Links | research papers and tutorials (BioNLP)

[List of journals relevant to computational biology]

BioNLP - mining biomedical literature

BioNLP by date - [By topic]

*** May 7 2012 ***
Boosting automatic event extraction from the literature using domain adaptation and coreference resolution
Makoto Miwa, Paul Thompson, and Sophia Ananiadou
Bioinformatics published 25 April 2012
DOI: 10.1093/bioinformatics/bts237
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts237v1?papetoc
(OA)

*** May 4 2012 ***
Using PharmGKB to Train text mining approaches for identifying potential gene targets for pharmacogenomic studies
S. Pakhomov, B.T. Mcinnes, J. Lamba, Y. Liu, G.B. Melton, Y. Ghodke, N. Bhise, V. Lamba, A.K. Birnbaum
J Biomed Inform, In Press, Available online 4 May 2012
DOI: 10.1016/j.jbi.2012.04.007

A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions
Jörg Hakenberg, Dmitry Voronov, Vo Ha Nguyen, Shanshan Liang, Saadat Anwar, Barry Lumpkin, Robert Leaman, Luis Tari, Chitta Baral
J Biomed Inform, In Press, Uncorrected Proof, Available online 30 April 2012
DOI: 10.1016/j.jbi.2012.04.006

A knowledge-driven conditional approach to extract pharmacogenomics specific drug.gene relationships from free text
Rong Xu, QuanQiu Wang
J Biomed Inform, In Press, Uncorrected Proof, Available online 27 April 2012
DOI: 10.1016/j.jbi.2012.04.011

Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports
Harsha Gurulingappa, Abdul Mateen Rajput, Angus Roberts, Juliane Fluck, Martin Hofmann-Apitius, Luca Toldo
J Biomed Inform, In Press, Uncorrected Proof, Available online 25 April 2012
DOI: 10.1016/j.jbi.2012.04.008

The EU-ADR corpus: Annotated drugs, diseases, targets, and their relationships
Erik M. van Mulligen, Annie Fourrier-Reglat, David Gurwitz, Mariam Molokhia, Ainhoa Nieto, Gianluca Trifiro, Jan A. Kors, Laura I. Furlong
J Biomed Inform, In Press, Uncorrected Proof, Available online 25 April 2012
DOI: 10.1016/j.jbi.2012.04.004

Systematic identification of pharmacogenomics information from clinical trials
Jiao Li, Zhiyong Lu
J Biomed Inform, In Press, Uncorrected Proof, Available online 23 April 2012
DOI: 10.1016/j.jbi.2012.04.005

*** Apr 27 2012 ***
Harmonization of gene/protein annotations: towards a gold standard MEDLINE
David Campos, Sergio Matos, Ian Lewin, Jose Luis Oliveira and Dietrich Rebholz-Schuhmann
Bioinformatics, Vol. 28 no. 9 2012, pages 1253-1261
doi: 10.1093/bioinformatics/bts125

*** Apr 20 2012 ***
Using text-mining techniques in electronic patient records to identify ADRs from medicine use
Warrer P, Hansen EH, Juhl-Jensen L, Aagaard L.
Br J Clin Pharmacol. 2012 May;73(5):674-84
doi: 10.1111/j.1365-2125.2011.04153.x.
PMID: 22122057

*** Mar 19 2012 ***
Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches
Thanh Thieu, Sneha Joshi, Samantha Warren, and Dmitry Korkin
Bioinformatics 2012 28: 867-875
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/28/6/867?etoc

*** Feb 28 2012 ***
Mining and evaluation of molecular relationships in literature
Christian Senger, Bjorn A. Gruning, Anika Erxleben, Kersten Doring, Hitesh Patel, Stephan Flemming, Irmgard Merfort, and Stefan Gunther
Bioinformatics 2012 28: 709-714
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/28/5/709?etoc

*** Feb 5 2012 ***
Training text chunkers on a silver standard corpus: can silver replace gold?
Kang N, van Mulligen EM, Kors JA
BMC Bioinformatics 2012, 13:17 (30 January 2012)
Abstract: http://www.biomedcentral.com/1471-2105/13/17/abstract
PubMed: 22289351

*** Feb 2 2012 ***
Caipirini: using gene sets to rank literature
Soldatos TG, O'Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos GA, Wanderley-Nogueira A, Soares-Cavalcanti N, Schneider R
BioData Mining 2012, 5:1 (1 February 2012)
Abstract: http://www.biodatamining.org/content/5/1/1/abstract

*** Jan 27 ***
Automatic categorization of diverse experimental information in the bioscience literature
Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli M, Marygold S, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW
BMC Bioinformatics 2012, 13:16 (26 January 2012)
Abstract: http://www.biomedcentral.com/1471-2105/13/16/abstract

*** Jan 2 2012 ***
PIE the search: searching PubMed literature for protein interaction information
Sun Kim, Dongseop Kwon, Soo-Yong Shin, and W. John Wilbur
Bioinformatics published 22 December 2011
DOI: 10.1093/bioinformatics/btr702
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btr702v1?papetoc

*** Dec 27 2011 ***
Constructing a semantic predication gold standard from the biomedical literature
Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC
BMC Bioinformatics 2011, 12:486 (20 December 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/486/abstract
PubMed: http://www.biomedcentral.com/pubmed/22185221

Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation
Seymour E, Damle R, Sette A, Peters B
BMC Bioinformatics 2011, 12:482 (19 December 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/482/abstract
PubMed: http://www.biomedcentral.com/pubmed/22182279

*** Dec 19 2011 ***
MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature
Fang Y, Lai P, Dai H, Hsu W
BMC Bioinformatics 2011, 12:471 (14 December 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/471/abstract

U-Compare bio-event meta-service: compatible BioNLP event extraction services
Kano Y, Bjorne J, Ginter F, Salakoski T, Buyko E, Hahn U, Cohen KB, Verspoor K, Roeder C, Hunter LE, Kilicoglu H, Bergler S, Landeghem SV, Parys TV, Peer YV, Miwa M, Ananiadou S, Neves M, Pascual-Montano A, Ozgur A, Radev DR, Riedel S, Saetre R, Chun H, Kim J, Pyysalo S, Ohta T, Tsujii J
BMC Bioinformatics 2011, 12:481 (18 December 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/481/abstract

*** Dec 5 2011 ***
Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices
Nathan Harmston, Wendy Filsell, and Michael Stumpf
Bioinformatics, 28:254-260, 2012; First published online: November 30, 2011
DOI: 10.1093/bioinformatics/btr640
(OA)

*** Nov 28 2011 ***
Nine papers on the BioNLP'09 Shared T
ask are now available in a specia
l issue of COIN, 27(4), November 27, 2011

*** Nov 24 2011 ***
Extraction of data deposition statements from the literature: a method for automatically tracking research results
Aurelie Neveol, W. John Wilbur, and Zhiyong Lu
Bioinformatics 2011, 27:3306-3312
DOI: 10.1093/bioinformatics/btr573
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/23/3306?etoc

BioTextQuest: a web-based biomedical text mining suite for concept discovery
Nikolas Papanikolaou, Evangelos Pafilis, Stavros Nikolaou, Christos A. Ouzounis, Ioannis Iliopoulos, and Vasilis J. Promponas
Bioinformatics 2011, 27:3327-3328
DOI: 10.1093/bioinformatics/btr564.
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/23/3327?etoc
(OA)

*** Nov 22 2011 ***
Special issue of BMC Bioinformatics on BioCreative III
http://www.biomedcentral.com/bmcbioinformatics/12?issue=S8
(OA)

*** Nov 21 2011 ***
A.J. Jimeno-Yepes, B.T. McInnes, A.R. Aronson
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation
BMC Bioinformatics, 12:223, 2011
(C) (WSD)

*** Nov 17 2011 ***
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries
Barbosa-Silva A, Fontaine J, Donnard ER, Stussi F, Ortega J, Andrade-Navarro MA
BMC Bioinformatics 2011, 12:435 (9 November 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/435/abstract

BioNOT: A searchable database of biomedical negated sentences
Agarwal, Yu, Kohane
BMC Bioinformatics 2011, 12:420
DOI: 10.1186/1471-2105-12-420
(C)

*** Oct 21 2011 ***
Extraction of data deposition statements from the literature: a method for automatically tracking research results
Aurelie Neveol, W. John Wilbur, and Zhiyong Lu
Bioinformatics published 13 October 2011
DOI: 10.1093/bioinformatics/btr573
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btr573v1?papetoc

*** Oct 17 2011 ***
LBM 2011 - List of accepted papers
http://lbm2011.biopathway.org/index.php?p=accepted_papers

The BioLexicon: a large-scale terminological resource for biomedical text mining
Thompson P, McNaught J, Montemagni S, Calzolari N, del Gratta R, Lee V, Marchi S, Monachini M, Pezik P, Quochi V, Rupp C, Sasaki Y, Venturi G, Rebholz-Schuhmann D, Ananiadou S
BMC Bioinformatics 2011, 12:397 (12 October 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/397/abstract

Enriching a biomedical event corpus with meta-knowledge annotation
Thompson P, Nawaz R, McNaught J, Ananiadou S
BMC Bioinformatics 2011, 12:393 (10 October 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/393/abstract
PubMed: http://www.biomedcentral.com/pubmed/21985429

*** Sep 30 2011 ***
pubmed2ensembl: A Resource for Mining the Biological Literature on Genes
Joachim Baran, Martin Gerner, Maximilian Haeussler, Goran Nenadic, Casey M. Bergman
PLoS ONE 6(9):e24716
DOI: 10.1371/journal.pone.0024716
Availability: http://www.pubmed2ensembl.org

*** Sep 29 2011 ***
Weakly-supervised learning of information structure of scientific abstracts - is it accurate enough to benefit real-world tasks in biomedicine?
Yufan Guo, Anna Korhonen, Ilona Silins, and Ulla Stenius
Bioinformatics (2011), first published online: September 22, 2011
DOI: 10.1093/bioinformatics/btr536
PMID: 21949269
Availability: http://www.cl.cam.ac.uk/~yg244/11bioinfo.html

Neighborhood hash graph kernel for protein.protein interaction extraction
Yijia Zhang, Hongfei Lin, Zhihao Yang, Yanpeng Li
Journal of Biomedical Informatics, 2011
DOI: 10.1016/j.jbi.2011.08.011

*** August 25 2011 ***
A Statistical Approach for Extracting Protein-Protein Interactions
Lindsey Bell, Jinfeng Zhang, Xufeng Niu
Short paper at ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011, August 1-3, Chicago
Corpus: http://stat.fsu.edu/~jinfeng/resources/PICAD.txt
(C) (PPI)

*** August 12 2011 ***
OrganismTagger: Detection, normalization, and grounding of organism entities in biomedical documents.
Naderi N, Kappler T, Baker CJ, Witte R
Bioinformatics. 2011 Aug 9
PMID: 21828087

Automatic Extraction of Angiogenesis Bio-Process from Text.
Wang X, McKendrick I, Barrett I, Dix I, French T, Tsujii J, Ananiadou S
Bioinformatics. 2011 Aug 5
PMID: 21821664

The GNAT library for local and remote gene mention normalization.
Hakenberg J, Gerner M, Haeussler M, Solt I, Plake C, Schroeder M, Gonzalez G, Nenadic G, Bergman CM
Bioinformatics. 2011 Aug 3
PMID: 21813477

*** August 1 2011 ***
Integration of Gene Normalization Stages and Co-reference Resolution Using a Markov-Logic Network
Hong-Jie Dai, Yen-Ching Chang, Richard Tzong-Han Tsai, Wen-Lian Hsu
Bioinformatics. 2011 Jun 17

Text mining and visualisation of Protein-Protein Interactions.
Tsai FS
Int J Comput Biol Drug Des. 2011;4(3):239-44
PMID: 21778557

*** July 20 2011 ***
Literature mining, ontologies and information visualization for drug repurposing
Christos Andronis, Anuj Sharma, Vassilis Virvilis, Spyros Deftereos, and Aris Persidis
Brief Bioinform 2011 12: 357-368
DOI: 10.1093/bib/bbr005
PMID: 21712342
Abstract: http://bib.oxfordjournals.org/cgi/content/abstract/12/4/357?etoc

*** July 10 2011 ***
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers
Philippe E Thomas, Roman Klinger, Laura I Furlong, Martin Hofmann-Apitius, and Christoph M Friedrich
BMC Bioinformatics 2011, 12(Suppl 4):S4
DOI: 10.1186/1471-2105-12-S4-S4
Paper: http://www.biomedcentral.com/1471-2105/12/S4/S4

