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Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
Martin Krallinger, Alexander Morgan, Larry Smith, Florian Leitner, Lorraine Tanabe, John Wilbur, Lynette Hirschman, Alfonso Valencia
Genome Biol. 2008; 9(Suppl 2): S1. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s1
PMCID:
PMC2559980
Abstract Full Text PDF–848K

Is Cited by the Following 24 Articles in this Archive:

Open semantic annotation of scientific publications using DOMEO
Paolo Ciccarese, Marco Ocana, Tim Clark
J Biomed Semantics. 2012; 3(Suppl 1): S1. Published online 2012 April 24. doi: 10.1186/2041-1480-3-S1-S1
PMCID:
PMC3337259
Abstract Full Text PDF–1.8M
Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions
Keiichi Mochida, Kazuo Shinozaki
Plant Cell Physiol. 2011 December; 52(12): 2017–2038. Published online 2011 December 6. doi: 10.1093/pcp/pcr153
PMCID:
PMC3233218
Abstract Full Text PDF–1.6M
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus
Dietrich Rebholz-Schuhmann, Antonio Jimeno Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B Laurila, Christopher JO Baker, Cheng-Ju Kuo, Simone Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura I Furlong, Michael Rautschka, Mariana Lara Neves, Alberto Pascual-Montano, Qi Wei, Nigel Collier, Md Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik van Mulligen, Jan Kors, Udo Hahn
J Biomed Semantics. 2011; 2(Suppl 5): S11. Published online 2011 October 6. doi: 10.1186/2041-1480-2-S5-S11
PMCID:
PMC3239301
Abstract Full Text PDF–647K
Biblio-MetReS: A bibliometric network reconstruction application and server
Anabel Usié, Hiren Karathia, Ivan Teixidó, Joan Valls, Xavier Faus, Rui Alves, Francesc Solsona
BMC Bioinformatics. 2011; 12: 387. Published online 2011 October 5. doi: 10.1186/1471-2105-12-387
PMCID:
PMC3228545
Abstract Full Text PDF–1.0M Supplementary Material
Overview of the BioCreative III Workshop
Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H Wu
BMC Bioinformatics. 2011; 12(Suppl 8): S1. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S1
PMCID:
PMC3269932
Abstract Full Text PDF–228K
BioCreative III interactive task: an overview
Cecilia N Arighi, Phoebe M Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle Gwinn Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois J Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E Thomas, Luca Toldo, Lynette Hirschman, Cathy H Wu
BMC Bioinformatics. 2011; 12(Suppl 8): S4. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S4
PMCID:
PMC3269939
Abstract Full Text PDF–1.4M Supplementary Material
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization
Cheng-Ju Kuo, Maurice HT Ling, Chun-Nan Hsu
BMC Bioinformatics. 2011; 12(Suppl 8): S6. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S6
PMCID:
PMC3269941
Abstract Full Text PDF–668K
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
Classifying protein-protein interaction articles using word and syntactic features
Sun Kim, W John Wilbur
BMC Bioinformatics. 2011; 12(Suppl 8): S9. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S9
PMCID:
PMC3269944
Abstract Full Text PDF–507K
pubmed2ensembl: A Resource for Mining the Biological Literature on Genes
Joachim Baran, Martin Gerner, Maximilian Haeussler, Goran Nenadic, Casey M. Bergman
PLoS One. 2011; 6(9): e24716. Published online 2011 September 29. doi: 10.1371/journal.pone.0024716
PMCID:
PMC3183000
Abstract Full Text PDF–857K Supplementary Material
Literature curation of protein interactions: measuring agreement across major public databases
Andrei L. Turinsky, Sabry Razick, Brian Turner, Ian M. Donaldson, Shoshana J. Wodak
Database (Oxford) 2010; 2010: baq026. Published online 2010 December 22. doi: 10.1093/database/baq026
PMCID:
PMC3011985
Abstract Full Text PDF–1.1M
The structural and content aspects of abstracts versus bodies of full text journal articles are different
K Bretonnel Cohen, Helen L Johnson, Karin Verspoor, Christophe Roeder, Lawrence E Hunter
BMC Bioinformatics. 2010; 11: 492. Published online 2010 September 29. doi: 10.1186/1471-2105-11-492
PMCID:
PMC3098079
Abstract Full Text PDF–419K
Discriminative and informative features for biomolecular text mining with ensemble feature selection
Sofie Van Landeghem, Thomas Abeel, Yvan Saeys, Yves Van de Peer
Bioinformatics. 2010 September 15; 26(18): i554–i560. Published online 2010 September 4. doi: 10.1093/bioinformatics/btq381
PMCID:
PMC2935429
Abstract Full Text PDF–853K
eGIFT: Mining Gene Information from the Literature
Catalina O Tudor, Carl J Schmidt, K Vijay-Shanker
BMC Bioinformatics. 2010; 11: 418. Published online 2010 August 9. doi: 10.1186/1471-2105-11-418
PMCID:
PMC2929241
Abstract Full Text PDF–677K Supplementary Material
Exploring species-based strategies for gene normalization
Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner, Jr., Lawrence E. Hunter
IEEE/ACM Trans Comput Biol Bioinform. Author manuscript; available in PMC 2010 August 30.
