-S5-O1
PMCID:
PMC2956388
Full Text PDF–390K
Simple tricks for improving pattern-based information extraction from the biomedical literature
Quang Long Nguyen, Domonkos Tikk, Ulf Leser
J Biomed Semantics. 2010; 1: 9. Published online 2010 September 24. doi: 10.1186/2041-1480-1-9
PMCID:
PMC2955645
Abstract Full Text PDF–735K Supplementary Material
A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature
Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg, Ulf Leser
PLoS Comput Biol. 2010 July; 6(7): e1000837. Published online 2010 July 1. doi: 10.1371/journal.pcbi.1000837
PMCID:
PMC2895635
Abstract Full Text PDF–2.2M Supplementary Material
Complex event extraction at PubMed scale
Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski
Bioinformatics. 2010 June 15; 26(12): i382–i390. Published online 2010 June 1. doi: 10.1093/bioinformatics/btq180
PMCID:
PMC2881365
Abstract Full Text PDF–414K
Document classification for mining host pathogen protein-protein interactions
Lanlan Yin, Guixian Xu, Manabu Torii, Zhendong Niu, Jose M. Maisog, Cathy Wu, Zhangzhi Hu, Hongfang Liu
Artif Intell Med. Author manuscript; available in PMC 2011 July 1.
Published in final edited form as: Artif Intell Med. 2010 July; 49(3): 155–160. Published online 2010 May 15. doi: 10.1016/j.artmed.2010.04.003
PMCID:
PMC2902599
Abstract Full Text PDF–831K
Learning an enriched representation from unlabeled data for protein-protein interaction extraction
Yanpeng Li, Xiaohua Hu, Hongfei Lin, Zhihao Yang
BMC Bioinformatics. 2010; 11(Suppl 2): S7. Published online 2010 April 16. doi: 10.1186/1471-2105-11-S2-S7
PMCID:
PMC3166043
Abstract Full Text PDF–731K
LINNAEUS: A species name identification system for biomedical literature
Martin Gerner, Goran Nenadic, Casey M Bergman
BMC Bioinformatics. 2010; 11: 85. Published online 2010 February 11. doi: 10.1186/1471-2105-11-85
PMCID:
PMC2836304
Abstract Full Text PDF–532K Supplementary Material
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships
Adriano Barbosa-Silva, Theodoros G Soldatos, Ivan LF Magalhães, Georgios A Pavlopoulos, Jean-Fred Fontaine, Miguel A Andrade-Navarro, Reinhard Schneider, J Miguel Ortega
BMC Bioinformatics. 2010; 11: 70. Published online 2010 February 1. doi: 10.1186/1471-2105-11-70
PMCID:
PMC3098111
Abstract Full Text PDF–381K Supplementary Material
BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature
Cheng-Ju Kuo, Maurice HT Ling, Kuan-Ting Lin, Chun-Nan Hsu
BMC Bioinformatics. 2009; 10(Suppl 15): S7. Published online 2009 December 3. doi: 10.1186/1471-2105-10-S15-S7
PMCID:
PMC2788358
Abstract Full Text PDF–321K
Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans
Ivan Iossifov, Raul Rodriguez-Esteban, Ilya Mayzus, Kathleen J. Millen, Andrey Rzhetsky
PLoS Comput Biol. 2009 November; 5(11): e1000559. Published online 2009 November 6. doi: 10.1371/journal.pcbi.1000559
PMCID:
PMC2767227
Abstract Full Text PDF–630K Supplementary Material
Construction of an annotated corpus to support biomedical information extraction
Paul Thompson, Syed A Iqbal, John McNaught, Sophia Ananiadou
BMC Bioinformatics. 2009; 10: 349. Published online 2009 October 23. doi: 10.1186/1471-2105-10-349
PMCID:
PMC2774701
Abstract Full Text PDF–381K Supplementary Material
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D
Yun Niu, David Otasek, Igor Jurisica
Bioinformatics. 2010 January 1; 26(1): 111–119. Published online 2009 October 22. doi: 10.1093/bioinformatics/btp602
PMCID:
PMC2796811
Abstract Full Text PDF–951K
Enhancing navigation in biomedical databases by community voting and database-driven text classification
Timo Duchrow, Timur Shtatland, Daniel Guettler, Misha Pivovarov, Stefan Kramer, Ralph Weissleder
BMC Bioinformatics. 2009; 10: 317. Published online 2009 October 3. doi: 10.1186/1471-2105-10-317
PMCID:
PMC2768718
Abstract Full Text PDF–1.0M
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. Published online 2009 July 28. doi: 10.1186/1471-2105-10-233
PMCID:
PMC2723093
Abstract Full Text PDF–263K Supplementary Material
The textual characteristics of traditional and Open Access scientific journals are similar
Karin Verspoor, K Bretonnel Cohen, Lawrence Hunter
BMC Bioinformatics. 2009; 10: 183. Published online 2009 June 15. doi: 10.1186/1471-2105-10-183
PMCID:
PMC2714574
Abstract Full Text PDF–472K
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