A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
Jeroen F J Laros, Andre Blavier, Johan T den Dunnen, and Peter E M Taschner
BMC Bioinformatics 2011, 12(Suppl 4):S5
DOI: 10.1186/1471-2105-12-S4-S5
Paper: http://www.biomedcentral.com/1471-2105/12/S4/S5

Deploying mutation impact text-mining software with the SADI Semantic Web Services framework
Alexandre Riazanov, Jonas Bergman Laurila, and Christopher JO Baker
BMC Bioinformatics 2011, 12(Suppl 4):S6
DOI: 10.1186/1471-2105-12-S4-S6
Paper: http://www.biomedcentral.com/1471-2105/12/S4/S6

*** June 29 2011 ***
CoPub update: CoPub 5.0 a text mining system to answer biological questions
Wilco W. M. Fleuren, Stefan Verhoeven, Raoul Frijters, Bart Heupers, Jan Polman, Rene van Schaik, Jacob de Vlieg, and Wynand Alkema
Nucl. Acids Res., 2011, 39:W450-W454.
Abstract: http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W450?etoc

Genie: literature-based gene prioritization at multi genomic scale
Jean-Fred Fontaine, Florian Priller, Adriano Barbosa-Silva, and Miguel A. Andrade-Navarro
Nucl. Acids Res., 2011, 39:W455-W461.
Abstract: http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W455?etoc

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature
Moushumi Sen Sarma, David Arcoleo, Radhika S. Khetani, Brant Chee, Xu Ling, Xin He, Jing Jiang, Qiaozhu Mei, ChengXiang Zhai, and Bruce Schatz
Nucl. Acids Res., 2011, 39:W462-W469.
Abstract: http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W462?etoc

Literature mining, ontologies and information visualization for drug repurposing
Christos Andronis, Anuj Sharma, Vassilis Virvilis, Spyros Deftereos, and Aris Persidis
Brief Bioinform published 28 June 2011
DOI: 10.1093/bib/bbr005
Abstract: http://bib.oxfordjournals.org/cgi/content/abstract/bbr005v1?papetoc

*** June 21 2011 ***
Combining literature text mining with microarray data: advances for system biology modeling
Alberto Faro, Daniela Giordano, and Concetto Spampinato
Brief Bioinform published 15 June 2011
DOI: 10.1093/bib/bbr018
Abstract: http://bib.oxfordjournals.org/cgi/content/abstract/bbr018v1?papetoc

Discovering and visualizing indirect associations between biomedical concepts
Yoshimasa Tsuruoka; Makoto Miwa; Kaisei Hamamoto; Jun'ichi Tsujii; Sophia Ananiadou
Bioinformatics 2011 27: i111-i119
http://bioinformatics.oxfordjournals.org/content/27/13/i111.short

*** June 16 2011 ***
Discovering and visualizing indirect associations between biomedical concepts
Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun'ichi Tsujii, and Sophia Ananiadou
Bioinformatics 2011 27: i111-i119
DOI: 10.1093/bioinformatics/btr214.
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/13/i111?etoc
(OA)

MeSH: a window into full text for document summarization
Sanmitra Bhattacharya, Viet Ha-Thuc, and Padmini Srinivasan
Bioinformatics 2011 27: i120-i128
DOI: 10.1093/bioinformatics/btr223.
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/13/i120?etoc
(OA)

Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases
Filipe Santana, Daniel Schober, Zulma Medeiros, Fred Freitas, and Stefan Schulz
Bioinformatics 2011 27: i349-i356
DOI: 10.1093/bioinformatics/btr226.
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/13/i349?etoc
(ONT) (OA)

*** June 14 2011 ***
Question Answering Systems in biology and medicine - the time is now
Jonathan D. Wren
Bioinformatics published 14 June 2011
DOI: 10.1093/bioinformatics/btr327
Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/btr327v1?papetoc

Proc. Machine Learning for Biomedical Literature Analysis and Text Retrieval in the International Conference for Machine Learning and Applications 2010
Supplement of BMC Bioinformatics
Contents of Volume 12 Suppl 3
Washington, DC, USA. 12-14 December 2010
Edited by Lana Yeganova and Rezarta Islamaj Dogan
ToC: http://www.biomedcentral.com/1471-2105/12?issue=S3

Building a biomedical tokenizer using the token lattice design pattern and the adapted Viterbi algorithm
Neil Barrett, Jens Weber-Jahnke
BMC Bioinformatics 2011, 12(Suppl 3):S1 (18 May 2011)

A system for de-identifying medical message board text
Adrian Benton, Shawndra Hill, Lyle Ungar, Annie Chung, Charles Leonard, Cristin Freeman, John H Holmes
BMC Bioinformatics 2011, 12(Suppl 3):S2 (18 May 2011)

A context-blocks model for identifying clinical relationships in patient records
Rezarta Islamaj Dogan, Aurelie Neveol, Zhiyong Lu
BMC Bioinformatics 2011, 12(Suppl 3):S3 (18 May 2011)

Collocation analysis for UMLS knowledge-based word sense disambiguation
Antonio Jimeno-Yepes, Bridget T Mclnnes, Alan R Aronson
BMC Bioinformatics 2011, 12(Suppl 3):S4 (18 May 2011)

Improving a gold standard: treating human relevance judgments of MEDLINE document pairs
W John Wilbur, Won Kim
BMC Bioinformatics 2011, 12(Suppl 3):S5 (18 May 2011)

Machine learning with naturally labeled data for identifying abbreviation definitions
Lana Yeganova, Donald C Comeau, W John Wilbur
BMC Bioinformatics 2011, 12(Suppl 3):S6 (18 May 2011)

A structural SVM approach for reference parsing
Xiaoli Zhang, Jie Zou, Daniel X Le, George R Thoma
BMC Bioinformatics 2011, 12(Suppl 3):S7 (18 May 2011)

*** June 6 2011 ***
Collocation analysis for UMLS knowledge-based word sense disambiguation
Antonio Jimeno-Yepes, Bridget T Mclnnes, and Alan R Aronson
BMC Bioinformatics 2011, 12(Suppl 3):S4
DOI: 10.1186/1471-2105-12-S3-S4

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation
Jimeno Yepes AJ, McInnes BT, Aronson AR
BMC Bioinformatics 2011, 12:223 (2 June 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/223/abstract

Integration and publication of heterogeneous text-mined relationships on the Semantic Web
J Biomed Semantics. 2011;2 Suppl 2:S10
PubMed: 21624156

*** June 2 2011 ***
Figure summarizer browser extensions for PubMed Central
Shashank Agarwal and Hong Yu
Bioinformatics 2011 27: 1723-1724
DOI: 10.1093/bioinformatics/btr194
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/12/1723?etoc

*** June 1 2011 ***
A statistical learning algorithm for word segmentation
Jerry R. Van Aken
Abstract: http://arxiv.org/abs/1105.6162
(OS)

*** May 31 2011 ***
Exploring subdomain variation in biomedical language
Lippincott T, O Seaghdha D, Korhonen A
BMC Bioinformatics 2011, 12:212 (27 May 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/212/abstract

*** May 27 2011 ***
Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry
Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J. and S. Ananiadou
PLoS ONE 6(5): e20181
Full text: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020181
(OA) (NER)

*** May 23 2011 ***
The Biomedical Discourse Relation Bank
Rashmi Prasad, Susan McRoy, Nadya Frid, Aravind Joshi, and Hong Yu
BMC Bioinformatics 2011, 12:188
DOI: 10.1186/1471-2105-12-188
Abstract: http://www.biomedcentral.com/1471-2105/12/188/abstract

*** May 20 2011 ***
MinePhos: A Literature Mining System for Protein Phoshphorylation Information Extraction.
Xu Y, Teng D, Lei Y.
IEEE/ACM Trans Comput Biol Bioinform. 2011 Apr 27. [Epub ahead of print]
DOI: 10.1109/TCBB.2011.85
PubMed: 21576755

ChemicalTagger: A tool for semantic text-mining in chemistry
Hawizy L, Jessop DM, Adams N, Murray-Rust P.
J Cheminform. 2011 May 16;3(1):17. [Epub ahead of print]
DOI: 10.1186/1758-2946-3-17
PubMed: 21575201

*** May 18 2011 ***
Program of BioNLP 2011 Shared Task
Portland, Oregon, 24 June 2011

Program of BioNLP 2011, a workshop of ACL/HLT 2011
Portland, Oregon, 23 June 2011
Electronic proceedings available after the workshop

*** May 17 2011 ***
Advancing Science through Mining Libraries, Ontologies and Communities.
Evans JA, Rzhetsky A.
J Biol Chem. 2011 May 12. [Epub ahead of print]
PubMed: 21566119

Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010.
de Bruijn B, Cherry C, Kiritchenko S, Martin J, Zhu X.
J Am Med Inform Assoc. 2011 May 12. [Epub ahead of print]
PubMed: 21565856

Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies.
Fan JW, Friedman C.
J Biomed Inform. 2011 Apr 28. [Epub ahead of print]
PubMed: 21549857

*** May 13 2011 ***
A MOD(ern) perspective on literature curation
Jodi Hirschman, Tanya Z. Berardini, Harold J. Drabkin, and Doug Howe
Mol Genet Genomics. 2010 May;283(5):415-25. Epub 2010 Mar 11.
DOI: 10.1007/s00438-010-0525-8
PubMed: 20221640
PMC: PMC2854346
Keywords: Annotation, Biocuration, Database, Genome, Literature, Model organism
Summary: provides insights into the literature curation process as performed at various model organism databases

*** May 12 2011 ***
Using information mining of the medical literature to improve drug safety.
Shetty KD, Dalal S
J Am Med Inform Assoc. 2011 May 5;
PubMed: 21546507

Using a shallow linguistic kernel for drug-drug interaction extraction.
Segura-Bedmar I, Martinez P, de Pablo-Sanchez C
J Biomed Inform. 2011 Apr 24;
PubMed: 21545845

BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs.
Lin FP, Anthony S, Polasek TM, Tsafnat G, Doogue MP
BMC Bioinformatics. 2011 Apr 21; 12(1):112
PubMed: 21510898

A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents.
Segura-Bedmar I, Martinez P, de Pablo-Sanchez C
BMC Bioinformatics. 2011;12 Suppl 2:S1
PubMed: 21489220

*** May 7 2011 ***
GenDrux: A biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer
Crasto C, Luo D, Yu F, Forero A, Chen D
BMC Medical Informatics and Decision Making 2011, 11:28 (5 May 2011)
DOI: 10.1186/1472-6947-11-28
Abstract: http://www.biomedcentral.com/1472-6947/11/28/abstract
Availability: http://www.microarray.uab.edu/drug_gene.pl

*** May 3 2011 ***
Mining MEDLINE for the Treatment of Osteoporosis
Yildirim P, Ceken C, Hassanpour R, Esmelioglu S, Tolun MR
J Med Syst. 2011 Apr 15
PubMed: 21494854

*** April 27 2011 ***
Proceedings of BioNLP 2011 - a workshop of ACL/HLT 2011, Portland, Oregon, USA, June 23-24, 2011
Program, talks, and posters: http://compbio.ucdenver.edu/BioNLP2011/program.shtml
Long/short papers & posters for the Shared Task (BioNLP-ST 2011) will be announced separately.
Full papers will be available online after June 24 2011.