Published in final edited form as: IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul–Sep; 7(3): 462–471. doi: 10.1109/TCBB.2010.48
PMCID:
PMC2929766
Abstract Full Text PDF–270K
Full Text and Figure Display Improves Bioscience Literature Search
Anna Divoli, Michael A. Wooldridge, Marti A. Hearst
PLoS One. 2010; 5(4): e9619. Published online 2010 April 14. doi: 10.1371/journal.pone.0009619
PMCID:
PMC2854679
Abstract Full Text PDF–1018K
Word add-in for ontology recognition: semantic enrichment of scientific literature
J Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex Wade, Oscar Naim, Gregory B Quinn, Philip E Bourne
BMC Bioinformatics. 2010; 11: 103. Published online 2010 February 24. doi: 10.1186/1471-2105-11-103
PMCID:
PMC2837026
Abstract Full Text PDF–658K
Disambiguating the species of biomedical named entities using natural language parsers
Xinglong Wang, Jun'ichi Tsujii, Sophia Ananiadou
Bioinformatics. 2010 March 1; 26(5): 661–667. Published online 2010 January 6. doi: 10.1093/bioinformatics/btq002
PMCID:
PMC2828111
Abstract Full Text PDF–181K
Automated Recognition of Brain Region Mentions in Neuroscience Literature
Leon French, Suzanne Lane, Lydia Xu, Paul Pavlidis
Front Neuroinformatics. 2009; 3: 29. Prepublished online 2009 July 7. Published online 2009 September 1. doi: 10.3389/neuro.11.029.2009
PMCID:
PMC2741206
Abstract Full Text PDF–282K
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
Martin Krallinger, Carlos Rodriguez-Penagos, Ashish Tendulkar, Alfonso Valencia
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W160–W165. Published online 2009 July 1. doi: 10.1093/nar/gkp484
PMCID:
PMC2703909
Abstract Full Text PDF–3.9M
The High Throughput Sequence Annotation Service (HT-SAS) – the shortcut from sequence to true Medline words
Szymon Kaczanowski, Pawel Siedlecki, Piotr Zielenkiewicz
BMC Bioinformatics. 2009; 10: 148. Published online 2009 May 16. doi: 10.1186/1471-2105-10-148
PMCID:
PMC2694793
Abstract Full Text PDF–266K Supplementary Material
Application and evaluation of automated semantic annotation of gene expression experiments
Leon French, Suzanne Lane, Tamryn Law, Lydia Xu, Paul Pavlidis
Bioinformatics. 2009 June 15; 25(12): 1543–1549. Published online 2009 April 17. doi: 10.1093/bioinformatics/btp259
PMCID:
PMC2687992
Abstract Full Text PDF–133K
Bayesian inference of protein–protein interactions from biological literature
Rajesh Chowdhary, Jinfeng Zhang, Jun S. Liu
Bioinformatics. 2009 June 15; 25(12): 1536–1542. Published online 2009 April 15. doi: 10.1093/bioinformatics/btp245
PMCID:
PMC2732911
Abstract Full Text PDF–176K
Biomedical Discovery Acceleration, with Applications to Craniofacial Development
Sonia M. Leach, Hannah Tipney, Weiguo Feng, William A. Baumgartner, Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter
PLoS Comput Biol. 2009 March; 5(3): e1000215. Published online 2009 March 27. doi: 10.1371/journal.pcbi.1000215
PMCID:
PMC2653649
Abstract Full Text PDF–1.6M Supplementary Material
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