*** April 21 2011 ***
Literature-based Resurrection of Neglected Medical Discoveries
Don R. Swanson
Journal of Biomedical Discovery and Collaboration, 2011, 6:34-47.
DOI: 10.5210/disco.v6i0.3515
Abstract: http://www.uic.edu/htbin/cgiwrap/bin/ojs/index.php/jbdc/article/view/3515
PDF: http://www.uic.edu/htbin/cgiwrap/bin/ojs/index.php/jbdc/article/view/3515/2953

*** April 20 2011 ***
Figure summarizer browser extensions for PubMed Central
Shashank Agarwal and Hong Yu
Bioinformatics (2011) First published online: April 14, 2011
DOI: 10.1093/bioinformatics/btr194
Abstract: http://bioinformatics.oxfordjournals.org/content/early/2011/04/14/bioinformatics.btr194.abstract?papetoc
Availability: http://figuresearch.askhermes.org/
Keywords: plug-in, web browser, search engine, summarization, figure caption
(WI)

*** April 15 2011 ***
Allie: a database and a search service of abbreviations and long forms
Yasunori Yamamoto, Atsuko Yamaguchi, Hidemasa Bono, and Toshihisa Takagi
Database (2011) 2011
DOI: 10.1093/database/bar013
URL: http://allie.dbcls.jp/
(WSD) (WI) (DB)

*** April 7 2011 ***
Inference of transcriptional regulatory network by bootstrapping patterns.
Wang HC, Chen YS, Kao HY, Tsai SJ
Bioinformatics. 2011 Mar 30. (2011) 27(10):1422-1428
DOI: 10.1093/bioinformatics/btr155
PubMed: 21450714
Webpage: http://140.116.99.138/~hcw0901/PubMedSearch.php
(AVO) (C)

*** April 4 2011 ***
Word sense disambiguation for event trigger word detection in biomedicine
Martinez D, Baldwin T
BMC Bioinformatics 2011, 12(Suppl 2):S4 (29 March 2011)
DOI: 10.1186/1471-2105-12-S2-S4
Article: http://www.biomedcentral.com/1471-2105/12/S2/S4
Keywords: BioNLP 2009 Shared Task (BioNLP-ST), CRF
(OA) (WSD)

Building the process-drug-side effect network to discover the relationship between biological Processes and side effects
Lee S, Lee KH , Song M, Lee D
BMC Bioinformatics 2011, 12(Suppl 2):S2 (29 March 2011)
DOI: 10.1186/1471-2105-12-S2-S2
Article: http://www.biomedcentral.com/1471-2105/12/S2/S2
Keywords: SIDER, ADR, GO
(OA)

Comparing and combining chunkers of biomedical text
Ning Kang, Erik M. van Mulligena, and Jan A. Kors
Journal of Biomedical Informatics, Volume 44, Issue 2, April 2011, Pages 354-360
DOI: 10.1016/j.jbi.2010.10.005
Keywords: Shallow parsing; Natural language processing; GENIA corpus; Chunking systems; Evaluation; Simple voting scheme

Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction
Aurelie Neveol, Rezarta Islamaj Dogan, and Zhiyong Lu
Journal of Biomedical Informatics, Volume 44, Issue 2, April 2011, Pages 310-318
DOI: 10.1016/j.jbi.2010.11.001
Keywords: PubMed queries; Biomedical entities; Annotation standards; Annotation methods

AskHERMES: An online question answering system for complex clinical questions Original Research Article
YongGang Cao, Feifan Liu, Pippa Simpson, Lamont Antieau, Andrew Bennett, James J. Cimino, John Ely, Hong Yu
Journal of Biomedical Informatics, Volume 44, Issue 2, April 2011, Pages 277-288
DOI: 10.1016/j.jbi.2011.01.004
Keywords: Clinical question answering; Question analysis; Passage retrieval; Summarization; Answer presentation

A comparison of two methods for retrieving ICD-9-CM data: The effect of using an ontology-based method for handling terminology changes Original Research Article
Alexander C. Yu, James J. Cimino
Journal of Biomedical Informatics, Volume 44, Issue 2, April 2011, Pages 289-298
DOI: 10.1016/j.jbi.2011.01.005
Keywords: Ontology; Terminology; Retrieval; ICD; Change management

*** April 1 2011 ***
Named Entity Recognition for Bacterial Type IV Secretion Systems
Sophia Ananiadou, Dan Sullivan, William Black, Gina-Anne Levow, Joseph J. Gillespie, Chunhong Mao, Sampo Pyysalo, BalaKrishna Kolluru, Junichi Tsujii and Bruno Sobral
PLoS ONE, 6(3):e14780, 2011
DOI: 10.1371/journal.pone.0014780
Article: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0014780
(NER) (OA)

Issue on "Ontologies for Clinical and Translational Research"
Journal of Biomedical Informatics, Volume 44, Issue 1, Pages 1-180 (February 2011)
Topics (among others): NLP for ontology learning; semantic similarity; desiderata; articles on particular ontologies
Table of Contents

*** March 29 2011 ***
GeneTUKit: a software for document-level gene normalization
Minlie Huang, Jingchen Liu, and Xiaoyan Zhu
Bioinformatics 2011 27:1032-1033
DOI: doi:10.1093/bioinformatics/btr042.
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/7/1032?etoc
(OA) (EMN) (T) (AVO)

GeneReporter--sequence-based document retrieval and annotation
Annekathrin Bartsch, Boyke Bunk, Isam Haddad, Johannes Klein, Richard Munch, Thorsten Johl, Uwe Karst, Lothar Jansch, Dieter Jahn, and Ida Retter
Bioinformatics 2011 27:1034-1035
DOI: doi:10.1093/bioinformatics/btr047.
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/7/1034?etoc
(OA)

A common layer of interoperability for biomedical ontologies based on OWL EL
Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala Wimalaratne, Dietrich Rebholz-Schuhmann, Paul Schofield, and Georgios V. Gkoutos
Bioinformatics 2011 27:1001-1008
DOI: 10.1093/bioinformatics/btr058.
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/7/1001?etoc

Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA
Huijun Wang, Ying Ding, Jie Tang, Xiao Dong, Bing He, Judy Qiu, David J. Wild
PLoS ONE 6(3):e17243, 2011
DOI: 10.1371/journal.pone.0017243

Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets
David Ruau, Michael Mbagwu, Joel T. Dudley, Vijay Krishnan, and Atul J. Butte
Journal of Biomedical Informatics, article in press, 2011
DOI: 10.1016/j.jbi.2011.03.007

System and method for extracting information from text using text annotation and fact extraction
Mark D. Wasson, James S. Wiltshire, Jr., Donald Loritz, Steve Xu, Shian-jung Dick Chen, Valentina Templar, Eleni Koutsomitopoulou
United States Patent 7912705
Publication date: 03/22/2011; filing date: 01/19/2010
Link: http://www.freepatentsonline.com/7912705.html
PDF: http://www.freepatentsonline.com/7912705.pdf
(PA)

*** March 26 2011 ***
Parsing citations in biomedical articles using conditional random fields
Zhang Q, Cao YG, Yu H
Comput Biol Med. 2011 Mar 16
PubMed: 21419403
Link: http://www.cs.uwm.edu/~qing/projects/cithit/index.html
Keywords: CRF, citation parser
Summary: Parses citations for author, title, journal, etc.
(T) (AVO)

*** March 21 2011 ***
Compounds In Literature (CIL): Screening for Compounds and Relatives in PubMed
Bjürn A. Grüning, Christian Senger, Anika Erxleben, Stephan Flemming, and Stefan Günther
Bioinformatics, 2011 27:1341-1342, published 16 March 2011
DOI: 10.1093/bioinformatics/btr130
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btr130v1?papetoc
PubMed: 21414988
Link: http://cil.pharmaceuticalbioinformatics.de
(NER) (WI)

*** March 17 2011 ***
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study
Maria C. Costanzo, Julie Park, Rama Balakrishnan, J. Michael Cherry, and Eurie L. Hong
Database (Oxford), published online March 15, 2011,
Abstract: http://database.oxfordjournals.org/cgi/content/abstract/2011/0/bar004?etoc

*** March 12 2011 ***
Mining semantic networks of bioinformatics e-resources from the literature
Afzal H, Eales J, Stevens R, Nenadic G
J Biomed Semantics. 2011;2 Suppl 1:S4
PubMed: 21388573
Article: http://www.jbiomedsem.com/content/2/S1/S4/?mkt=
Link: http://gnode1.mib.man.ac.uk/bioinf/semnets.html
(OA)

*** March 9 2011 ***
A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment
Guo Y, Korhonen A, Liakata M, Silins I, Hogberg J, Stenius U
BMC Bioinformatics 2011, 12(1):69 (8 March 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/69/abstract
DOI: 10.1186/1471-2105-12-69
PubMed: 21385430

** March 7 2011 ***
Omics and literature mining
V. Kumar
Methods Mol Biol. 2011;719:457-77
PubMed: 21370097

Chemical-protein interactome and its application in off-target identification.
Yang L, Wang KJ, Wang LS, Jegga AG, Qin SY, He G, Chen J, Xiao Y, He L
Interdiscip Sci. 2011 Mar;3(1):22-30
PubMed: 21369884
(R) (ATM) (PPI)

AGRA: Analysis of Gene Ranking Algorithms.
Kocbek S, Sætre R, Stiglic G, Kim JD, Pernek I, Tsuruoka Y, Kokol P, Ananiadou S, Tsujii J
Bioinformatics 2011 27:1185-1186, Feb 23
PubMed: 21349873
(OA)

Concept Discovery for Pathology Reports using an N-gram Model.
Yip V, Mete M, Topaloglu U, Kockara S
AMIA Summits Transl Sci Proc. 2010;2010:43-7
PubMed: 21347147

Improving Search for Evidence-based Practice using Information Extraction.
Zhao J, Kan MY, Procter PM, Zubaidah S, Yip WK, Li GM
AMIA Annu Symp Proc. 2010;2010:937-41
PubMed: 21347116

eEvidence: Information Seeking Support for Evidence-based Practice: An Implementation Case Study.
Zhao J, Kan MY, Procter PM, Zubaidah S, Yip WK, Li GM
AMIA Annu Symp Proc. 2010;2010:932-6
PubMed: 21347115

Discovering peripheral arterial disease cases from radiology notes using natural language processing.
Savova GK, Fan J, Ye Z, Murphy SP, Zheng J, Chute CG, Kullo IJ
AMIA Annu Symp Proc. 2010;2010:722-6
PubMed: 21347073

Natural language processing for lines and devices in portable chest x-rays.
Rubin D, Wang D, Chambers DA, Chambers JG, South BR, Goldstein MK
AMIA Annu Symp Proc. 2010;2010:692-6
PubMed: 21347067

BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction.
Jonnalagadda S, Gonzalez G
AMIA Annu Symp Proc. 2010;2010:351-5
PubMed: 21346999

Throw the bath water out, keep the baby: keeping medically-relevant terms for text mining.
Jarman J, Berndt DJ
AMIA Annu Symp Proc. 2010;2010:336-40
PubMed: 21346996

Using ontology network structure in text mining.
Berndt DJ, McCart JA, Luther SL
AMIA Annu Symp Proc. 2010;2010:41-5
PubMed: 21346937

Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles.
Tsai RT, Lai PT
BMC Bioinformatics. 2011 Feb 23;12(1):60
PubMed: 21342534
(IE) (EMN) (PPI)
Keywords: BioCreative II.5 INT, BioCreative II.5 IPT, SVM, re-ranking

k-Information Gain Scaled Nearest Neighbors: A Novel Approach to Classifying Protein-Protein Interaction-Related Documents.
Ambert KH, Cohen AM
IEEE/ACM Trans Comput Biol Bioinform. 2011 Feb 16;
PubMed: 21339533

Explicitly searching for useful inventions: dynamic relatedness and the costs of connecting versus synthesizing.
Hsieh C
Scientometrics. 2011 Feb;86(2):381-404
PubMed: 21297855

*** March 5 2011 ***
Clinical Synopsis Search in OMIM
Raphael Cohen, Avitan Gefen, Michael Elhadad and Ohad S Birk
BMC Bioinformatics 2011, 12:65
DOI: 10.1186/1471-2105-12-65
Abstract: http://www.biomedcentral.com/1471-2105/12/65/abstract

*** March 3 2011 ***
Natural Language Processing (almost) from Scratch
Ronan Collobert, Jason Weston, Leon Bottou, Michael Karlen, Koray Kavukcuoglu, and Pavel Kuksa
arXiv: http://arxiv.org/abs/1103.0398S
(NLP) (ML) (M) (OA) (AVO) (OS)

*** Feb 24 2011 ***
Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles
Tsai R, Lai P
BMC Bioinformatics 2011, 12:60 (23 February 2011)
DOI: 10.1186/1471-2105-12-60
Abstract: http://www.biomedcentral.com/1471-2105/12/60/abstract
(PPI) (REL) (BioCreative II.5)

*** Feb 23 2011 ***
Drug repurposing and adverse event prediction using high-throughput literature analysis.
Spyros N. Deftereos, Christos Andronis, Ellen J. Friedla, Aris Persidis, Andreas Persidis
In: Wiley Interdisciplinary Reviews: Systems Biology and Medicine
Article first published online: 16 Feb 2011
Article: http://onlinelibrary.wiley.com/doi/10.1002/wsbm.147/full
DOI: 10.1002/wsbm.147

*** Feb 20 2011 ***
Condensing biomedical journal texts through paragraph ranking
Jung-Hsien Chiang, Heng-Hui Liu, and Yi-Ting Huang
Bioinformatics published 16 February 2011
Bioinformatics 2011 27:1143-1149
DOI: 10.1093/bioinformatics/btr080
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btr080v1?papetoc

*** Feb 18 2011 ***
Annotating genes and genomes with DNA sequences extracted from biomedical articles
Bioinformatics. 2011 Feb 16.
Haeussler M, Gerner M, Bergman CM.
PubMed: 21325301
URL: http://text2genome.org
(T) (OA)

Extracting causal relations on HIV drug resistance from literature
Quoc-Chinh Bui, Breanndan O Nuallain, Charles A Boucher, and Peter MA Sloot
BMC Bioinformatics 2010, 11:101
DOI: 10.1186/1471-2105-11-101

*** Feb 16 2011 ***
GeneTUKit: a software for document-level gene normalization
Minlie Huang, Jingchen Liu, and Xiaoyan Zhu
Bioinformatics published 8 February 2011
DOI: 10.1093/bioinformatics/btr042
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btr042v1?papetoc
(EMN) (OA) (BioCreative III)

Towards classifying species in systems biology papers using text mining
Wei Q, Collier N.
BMC Res Notes. 2011 Feb 4;4(1):32
PubMed: 21294879
(OA)

In silico discovery and experimental validation of new protein-protein interactions.
van Haagen HH, 't Hoen PA, de Morree A, van Roon-Mom WM, Peters DJ, Roos M, Mons B, van Ommen GJ, Schuemie MJ.
Proteomics. 2011 Jan 7.
DOI: 10.1002/pmic.201000398
PubMed: 21280221

*** Feb 2 2011 ***
Computational Polypharmacology with Text Mining and Ontologies
Conrad Plake and Michael Schroeder
Curr Pharm Biotechnol. 2010 Dec 6
PubMed: 21133848

*** Jan 30 2011 ***
Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature
Emily Doughty, Attila Kertesz-Farkas, Olivier Bodenreider, Gary Thompson, Asa Adadey, Thomas Peterson, and Maricel G. Kann
Bioinformatics 2011 27: 408-415
DOI: 10.1093/bioinformatics/btq667.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/3/408?etoc

*** Jan 23 2011 ***
Automated Information Extraction and Structure-Activity Relationship Analysis of Cytochrome P450 Substrates
Yamashita F, Feng C, Yoshida S, Itoh T, Hashida M
J Chem Inf Model. 2011 Jan 19
PubMed: 21247177

PubMed and beyond: a survey of web tools for searching biomedical literature
Lu Z
Database (Oxford). 2011; 2011:baq036
PubMed: 21245076
DOI: 10.1093/database/baq036
PMID: 21245076
(R)

*** Jan 19 2011 ***
Disclosing ambiguous gene aliases by automatic literature profiling
Coimbra RS, Vanderwall DE, Oliveira GC
BMC Genomics. 2010;11 Suppl 5:S3
PubMed: 21210969

*** Jan 5 2011 ***
Literature-aided interpretation of gene expression data with the weighted global test
Rob Jelier, Jelle J. Goeman, Kristina M. Hettne, Martijn J. Schuemie, Johan T. den Dunnen, and Peter A.C. 't Hoen
Brief Bioinform. 2010 Dec 22
Abstract: http://bib.oxfordjournals.org/cgi/content/abstract/bbq082v1?papetoc
DOI: 10.1093/bib/bbq082
PubMed: 21183478

Algorithms and semantic infrastructure for mutation impact extraction and grounding
Laurila JB, Naderi N, Witte R, Riazanov A, Kouznetsov A, Baker CJ
BMC Genomics. 2010;11 Suppl 4:S24
In Proc Asia Pacific Bioinformatics Network (APBioNet) Int Conf Bioinformatics (InCoB), Tokyo, Japan, Sep 26-28, 2010.
Paper: http://www.biomedcentral.com/1471-2164/11/S4/S24
PubMed: 21143808

Text mining for systems modeling
Kowald A, Schmeier S
Methods Mol Biol. 2011;696:305-18
PubMed: 21063956

UKPMC: a full text article resource for the life sciences
McEntyre JR, Ananiadou S, Andrews S, Black WJ, Boulderstone R, Buttery P, Chaplin D, Chevuru S, Cobley N, Coleman LA, Davey P, Gupta B, Haji-Gholam L, Hawkins C, Horne A, Hubbard SJ, Kim JH, Lewin I, Lyte V, Macintyre R, Mansoor S, Mason L, McNaught J, Newbold E, Nobata C, Ong E, Pillai S, Rebholz-Schuhmann D, Rosie H, Rowbotham R, Rupp CJ, Stoehr P, Vaughan P
Nucleic Acids Res. 2010 Nov 9
PubMed: 21062818

A hybrid approach to extract protein-protein interactions.
Bui QC, Katrenko S, Sloot PM
Bioinformatics. 2010 Nov 8;
PubMed: 21062765

The Text-mining based PubChem Bioassay neighboring analysis.
Han L, Suzek TO, Wang Y, Bryant SH
BMC Bioinformatics. 2010 Nov 8;11(1):549
PubMed: 21059237

Comparing and combining chunkers of biomedical text.
Kang N, Van Mulligen EM, Kors JA
J Biomed Inform. 2010 Nov 3;
PubMed: 21056118

Recent progress in automatically extracting information from the pharmacogenomic literature
Garten Y, Coulet A, Altman RB
Pharmacogenomics. 2010 Oct;11(10):1467-89
PubMed: 21047206

*** Dec 25 2010 ***
Selected Papers from LBM2009: Introduction WRESTLING WITH BIOMEDICAL RESEARCH RESULTS: LANGUAGE RESOURCES AND LITERATURE ANALYSIS
D. REBHOLZ-SCHUHMANN, NIGEL COLLIER, JONG C. PARK and LIMSOON WONG
Journal of Bioinformatics and Computational Biology, Volume: 8, Issue: 1 (February 2010), Page: 129-130
DOI: 10.1142/S0219720010004586
Abstract: http://www.worldscinet.com/jbcb/08/0801/S0219720010004598.html
(OA)

THE VALUE OF AN IN-DOMAIN LEXICON IN GENOMICS QA
YUTAKA SASAKI, JOHN MCNAUGHT and SOPHIA ANANIADOU
Journal of Bioinformatics and Computational Biology, Volume: 8, Issue: 1 (February 2010), Page: 147-161
DOI: 10.1142/S0219720010004513
Abstract: http://www.worldscinet.com/jbcb/08/0801/S0219720010004513.html
(QA)

CALBC SILVER STANDARD CORPUS
DIETRICH REBHOLZ-SCHUHMANN, ANTONIO JOSE JIMENO YEPES, ERIK M. VAN MULLIGEN, NING KANG, JAN KORS, DAVID MILWARD, PETER CORBETT, EKATERINA BUYKO, ELENA BEISSWANGER and UDO HAHN
Journal of Bioinformatics and Computational Biology, Volume: 8, Issue: 1 (February 2010), Page: 163-179
DOI: 10.1142/S0219720010004562
Abstract: http://www.worldscinet.com/jbcb/08/0801/S0219720010004562.html
(C) (NER)

*** Dec 10 2010 ***
Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature
E. Doughty, A. Kertesz-Farkas, O. Bodenreider, G. Thompson, A. Adadey, T.
Peterson, and M. G. Kann
Bioinformatics 27(3):408-415, 2011; advance access publication 7 December 2010
DOI: 10.1093/bioinformatics/btq667
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq667v1?papetoc

*** Dec 1 2010 ***
Interoperability between phenotype and anatomy ontologies
Robert Hoehndorf, Anika Oellrich, and Dietrich Rebholz-Schuhmann
Bioinformatics 2010 26:3112-3118
DOI: 10.1093/bioinformatics/btq578
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/24/3112?etoc
(OA)

What the papers say: text mining for genomics and systems biology
Harmston N, Filsell W, Stumpf MP
Hum Genomics. 2010 Oct;5(1):17-29
PMID: 21106487

*** Nov 24 2010 ***
Detecting hedge cues and their scope in biomedical text with conditional random fields
Shashank Agarwal, Hong Yu
Journal of Biomedical Informatics, Volume 43, Issue 6, December 2010, Pages 953-961
DOI: 10.1016/j.jbi.2010.08.003

Automatically extracting information needs from complex clinical questions
Yong-gang Cao, James J. Cimino, John Ely, Hong Yu
Journal of Biomedical Informatics, Volume 43, Issue 6, December 2010, Pages 962-971
DOI: 10.1016/j.jbi.2010.07.007

Disambiguation in the biomedical domain: The role of ambiguity type
Mark Stevenson, Yikun Guo
Journal of Biomedical Informatics, Volume 43, Issue 6, December 2010, Pages 972-981
DOI: 10.1016/j.jbi.2010.08.009
(WSD)

Using text to build semantic networks for pharmacogenomics
Journal of Biomedical Informatics, Volume 43, Issue 6, December 2010, Pages 1009-1019
Adrien Coulet, Nigam H. Shah, Yael Garten, Mark Musen, Russ B. Altman
DOI: 10.1016/j.jbi.2010.08.005

A concept-driven biomedical knowledge extraction and visualization framework for conceptualization of text corpora
Journal of Biomedical Informatics, Volume 43, Issue 6, December 2010, Pages 1020-1035
Jahiruddin, Muhammad Abulaish, Lipika Dey
DOI: 10.1016/j.jbi.2010.09.008

*** Nov 9 2010 ***
A hybrid approach to extract protein-protein interactions
Quoc-Chinh Bui, Sophia Katrenko, and Peter M.A. Sloot
Bioinformatics, First published online: November 8, 2010
DOI: 10.1093/bioinformatics/btq620
Abstract: http://bioinformatics.oxfordjournals.org/content/early/2010/11/08/bioinformatics.btq620

*** Nov 1 2010 ***
BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects
Xin He, Yanen Li, Radhika Khetani, Barry Sanders, Yue Lu, Xu Ling, ChengXiang Zhai, and Bruce Schatz
Nucl. Acids Res. (2010) 38(suppl 2): W175-W181
DOI: 10.1093/nar/gkq544

*** Oct 31 2010 ***
Automated ancillary cancer history classification for mesothelioma patients from free-text clinical reports.
Wilson RA, Chapman WW, Defries SJ, Becich MJ, Chapman BE
J Pathol Inform. 2010;1:24
PubMed: 21031012
Keywords: Hx, Dynamic-Window, ConText, Cohen's kappa, classification
(ATM) (IR)

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.
Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, Schomburg D
Nucleic Acids Res. 2010 Oct 28;
PubMed: 21030441
Keywords: GeneOntology, OBO Foundry
Website: http://www.BTO.brenda-enzymes.org
(ONT)

A re-evaluation of biomedical named entity-term relations.
Ohta T, Pyysalo S, Kim JD, Tsujii J
J Bioinform Comput Biol. 2010 Oct;8(5):917-28
Ohta T, Pyysalo S, Kim JD, Tsujii J
PubMed: 20981895
(REL)

Literature-based discovery of diabetes- and ROS-related targets.
Hur J, Sullivan KA, Schuyler AD, Hong Y, Pande M, States DJ, Jagadish HV, Feldman EL
BMC Med Genomics. 2010 Oct 27;3(1):49
PubMed: 20979611
Tools: SciMiner
Website: http://jdrf.neurology.med.umich.edu/ROSDiabetes/
(ATM)

Combining free text and structured electronic medical record entries to detect acute respiratory infections.
Delisle S, South B, Anthony JA, Kalp E, Gundlapallli A, Curriero FC, Glass GE, Samore M, Perl TM
PLoS One. 2010;5(10):e13377
PubMed: 20976281
Keywords: IR, logistic regression, backward elimination
(OA) (IR)

Development of the method for the similarity detection of descriptions in radiology reports using structuring technology
Futami H, Yamagishi H, Kawaguchi O, Tsukamoto N, Fujii H, Kasamatsu T, Ando Y, Osada M, Kubo A
Nippon Hoshasen Gijutsu Gakkai Zasshi. 2010 Sep 20;66(9):1229-36
PubMed: 20975244
(IR)

Design and evaluation of an ontology based information extraction system for radiological reports.
Soysal E, Cicekli I, Baykal N
Comput Biol Med. 2010 Oct 20;
PubMed: 20970122
(IR) (IE) (ONT)

Interruption of β-catenin supresses the EGFR pathway by blocking multiple oncogenic targets in human glioma cells.
Yue X, Lan F, Yang W, Yang Y, Han L, Zhang A, Liu J, Zeng H, Jiang T, Pu P, Kang C
Brain Res. 2010 Oct 19;
PubMed: 20969832
(ATM) (I)

Biomedical negation scope detection with conditional random fields.
Agarwal S, Yu H
J Am Med Inform Assoc. 2010 Nov 1;17(6):696-701
PubMed: 20962133
Keywords: NLP, negation, hedge, CRF, Java
Website: http://negscope.askhermes.org
(IE) (IR) (AVO)

*** Oct 29 2010 ***
Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP.
Fox AD, Baumgartner WA, Johnson HL, Hunter LE, Slonim DK
Lect Notes Comput Sci. 2010 May 13;6004:43-52
PubMed: 20953344
Keywords: OpenDMAP, patterns
(IE) (PPI)

Knowledge representation and management: transforming textual information into useful knowledge.
Rassinoux AM
Yearb Med Inform. 2010;:64-7
PubMed: 20938573
(KR)

Interoperability between phenotype and anatomy ontologies
Robert Hoehndorf, Anika Oellrich and Dietrich Rebholz-Schuhmann
Bioinformatics, advance access, Oct 22 2010
DOI: 10.1093/bioinformatics/btq578
Website: http://bioonto.de/pmwiki.php/Main/PheneOntology
(ONT)

*** Oct 25 2010 ***
A systematic literature review of automated clinical coding and classification systems.
Stanfill MH, Williams M, Fenton SH, Jenders RA, Hersh WR
J Am Med Inform Assoc. 2010 Nov 1;17(6):646-51.
PubMed: 20962126

*** Oct 22 2010 ***
Click-words: learning to predict document keywords from a user perspective
Rezarta Islamaj Dogan and Zhiyong Lu
Bioinformatics 26(21):2767-2775, 2010
DOI: 10.1093/bioinformatics/btq459
http://bioinformatics.oxfordjournals.org/content/26/21/2767

PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids
Miguel Garcia-Remesal, Alejandro Cuevas, David Perez-Rey, Luis Martin, Alberto Anguita, Diana de la Iglesia, Guillermo de la Calle, Jose Crespo, and Victor Maojo
Bioinformatics 26(21):2801-2802, 2010
DOI: 10.1093/bioinformatics/btq520
http://bioinformatics.oxfordjournals.org/content/26/21/2801

Graph-based Word Sense Disambiguation of Biomedical Documents
Eneko Agirre, Aitor Soroa, and Mark Stevenson
Bioinformatics 2010, 26:2889-2896, advance access 7 October 2010
DOI: 10.1093/bioinformatics/btq555
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content
/abstract/26/22/2889?etoc
Website: http://ixa2.si.ehu.es/ukb/
(WSD) (OS) (AVO)

*** Oct 18 2010 ***
Knowledge representation and management: transforming textual information into useful knowledge.
Yearb Med Inform. 2010; 64-7
Rassinoux AM
PubMed: 20938573

*** Oct 6 2010 ***
Workshop on Advances in Bio Text Mining
Ghent, Belgium. 10-11 May 2010
Edited by Thomas Abeel and Sofie Van Landeghem
About 15 extended abstracts are available online
ToC: http://www.biomedcentral.com/1471-2105/11?issue=S5
(P)

Pitfalls in applying text mining to scientific literature
Jean-Marc Neefs
BMC Bioinformatics 2010, 11(Suppl 5):O4 (6 October 2010)

Species identification for gene name normalization
Illes Solt, Domonkos Tikk, Ulf Leser
BMC Bioinformatics 2010, 11(Suppl 5):P5 (6 October 2010)
(NER) (NEN)

A fast and effective dependency graph kernel for PPI relation extraction
Domonkos Tikk, Peter Palaga, Ulf Leser
BMC Bioinformatics 2010, 11(Suppl 5):P8 (6 October 2010)
(PPI) (K)

*** Oct 5 2010 ***
A New Pivoting and Iterative Text Detection Algorithm for Biomedical Images.
J Biomed Inform. 2010 Sep 28;
Xu S, Krauthammer M
PubMed: 20887803

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases.
PLoS Comput Biol. 2010;6(9):
Frijters R, van Vugt M, Smeets R, van Schaik R, de Vlieg J, Alkema W
PubMed: 20885778
(REL)

*** Oct 1 2010 ***
A Framework for Semi-Supervised Feature Generation and its Applications in Biomedical Literature Mining.
IEEE/ACM Trans Comput Biol Bioinform. 2010 Sep 22;
Li Y, Hu X, Lin H, Yang Z
PubMed: 20876938
(ML) (F)

Developing a disease outbreak event corpus.
J Med Internet Res. 2010;12(3):e43
Conway M, Kawazoe A, Chanlekha H, Collier N
PubMed: 20876049
(C)

A Concept-Driven Biomedical Knowledge Extraction and Visualization Framework for Conceptualization of Text Corpora.
J Biomed Inform. 2010 Sep 23;
Uddin J, Abulaish M, Dey L
PubMed: 20870033

Simple tricks for improving pattern-based information extraction from the biomedical literature.
J Biomed Semantics. 2010 Sep 24;1(1):9
Nguyen QL, Tikk D, Leser U
PubMed: 20868467
(REL)

The structural and content aspects of abstracts versus bodies of full text journal articles are different
Cohen K, Johnson HL, Verspoor K, Roeder C, Hunter LE
BMC Bioinformatics 2010, 11:492 (29 September 2010)
PubMed: 20920264
DOI: doi:10.1186/1471-2105-11-492
Abstract: http://www.biomedcentral.com/1471-2105/11/492/abstract

ExaCT: automatic extraction of clinical trial characteristics from journal publications.
Kiritchenko S, de Bruijn B, Carini S, Martin J, Sim I
BMC Med Inform Decis Mak. 2010 Sep 28;10(1):56
PubMed: 20920176

Exploring species-based strategies for gene normalization.
Verspoor K, Roeder C, Johnson HL, Cohen KB, Baumgartner WA Jr, Hunter LE.
IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):462-71.
PubMed: 20671318

*** Sep 25 2010 ***
Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documents.
J Am Med Inform Assoc. 2010 Sep 1;17(5):559-562
Meystre SM, Thibault J, Shen S, Hurdle JF, South BR
PubMed: 20819864

Linguistic approach for identification of medication names and related information in clinical narratives.
J Am Med Inform Assoc. 2010 Sep 1;17(5):549-554
Hamon T, Grabar N
PubMed: 20819862

Medication information extraction with linguistic pattern matching and semantic rules.
J Am Med Inform Assoc. 2010 Sep 1;17(5):532-535
Spasic I, Sarafraz F, Keane JA, Nenadic G
PubMed: 20819858

High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge.
J Am Med Inform Assoc. 2010 Sep 1;17(5):524-527
Patrick J, Li M
PubMed: 20819856

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.
J Am Med Inform Assoc. 2010 Sep 1;17(5):507-513
Savova GK, Masanz JJ, Ogren PV, Zheng J, Sohn S, Kipper-Schuler KC, Chute CG
PubMed: 20819853

Structured digital tables on the Semantic Web: toward a structured digital literature.
Mol Syst Biol. 2010 Aug 24;6:403
Cheung KH, Samwald M, Auerbach RK, Gerstein MB
PubMed: 20739925

The FEBS Letters SDA corpus: A collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community.
FEBS Lett. 2010 Aug 20;
Leitner F, Krallinger M, Cesareni G, Valencia A
PubMed: 20728446

Detecting hedge cues and their scope in biomedical literature with conditional random fields.
J Biomed Inform. 2010 Aug 13;
Agarwal S, Yu H
PubMed: 20709188

An Overview of BioCreative II.5.
IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):385-99
Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A
PubMed: 20704011

*** Sep 7 2010 ***
Discovering drug-drug interactions: a text-mining and reasoning approach based on properties of drug metabolism
Luis Tari, Saadat Anwar, Shanshan Liang, James Cai, and Chitta Baral
Bioinformatics 2010 26: i547-i553; doi:10.1093/bioinformatics/btq382.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/18/i547?etoc
(OA)

Discriminative and informative features for biomolecular text mining with ensemble feature selection
Sofie Van Landeghem, Thomas Abeel, Yvan Saeys, and Yves Van de Peer
Bioinformatics 2010 26: i554-i560; doi:10.1093/bioinformatics/btq381.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/18/i554?etoc
(OA)

Utopia documents: linking scholarly literature with research data
T. K. Attwood, D. B. Kell, P. McDermott, J. Marsh, S. R. Pettifer, and D. Thorne
Bioinformatics 2010 26: i568-i574; doi:10.1093/bioinformatics/btq383.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/18/i568?etoc
(OA)

Interactive and fuzzy search: a dynamic way to explore MEDLINE
Jiannan Wang, Inci Cetindil, Shengyue Ji, Chen Li, Xiaohui Xie, Guoliang Li, and Jianhua Feng
Bioinformatics 2010 26: 2321-2327; doi:10.1093/bioinformatics/btq414.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/18/2321?etoc

*** Aug 19 2010 ***
Text Mining Meets Workflow: Linking U-Compare with Taverna
Yoshinobu Kano, Paul Dobson, Mio Nakanishi, Jun'ichi Tsujii, and Sophia Ananiadou
Bioinformatics published 12 August 2010, Open Access
DOI: 10.1093/bioinformatics/btq464
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq464
(OA)

*** Aug 10 2010 ***
eGIFT: Mining Gene Information from the Literature
Tudor CO, Schmidt CJ, Vijay-Shanker K
BMC Bioinformatics 2010, 11:418 (9 August 2010)
Abstract: http://www.biomedcentral.com/1471-2105/11/418/abstract

*** Aug 9 2010 ***
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
Uppsala, Sweden, 15 July 2010
http://www.aclweb.org/anthology/W/W10/#1900

*** Aug 3 2010 ***
A method for automatically extracting infectious disease-related primers and probes from the literature
Garcia-Remesal M, Cuevas A, Lopez-Alonso V, Lopez-Campos G, de la Calle G, de la Iglesia D, Perez-Rey D, Crespo J, Martin-Sanchez F, Maojo V
BMC Bioinformatics 2010, 11:410 (3 August 2010)
Abstract: http://www.biomedcentral.com/1471-2105/11/410/abstract

*** July 16 2010 ***
Automatic indexing and retrieval of encounter-specific evidence for point-of-care support
Dympna M. O'Sullivan, Szymon A. Wilk, Wojtek J. Michalowski, and Ken J. Farion
Journal of Biomedical Informatics, Volume 43, Issue 4, August 2010, Pages 623-631
DOI: 10.1016/j.jbi.2010.03.003

Text mining for traditional Chinese medical knowledge discovery: A survey
Xuezhong Zhou, Yonghong Peng, and Baoyan Liu
Journal of Biomedical Informatics, Volume 43, Issue 4, August 2010, Pages 650-660
DOI: 10.1016/j.jbi.2010.01.002

Selecting information in electronic health records for knowledge acquisition
Xiaoyan Wang, Herbert Chase, Marianthi Markatou, George Hripcsak, and Carol Friedman
Journal of Biomedical Informatics, Volume 43, Issue 4, August 2010, Pages 595-601
DOI: 10.1016/j.jbi.2010.03.011

*** July 14 2010 ***
Interactive and Fuzzy Search: A Dynamic Way to Explore MEDLINE
Jiannan Wang, Inci Cetindil, Shengyue Ji, Chen Li, Xiaohui Xie, Guoliang Li, and Jianhua Feng
Bioinformatics, Advance Access published online on July 12, 2010
DOI: 10.1093/bioinformatics/btq414

UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text
Dina Demner-Fushman, James G. Mork, Sonya E. Shooshan, and Alan R. Aronson
Journal of Biomedical Informatics, Volume 43, Issue 4, August 2010, Pages 587-594
DOI: 10.1016/j.jbi.2010.02.005

Mining connections between chemicals, proteins, and diseases extracted from Medline annotations
Nancy C. Baker and Bradley M. Hemminger
Journal of Biomedical Informatics, Volume 43, Issue 4, August 2010, Pages 510-519
DOI: 10.1016/j.jbi.2010.03.008

KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes
Stephanie Heinen, Bernhard Thielen, and Dietmar Schomburg
BMC Bioinformatics 2010, 11:375
DOI: 10.1186/1471-2105-11-375

Literature-Based Discovery of IFN-gamma and Vaccine-Mediated Gene Interaction Networks.
Ozg&uumnl;r A, Xiang Z, Radev DR, He Y
J Biomed Biotechnol., 2010, 426479
PubMed: 20625487

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.
Tikk D, Thomas P, Palaga P, Hakenberg J, Leser U
PLoS Comput Biol., 2010, 6:e1000837
PubMed: 20617200
(ML) (K) (PPI) (R)

A text-mining technique for extracting gene-disease associations from the biomedical literature.
Al-Mubaid H, Singh RK
Int J Bioinform Res Appl. 2010; 6(3):270-86
PubMed: 20615835
(REL)

*** June 15 2010 ***
Event extraction for systems biology by text mining the literature
Ananiadou, S., Pyysalo, S., Tsujii, J. and D.B. Kell
Trends in Biotechnology (01 June 2010)
(R) (REL)

*** June 8 2010 ***
Semi-automated ontology generation within OBO-Edit
Thomas Wächter and Michael Schroeder
Bioinformatics 2010 26: i88-i96; doi:10.1093/bioinformatics/btq188
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/12/i88?etoc
(OA) (ONT)

PathText: a text mining integrator for biological pathway visualizations
Brian Kemper, Takuya Matsuzaki, Yukiko Matsuoka, Yoshimasa Tsuruoka, Hiroaki Kitano, Sophia Ananiadou, and Jun'ichi Tsujii
Bioinformatics 2010 26: i374-i381; doi:10.1093/bioinformatics/btq221
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/12/i374?etoc
(OA)

Complex event extraction at PubMed scale
Jari Bjorne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, and Tapio Salakoski
Bioinformatics 2010 26: i382-i390; doi:10.1093/bioinformatics/btq180
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/12/i382?etoc
(OA) (REL)

*** June 2 2010 ***
EnvMine: A text-mining system for the automatic extraction of contextual information.
Javier Tamames and Victor de Lorenzo
BMC Bioinformatics 2010, 11:294
DOI: 10.1186/1471-2105-11-294
Paper: http://www.biomedcentral.com/1471-2105/11/294

*** May 30 2010 ***
A UIMA Wrapper for the NCBO Annotator
Christophe Roeder, Clement Jonquet, Nigam H. Shah, William A. Baumgartner Jr, and Lawrence Hunter
Bioinformatics, advacne access May 26, 2010
DOI: 10.1093/bioinformatics/btq250
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq250
(F) (ONT) (OS)

*** May 18 2010 ***
Mounir Errami, Zhaohui Sun, Angela C. George, Tara C. Long, Michael A. Skinner, Jonathan D. Wren, and Harold R. Garner
Identifying duplicate content using statistically improbable phrases
Bioinformatics 2010, 26(11):1453-1457, open access
DOI: 10.1093/bioinformatics/btq146
PubMed: 20472545
Paper: http://bioinformatics.oxfordjournals.org/cgi/content/full/26/11/1453
(OA) (IR)

*** May 11 2010 ***
caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research.
Crowley RS, Castine M, Mitchell K, Chavan G, McSherry T, Feldman M.
J Am Med Inform Assoc. 2010 May 1;17(3):253-64
PubMed: 20442142
(I)

Multi-way association extraction and visualization from biological text documents using hyper-graphs: Applications to genetic association studies for diseases.
Mukhopadhyay S, Palakal M, Maddu K.
Artif Intell Med. 2010 Apr 8.
PubMed: 20382004

Automated detection of follow-up appointments using text mining of discharge records.
Ruud KL, Johnson MG, Liesinger JT, Grafft CA, Naessens JM.
Int J Qual Health Care. 2010 Mar 27
PubMed: 20348557

*** May 7 2010 ***
#Some papers from the proceedings of the Third International Workshop on Data and Text Mining in Bioinformatics (DTMBio) 2009, Hong Kong, 6 November 2009, appeared as Supplementary issue 2 in BMC Bioinformatics 2010: http://www.biomedcentral.com/1471-2105/11?issue=S2

Learning an enriched representation from unlabeled data for protein-protein interaction extraction.
Yanpeng Li, Xiaohua Hu, Hongfei Lin, and Zhihao Yang
BMC Bioinformatics, 11(Suppl 2):S7, 2010
DOI: 10.1186/1471-2105-11-S2-S7
Paper: http://www.biomedcentral.com/1471-2105/11/S2/S7
PubMed: 20406505

Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents
Isabel Segura-Bedmar, Mario Crespo, Cesar de Pablo-Sanchez, and Paloma Martinez
BMC Bioinformatics, 11(Suppl 2):S1, 2010
DOI: 10.1186/1471-2105-11-S2-S1
Paper: http://www.biomedcentral.com/1471-2105/11/S2/S1
PubMed: 20406499

MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge
Ali Z Ijaz, Min Song, and Doheon Lee
BMC Bioinformatics, 11(Suppl 2):S3, 2010
DOI: 10.1186/1471-2105-11-S2-S3
Paper: http://www.biomedcentral.com/1471-2105/11/S2/S3
PubMed: 20406501

Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS
Hwanjo Yu, Taehoon Kim, Jinoh Oh, Ilhwan Ko, Sungchul Kim, and Wook-Shin Han
BMC Bioinformatics, 11(Suppl 2):S6, 2010
DOI: 10.1186/1471-2105-11-S2-S6
Paper: http://www.biomedcentral.com/1471-2105/11/S2/S6
PubMed: 20406504

*** April 27 2010 ***
Concept-based query expansion for retrieving gene related publications from MEDLINE
Sergio Matos, Joel P Arrais, Joao Maia-Rodrigues, and Jose Luis Oliveira
BMC Bioinformatics, 11(1):212, 2010
DOI: 10.1186/1471-2105-11-212
Paper: http://www.biomedcentral.com/1471-2105/11/212/
PubMed: 20426836

*** April 13 2010 ***
Domain adaptation for semantic role labeling in the biomedical domain
Daniel Dahlmeier and Hwee Tou Ng
Bioinformatics 2010, 26(8):1098-1104
DOI: 10.1093/bioinformatics/btq075
Paper: http://bioinformatics.oxfordjournals.org/cgi/content/full/26/8/1098

*** Apr 2 2010 ***
Building a High Quality Sense Inventory for Improved Abbreviation Disambiguation
Naoaki Okazaki, Sophia Ananiadou, and Jun'ichi Tsujii
Bioinformatics Advance Access first published online on March 25, 2010
DOI: 10.1093/bioinformatics/btq129
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq129

Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining.
Hettne KM, Williams AJ, van Mulligen EM, Kleinjans J, Tkachenko V, Kors JA.
J Cheminform. 2010 Mar 23;2(1):3.
PubMed: 20331846

Moara: a Java library for extracting and normalizing gene and protein mentions.
Neves ML, Carazo JM, Pascual-Montano A.
BMC Bioinformatics. 2010 Mar 26;11:157.
PubMed: 20346105

miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature.
Naeem H, Kü:ffner R, Csaba G, Zimmer R.
BMC Bioinformatics. 2010 Mar 16;11:135.
PubMed: 20233441

*** Apr 1 2010 ***
Biomedical Semantics: the Hub for Biomedical Research 2.0
Dietrich Rebholz-Schuhmann, Goran Nenadic
Journal of Biomedical Semantics 2010, 1:5 (31 March 2010)
DOI: 10.1186/2041-1480-1-5
Abstract: http://www.jbiomedsem.com/content/1/1/5

Applying the functional abnormality ontology pattern to anatomical functions
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso
Journal of Biomedical Semantics 2010, 1:4 (31 March 2010)
DOI: 10.1186/2041-1480-1-4
Abstract: http://www.jbiomedsem.com/content/1/1/4

Analysis of syntactic and semantic features for fine-grained event-spatial understanding in outbreak news reports
Hutchatai Chanlekha, Nigel Collier
Journal of Biomedical Semantics 2010, 1:3 (31 March 2010)
DOI: 10.1186/2041-1480-1-3
Abstract: http://www.jbiomedsem.com/content/1/1/3

What's unusual in online disease outbreak news?
Nigel Collier
Journal of Biomedical Semantics 2010, 1:2 (31 March 2010)
DOI: 10.1186/2041-1480-1-2
Abstract: http://www.jbiomedsem.com/content/1/1/2

Rewriting and suppressing UMLS terms for improved biomedical term identification
Kristina M Hettne, Erik M van Mulligen, Martijn J Schuemie, Bob J.A
Schijvenaars, Jan A Kors
Journal of Biomedical Semantics 2010, 1:1 (31 March 2010)
DOI: 10.1186/2041-1480-1-1
Abstract: http://www.jbiomedsem.com/content/1/1/1

*** Mar 15 2010 ***
Measuring prediction capacity of individual verbs for the identification of protein interactions
Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Miguel Arregui, and Harald Kirsch
Journal of Biomedical Informatics
Volume 43, Issue 2, April 2010, Pages 200-207
DOI: 10.1016/j.jbi.2009.09.007

*** Mar 5 2010 ***
PaperMaker: Validation of biomedical scientific publications
D Rebholz-Schuhmann, S Kavaliauskas, and P Pezik
Bioinformatics, 2010, 26:982-984
DOI: 10.1093/bioinformatics/btq060
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq060
PubMed: 20200010

*** Feb 26 2010 ***
Event Extraction with Complex Event Classification using Rich Features
Makoto Miwa, Rune Saetre, Jin-Dong Kim, Jun'ichi Tsujii
Journal of Bioinformatics & Computational Biology; February 2010, Vol. 8 Issue 1, p131-146

Wrestling with Biomedical Research Results: Language Resources and Literature Analysis
Dietrich Rebholz-Schumann, Nigel Collier, Jong C. Park, Limsoon Wong
Journal of Bioinformatics & Computational Biology, February 2010, Vol. 8 Issue 1, p129-130

The Value of an In-Domain Lexicon in Genomics QA
Yutaka Sasaki, John McNaught, Sophia Ananiadou
Journal of Bioinformatics & Computational Biology, February 2010, Vol. 8 Issue 1, p147-161

Random Drift versus Selection in Academic Vocabulary: An Evolutionary Analysis of Published Keywords
R. Alexander Bentley
PLoS ONE 3(8): e3057
DOI: 10.1371/journal.pone.0003057
Full text: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003057

PPI Finder: A Mining Tool for Human Protein-Protein Interactions
Min He, Yi Wang, Wei Li
PLoS ONE 4(2):e4554, February 23, 2009.
DOI: 10.1371/journal.pone.0004554
Full text: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004554
PubMed: 19234603

*** Feb 22 2010 ***
Extracting causal relations on HIV drug resistance from literature
Quoc-Chinh Bui, Breanndan O Nuallain, Charles A Boucher, and Peter M.A. Sloot
BMC Bioinformatics 2010, 11:101
DOI: 10.1186/1471-2105-11-101
Paper: http://www.biomedcentral.com/1471-2105/11/101

Integrating text mining into the MGI biocuration workflow.
Dowell KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA.
Database (Oxford). 2009:bap019
PubMed: 20157492

LINNAEUS: A species name identification system for biomedical literature.
Gerner M, Nenadic G, Bergman CM.
BMC Bioinformatics. 2010 Feb 11; 11(1):85
PubMed: 20149233

Literature mining: Speed reading.
Lok C.
Nature. 2010 Jan 28; 463(7280):416-8. No abstract available.
PubMed: 20110962

*** Feb 2 2010 ***
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships
Adriano Barbosa-Silva, Theodoros G Soldatos, Ivan L F Magalhaes, Georgios A Pavlopoulos, Jean-Fred Fontaine, Miguel A Andrade-Navarro, Reinhard Schneider, and J. Miguel Ortega
BMC Bioinformatics 2010, 11:70
DOI: 10.1186/1471-2105-11-70
Paper: http://www.biomedcentral.com/1471-2105/11/70/

*** Jan 27 2010 ***
Semi-automated screening of biomedical citations for systematic reviews
Byron C Wallace, Thomas A Trikalinos, Joseph Lau, Carla E Brodley, and Christopher H Schmid
BMC Bioinformatics 2010, 11:55
DOI: 10.1186/1471-2105-11-55
Paper: http://www.biomedcentral.com/1471-2105/11/55/

GOClonto: An ontological clustering approach for conceptualizing PubMed abstracts
Hai-Tao Zheng, Charles Borchert, Hong-Gee Kim
Journal of Biomedical Informatics, Volume 43, Issue 1, pages 31-40, 2010
DOI: 10.1016/j.jbi.2009.07.006

BioPPISVMExtractor: A protein-protein interaction extractor for biomedical literature using SVM and rich feature sets
Zhihao Yang, Hongfei Lin, Yanpeng Li
Journal of Biomedical Informatics, Volume 43, Issue 1, pages 88-96, 2010
DOI: 10.1016/j.jbi.2009.08.013

*** Jan 21 2010 ***
Automatic symptom name normalization in clinical records of traditional Chinese medicine
Yaqiang Wang, Zhonghua Yu, Yongguang Jiang, Kaikuo Xu, and Xia Chen
BMC Bioinformatics 2010, 11:40
DOI: 10.1186/1471-2105-11-40
Paper: http://www.biomedcentral.com/1471-2105/11/40/

Chi-square-based Scoring Function for Categorization of MEDLINE Citations.
Kastrin A, Peterlin B, Hristovski D.
Methods Inf Med. 2010 Jan 20;49(2)
PubMed: 20091016

SPECTRa-T: Machine-Based Data Extraction and Semantic Searching of Chemistry e-Theses.
Downing J, Harvey MJ, Morgan PB, Murray-Rust P, Rzepa HS, Stewart DC, Tonge AP, Townsend JA.
J Chem Inf Model. 2010 Jan 20
PubMed: 20088574

*** Jan 15 2010 ***
Text mining for traditional Chinese medical knowledge discovery: A survey.
Zhou X, Peng Y, Liu B.
J Biomed Inform. 2010 Jan 13
PubMed: 20074663

Gene prioritization and clustering by multi-view text mining.
Yu S, Tranchevent LC, De Moor B, Moreau Y.
BMC Bioinformatics. 2010 Jan 14;11(1):28
PubMed: 20074336

Disambiguating the Species of Biomedical Named Entities Using Natural Language Parsers.
Xinglong Wang, Jun'ichi Tsujii, and Sophia Ananiadou
Bioinformatics. 2010 Jan 6, 26:661-667
DOI: 10.1093/bioinformatics/btq002
PubMed: 20053840

Biomedical text mining and its applications.
Rodriguez-Esteban R.
PLoS Comput Biol. 2009 Dec;5(12):e1000597
PubMed: 20041219

Cheminformatics analysis of assertions mined from literature that describe drug-induced liver injury in different species
Fourches D, Barnes JC, Day NC, Bradley P, Reed JZ, Tropsha A.
Chem Res Toxicol. 2010 Jan;23(1):171-83.
PubMed: 20014752

Exploitation of ontological resources for scientific literature analysis: Searching genes and related diseases.
Jimeno-Yepes A, Berlanga-Llavori R, Rebholz-Schuhmann D.
Conf Proc IEEE Eng Med Biol Soc. 2009;1:7073-8
PubMed: 19964204

Analysis of biological processes and diseases using text mining approaches.
Krallinger M, Leitner F, Valencia A.
Methods Mol Biol. 2010;593:341-82
PubMed: 19957157

*** Jan 14 2010 ***
Proceedings of the GPD-Rxn Workshop: Genotype-Phenotype-Drug Relationship Extraction from Text, in conjunction with PSB 2010
Adrien Coulet, Nigam Shah, Larry Hunter, Chitta Baral and Russ B. Altman (editors)
Workshop: http://psb.stanford.edu/psb10/gpdrxn-workshop.html
Agenda: http://psb.stanford.edu/psb10/gpdrxn-workshop2.pdf
(PC)

Tool Performance and Semantic Type Distribution for Genotype-Phenotype-Drug Relationship Mining from Text
Kevin Bretonnel Cohen, HL Johnson, K Verspoor, C Roeder, and L Hunter

A Dictionary Approach to the Identification of Small Molecules and Drugs in Free Text
Kristina M Hettne, RH Stierum, MJ Schuemie, PJM Hendriksen, BJA Schijvenaars, EM van Mulligen, J Kleinjans, and J Kors

Pharmacokinetics Ontology Development
Zhiping Wang, SK Quinney, and L Li

Pharmacokinetics Parameter Text Mining
Yuming Zhao, W Zhiping, and L Li

Taking a SNPShot of PubMed - a repository of genetic variants and their drug response phenotypes
Jörg Hakenberg, D Voronov, VH Nguyen, S Liang, B Lumpkin, S Anwar, R Leaman, LN Tari, and C Baral

Linking a Gene/Protein-Focused Relation Extractor to the Pharmacogenomic Domain
Ekaterina Buyko, and U Hahn

Extraction and Integration of Pharmacogenomic Relationships from Medline Abstracts
Adrien Coulet, N Shah, and RB Altman

Identifying Novel Drug Indications using Ontology-based Mashups of Disease, Phenotype and Drug Information
Cartic Ramakrishnan, K Kundu, A Qu, A Jegga, EK Neumann, and BJ Aronow

Towards mining drug-phenotype data: context based calculation of probabilistic semantic similarity
Lixia Yao, J. Evans, and A. Rzhetsky

** Dec 14 2009 ***
HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features.
Tsai RT, Lai PT, Dai HJ, Huang CH, Bow YY, Chang YC, Pan WH, Hsu WL.
BMC Bioinformatics. 2009 Dec 3;10 Suppl 15:S9
PubMed: 19958519

BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature.
Kuo CJ, Ling MH, Lin KT, Hsu CN.
BMC Bioinformatics. 2009 Dec 3;10 Suppl 15:S7
PubMed: 19958517

*** Dec 10 2009 ***
Investigating heterogeneous protein annotations toward cross-corpora utilization
Wang Y, Kim J, Saetre R, Pyysalo S, Tsujii J
BMC Bioinformatics 2009, 10:403 (9 December 2009)
Abstract: http://www.biomedcentral.com/1471-2105/10/403/abstract

Understanding PubMed user search behavior through log analysis
Islamaj Dogan R, Murray GC, Neveol A, Lu Z.
Database (Oxford), article ID bap018, 2009. Epub 2009 Nov 27
DOI: 10.1093/database/bap018
PubMed: 20157491
PMC: PMC2797455

*** Nov 24 2009 ***
Concepts and Synonymy in the UMLS Metathesaurus
Gary Merrill
Discovery and Collaboration (DISCO), 4:7, 2009
Abstract: http://www.uic.edu/htbin/cgiwrap/bin/ojs/index.php/jbdc/article/view/2663
PDF: http://www.uic.edu/htbin/cgiwrap/bin/ojs/index.php/jbdc/article/view/2663/2346

Novel protein-protein interactions inferred from literature context.
van Haagen HH, 't Hoen PA, Botelho Bovo A, de Morree A, van Mulligen EM, Chichester C, Kors JA, den Dunnen JT, van Ommen GJ, van der Maarel SM, Kern VM, Mons B, Schuemie MJ.
PLoS One. 2009 Nov 18;4(11):e7894
DOI: 10.1371/journal.pone.0007894
Open access article: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007894
PubMed: 19924298

*** Nov 12 2009 ***
Linguistic feature analysis for protein interaction extraction
Timur Fayruzov, Martine De Cock, Chris Cornelis, and Veronique Hoste
BMC Bioinformatics. 2009 Nov 12;10(1):374
http://www.biomedcentral.com/1471-2105/10/374
DOI: 10.1186/1471-2105-10-374
PubMed: 19909518

*** Nov 10 2009 ***
Improving the prediction of pharmacogenes using text-derived drug-gene relationships
Garten Y, Tatonetti NP, Altman RB.
Pac Symp Biocomput. 2010:305-14
PubMed: 19908383

Beyond genes, proteins, and abstracts: Identifying scientific claims from full-text biomedical articles
Catherine Blake
Journal of Biomedical Informatics
Volume 43, Issue 2, April 2010, Pages 173-189
DOI: 10.1016/j.jbi.2009.11.001
PubMed: 19900574

Textpresso site-specific recombinases: A text-mining server for the recombinase literature including Cre mice and conditional alleles
Urbanski WM, Condie BG.
Genesis. 2009 Oct 30.
PubMed: 19882667

Construction of an annotated corpus to support biomedical information extraction
Thompson P, Iqbal SA, McNaught J, Ananiadou S.
BMC Bioinformatics. 2009 Oct 23;10:349.
PubMed: 19852798

*** Oct 22 2009 ***
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D
Niu Y, Otasek D, Jurisica I.
Bioinformatics. 2009 Oct 22.
PubMed: 19850753

Predicting citation count of Bioinformatics papers within four years of publication
Ibanez A, Larranaga P, Bielza C.
Bioinformatics. 2009 Oct 9.
PubMed: 19819886

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)
Wiegers TC, Davis AP, Cohen KB, Hirschman L, Mattingly CJ.
BMC Bioinformatics. 2009 Oct 8;10:326.
PubMed: 19814812

*** Oct 1 2009 ***
GoWeb: a semantic search engine for the life science web
Dietze H, Schroeder M.
BMC Bioinformatics. 2009 Oct 1;10 Suppl 10:S7.
PubMed: 19796404

Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion
Agarwal S, Yu H.
Bioinformatics. 2009 Dec 1;25(23):3174-3180
PubMed: 19783830

Extraction of human kinase mutations from literature, databases and genotyping studies
Krallinger M, Izarzugaza JM, Rodriguez-Penagos C, Valencia A.
BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S1.
PubMed: 19758464
Supplementary information: http://www.biomedcentral.com/content/supplementary/1471-2105-10-s8-s1-s1.pdf

The first step in the development of Text Mining technology for Cancer Risk Assessment: identifying and organizing scientific evidence in risk assessment literature
Korhonen A, Silins I, Sun L, Stenius U.
BMC Bioinformatics. 2009 Sep 22;10:303.
PubMed: 19772619

Automated recognition of brain region mentions in neuroscience literature.
French L, Lane S, Xu L, Pavlidis P.
Front Neuroinformatics. 2009;3:29.
PubMed: 19750194

Automatic medical knowledge acquisition using question-answering
Pasche E, Teodoro D, Gobeill J, Ruch P, Lovis C.
Stud Health Technol Inform. 2009;150:569-73.
PubMed: 19745375

Current issues in biomedical text mining and natural language processing
Chapman WW, Cohen KB.
J Biomed Inform. 2009 Oct;42(5):757-9.
PubMed: 19735740

Pathway enrichment based on text mining and its validation on carotenoid and vitamin A metabolism
Waagmeester A, Pezik P, Coort S, Tourniaire F, Evelo C, Rebholz-Schuhmann D.
OMICS. 2009 Oct;13(5):367-79.
PubMed: 19715393

Two-phase biomedical named entity recognition using CRFs
Li L, Zhou R, Huang D.
Comput Biol Chem. 2009 Aug;33(4):334-8
PubMed: 19656727

PubMed-EX: A web browser extension to enhance PubMed search with text mining features
Richard Tzong-Han Tsai, Hong-Jie Dai, Po-Ting Lai, and Chi-Hsin Huang
Bioinformatics. 2009 Nov 15;25(22):3031-2
DOI: 10.1093/bioinformatics/btp475
PubMed: 19654114

Getting started in text mining: part two.
Rzhetsky A, Seringhaus M, Gerstein MB.
PLoS Comput Biol. 2009 Jul;5(7):e1000411
PubMed: 19649304
(R)

*** Sep 25 2009 ***
Challenges for automatically extracting molecular interactions from full-text articles
Tara McIntosh and James R Curran
BMC Bioinformatics 2009, 10:311
DOI: 10.1186/1471-2105-10-311

*** Sep 23 2009 ***
The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature
Korhonen A, Silins I, Sun L, Stenius U
BMC Bioinformatics 2009, 10:303 (22 September 2009)
Abstract: http://www.biomedcentral.com/1471-2105/10/303/abstract

*** Sep 17 2009 ***
A Dictionary to Identify Small Molecules and Drugs in Free Text
Kristina M Hettne, Rob H Stierum, Martijn J Schuemie, Peter JM Hendriksen,
Bob JA Schijvenaars, Erik M van Mulligen, Jos Kleinjans, and Jan A Kors
Bioinformatics published 16 September 2009
DOI: 10.1093/bioinformatics/btp535
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp535v1?papetoc

*** Aug 27 2009 ***
GeneNarrator: Mining the Literaturome for Relations Among Genes
Jing Ding, Daniel Berleant, Jun Xu, Kenton Juhlin, Eve Wurtele, Andy Fulmer
J Proteomics Bioinform, 2(8):360-371
DOI: 10.4172/jpb.1000096
Abstract: http://www.omicsonline.com/ArchiveJPB/2009/August/02/JPB2.360.html

*** Jul 17 2009 ***
Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity
Shanfeng Zhu, Jia Zeng, and Hiroshi Mamitsuka
Bioinformatics 2009 25: 1944-1951
DOI: 10.1093/bioinformatics/btp338.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/15/1944?etoc

*** Jul 6 2009 ***
Bayesian inference of protein-protein interactions from biological literature
Rajesh Chowdhary, Jinfeng Zhang, and Jun S. Liu
Bioinformatics 2009 25(12):1536-1542;
DOI: 10.1093/bioinformatics/btp245

Categorization of services for seeking information in biomedical literature: a typology for improvement of practice
Jung-jae Kim and Dietrich Rebholz-Schuhmann
Brief Bioinform 2008 9: 452-465
DOI: 10.1093/bib/bbn032.
http://bib.oxfordjournals.org/cgi/content/abstract/9/6/452?etoc

*** Jul 2 2009 ***
A neural network-based biomarker association information extraction approach for cancer classification
Hong-Qiang Wang, Hau-San Wong, Hailong Zhu, Timothy T.C. Yip
Journal of Biomedical Informatics, Volume 42, Issue 4, Pages 654-666, 2009

Sequential result refinement for searching the biomedical literature
L.Y. Tanaka, J.R. Herskovic, M.S. Iyengar, E.V. Bernstam
Journal of Biomedical Informatics, Volume 42, Issue 4, Pages 678-684, 2009

Translating medical terminologies through word alignment in parallel text corpora
Louise Deléger, Magnus Merkel, Pierre Zweigenbaum
Journal of Biomedical Informatics, Volume 42, Issue 4, Pages 692-701, 2009

Literature mining on pharmacokinetics numerical data: A feasibility study
Zhiping Wang, Seiongho Kim, Sara K. Quinney, Yingying Guo, Stephen D. Hall, Luis M. Rocha, Lang Li
Journal of Biomedical Informatics, Volume 42, Issue 4, Pages 726-735, 2009

*** Jun 29 2009 ***
Miguel Vazquez, Pedro Carmona-Saez, Ruben Nogales-Cadenas, Monica Chagoyen, Francisco Tirado, Jose Maria Carazo, and Alberto Pascual-Montano
SENT: semantic features in text
Nucleic Acids Research Advance Access published on May 20, 2009
Nucl. Acids Res. 2009 37: W153-W159
DOI: 10.1093/nar/gkp39

*** Jun 19 2009 ***
Feature Selection Techniques for Maximum Entropy based Biomedical Named Entity Recognition.
Saha SK, Sarkar S, Mitra P.
J Biomed Inform. 2009 Jan 22
PubMed: 19535010

*** Jun 18 2009 ***
The textual characteristics of traditional and Open Access scientific journals are similar
Karin Verspoor, K. Bretonnel Cohen, Lawrence Hunter
BMC Bioinformatics 2009, 10:183 (15 June 2009)
PubMed: 19527520
DOI: 10.1186/1471-2105-10-183
PDF: http://www.biomedcentral.com/content/pdf/1471-2105-10-183.pdf

*** Jun 16 2009 ***
Modeling actions of PubMed users with n-gram language models
Jimmy Lin and W. John Wilbur
Information Retrieval, Volume 12, Number 4 / August, 2009, Springer
DOI: 10.1007/s10791-008-9067-7
PDF: http://www.springerlink.com/content/t4316k8547863085/fulltext.pdf

A CitationRank Algorithm Inheriting Google Technology Designed to Highlight Genes Responsible for Serious Adverse Drug Reaction
Lun Yang, Langlai Xu, and Lin He
Bioinformatics Advance Access published online on June 15, 2009
DOI: 10.1093/bioinformatics/btp369
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp369
PDF: http://bioinformatics.oxfordjournals.org/cgi/reprint/btp369.pdf

*** Jun 15 2009 ***
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.
Krallinger M, Rodriguez-Penagos C, Tendulkar A, Valencia A.
Nucleic Acids Res. 2009 Jun 11
PubMed: 19520768

Interactive Text Mining with Pipeline Pilot: A Bibliographic Web-Based Tool for PubMed.
Vellay SG, Latimer NE, Paillard G.
Infect Disord Drug Targets. 2009 Jun;9(3):366-74.
PubMed: 19519489

Gene expression mining in type 2 diabetes research.
Dunbar DR.
Methods Mol Biol. 2009;560:263-71.
PubMed: 19504255

*** Jun 11 2009 ***
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, Shaker M, Pot D
BMC Bioinformatics 2009, 10:177
Abstract: http://www.biomedcentral.com/1471-2105/10/177/abstract

*** Jun 9 2009 ***
Protein-protein interaction extraction by leveraging multiple kernels and parsers.
Miwa M, Saetre R, Miyao Y, Tsujii J.
Int J Med Inform. 2009 Jun 3
PubMed: 19501018
DOI: 10.1016/j.ijmedinf.2009.04.010

*** Jun 4 2009 ***
Proceedings of the BioNLP 2009 workshop, in conjunction with NA-ACL 2009, Boulder, Colorado, USA
Website: http://compbio.uchsc.edu/BioNLP2009/program.shtml

Proceedings of the BioNLP 2009 Shared Task, in conjunction with the BioNLP 2009 workshop, in conjunction with NA-ACL 2009, Boulder, Colorado, USA
Website: http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/SharedTask/program.shtml

Exploring Two Biomedical Text Genres for Disease Recognition
Neveol A., Kim W., Wilbur WJ., Lu Z.
Proc BioNLP Workshop at NAACL 2009

*** May 30 2009 ***
Ontology quality assurance through analysis of term transformations.
Verspoor K, Dvorkin D, Cohen KB, Hunter L.
Bioinformatics. 2009 Jun 15;25(12):i77-84.
PubMed: 19478020
(ONT)

*** May 25 2009 ***
GoGene: gene annotation on the fast lane.
Conrad Plake, Loic Royer, Rainer Winnenburg, Jörg Hakenberg, Michael Schroeder
Nucl. Acids Res. 2009 37: W300-W304
DOI: 10.1093/nar/gkp429
PubMed: 19465383
Abstract: http://nar.oxfordjournals.org/cgi/content/abstract/gkp429v1
(T)

Classifying disease outbreak reports using n-grams and semantic features.
Conway M, Doan S, Kawazoe A, Collier N.
Int J Med Inform. 2009 May 14
PubMed: 19447070

*** May 18 2009 ***
LitInspector: literature and signal transduction pathway mining in PubMed abstracts
Matthias Frisch, Bernward Klocke, Manuela Haltmeier, and Kornelie Frech
Nucl. Acids Res. 2009 37(Suppl. 2):W135-W140
DOI: 10.1093/nar/gkp303

*** May 15 2009 ***
Figure mining for biomedical research.
Rodriguez-Esteban Raul and Iossifov Ivan
Bioinformatics, Advance Access published on May 13, 2009
DOI: 10.1093/bioinformatics/btp318
PubMed: 19439564

*** May 12 2009 ***
MedlineRanker: flexible ranking of biomedical literature.
Jean-Fred Fontaine, Adriano Barbosa-Silva, Martin Schaefer, Matthew R. Huska, Enrique M. Muro, and Miguel A. Andrade-Nav
arro
Nucl. Acids Res. 2009 37(Suppl. 2):W141-W146
DOI: 10.1093/nar/gkp353
PubMed: 19429696

MaHCO: An Ontology of the Major Histocompatibility Complex for Immunoinformatic Applications and Text Mining.
Deluca DS, Beisswanger E, Wermter J, Horn PA, Hahn U, Blasczyk R.
Bioinformatics. 2009 May 7.
PubMed: 19429601

*** May 6 2009 ***
Improving classification in protein structure databases using text mining
Antonis Koussounadis, Oliver C Redfern, David T Jones
BMC Bioinformatics 2009, 10:129
DOI: 10.1186/1471-2105-10-129
Abstract: http://www.biomedcentral.com/1471-2105/10/129/abstract
PubMed: 19416501

*** Cinco de Mayo 2009 ***
U-Compare: share and compare text mining tools with UIMA
Yoshinobu Kano, William A. Baumgartner, Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, and Jun'ichi Tsujii
Bioinformatics 2009, 25:1997-1998
DOI: 10.1093/bioinformatics/btp289
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp289
Paper: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/15/1997?etoc
PubMed: 19414535

Survey-based naming conventions for use in OBO Foundry ontology development
Daniel Schober, Barry Smith, Suzanna E Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F Taylor, Philippe Rocca-Serra, and Susanna-Assunta Sansone
BMC Bioinformatics 2009, 10:125
DOI: 10.1186/1471-2105-10-125
Abstract: http://www.biomedcentral.com/1471-2105/10/125/abstract

@Note: A workbench for Biomedical Text Mining.
Lourenco A, Carreira R, Carneiro S, Maia P, Glez-Pena D, Fdez-Riverola F, Ferreira EC, Rocha I, Rocha M.
J Biomed Inform. 2009 Apr 22
PubMed: 19393341

*** Apr 23 2009 ***
Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article
David Shotton, Katie Portwin, Graham Klyne, Alistair Miles
PLoS Comput Biol 5(4):e1000361.
Fulltext: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000361

A System for Classifying Disease Co-morbidity Status from Medical Discharge Summaries Using Automated Hotspot and Negated Concept Detection.
Ambert KH, Cohen AM.
J Am Med Inform Assoc. 2009 Apr 23
PubMed: 19390099

A Text Mining Approach to the Prediction of a Disease Status from Clinical Discharge Summaries.
Yang H, Spasic I, Keane JA, Nenadic G.
J Am Med Inform Assoc. 2009 Apr 23
PubMed: 19390098

Literature-based priors for gene regulatory networks
E. Steele, A. Tucker, P.A.C. 't Hoen, and M.J. Schuemie
Bioinformatics published 23 April 2009
DOI: 10.1093/bioinformatics/btp277
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp277

MeSH Up: Effective MeSH Text Classification for Improved Document Retrieval
Dolf Trieschnigg, Piotr Pezik, Vivian Lee, Franciska de Jong, Wessel
Kraaij, and Dietrich Rebholz-Schuhmann
Bioinformatics, 2009, 25:1412-1418
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/11/1412?etoc
DOI: 10.1093/bioinformatics/btp249
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp249

*** Apr 16 2009 ***
Assigning Roles to Protein Mentions: the Case of Transcription Factors.
Yang H, Keane J, Bergman CM, Nenadic G.
J Biomed Inform. 2009 Apr 10
PubMed: 19364541

Creating reference datasets for systems biology applications using text mining.
Krallinger M, Rojas AM, Valencia A.
Ann N Y Acad Sci. 2009 Mar;1158:14-28.
PubMed: 19348628

Literature Mining on Pharmacokinetics Numerical Data: A Feasibility Study.
Wang Z, Kim S, Quinney SK, Guo Y, Hall SD, Rocha LM, Li L.
J Biomed Inform. 2009 Apr 1
PubMed: 19345282

KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways.
Spasic I, Simeonidis E, Messiha HL, Paton NW, Kell DB.
Bioinformatics. 2009, 25:1404-1411
DOI: 10.1093/bioinformatics/btp175.
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/11/1404?etoc
PubMed: 19336445

Text-mining approach to evaluate terms for ontology development.
Tsoi LC, Patel R, Zhao W, Jim Zheng W.
J Biomed Inform. 2009 Mar 24
PubMed: 19318137

*** Mar 12 2009 ***
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.
Garten Y, Altman RB.
BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:S6.
PubMed: 19208194

Discovering Genes-Diseases Associations from Specialized Literature Using the GRID.
Faro A, Giordano D, Maiorana F, Spampinato C.
IEEE Trans Inf Technol Biomed. 2008 Oct 31
PubMed: 19273026

Prediction of EST Functional Relationships via Literature Mining With User-Specified Parameters.
Wang HC, Huang TH.
IEEE Trans Biomed Eng. 2008 Dec 2
PubMed: 19272867
Abstract: http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=4694115

Text mining in healthcare. Applications and opportunities.
Raja U, Mitchell T, Day T, Hardin JM.
J Healthc Inf Manag. 2008 Summer;22(3):52-6.
PubMed: 19267032

A functional network module for Smith-Magenis syndrome.
Girirajan S, Truong H, Blanchard C, Elsea S.
Clin Genet. 2009 Feb 17
PubMed: 19236431

*** Feb 22 2009 ***
Collaborative text-annotation resource for disease-centered relation extraction from biomedical text.
Cano C, Monaghan T, Blanco A, Wall DP, Peshkin L.
J Biomed Inform. 2009 Feb 13
PubMed: 19232400
DOI: 10.1016/j.jbi.2009.02.001

SciMiner: Web-based literature mining tool for target identification and functional enrichment analysis.
Hur J, Schuyler AD, States DJ, Feldman EL.
Bioinformatics. 2009 Feb 2
PubMed: 19188191

Building a semantically annotated corpus of clinical texts
Angus Roberts, Robert Gaizauskas, Mark Hepple, George Demetriou, Yikun Guo, Ian Roberts and Andrea Setzer
Journal of Biomedical Informatics
DOI: 10.1016/j.jbi.2008.12.013

*** Feb 3 2009 ***
Arrowsmith two-node search interface: A tutorial on finding meaningful links between two disparate sets of articles in MEDLINE.
N.R. Smalheiser, V.I. Torvik, and W. Zhou
Comput Methods Programs Biomed. 2009 Jan 29
PubMed: 19185946
DOI: 10.1016/j.cmpb.2008.12.006

*** Jan 26 2009 ***
Towards identifying intervention arms in randomized controlled trials: Extracting coordinating constructions.
Chung GY.
J Biomed Inform. 2009 Jan 4
PubMed: 19166975

*** Jan 22 2009 ***
Extraction of CYP Chemical Interactions from Biomedical Literature Using Natural Language Processing Methods.
Dazhi Jiao and David J. Wild
J Chem Inf Model. 2009, 49(2):263-9.
DOI: 10.1021/ci800332w
Abstract: http://pubs.acs.org/doi/abs/10.1021/ci800332w
PubMed: 19154181

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy
Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Joerg Hakenberg, Khaled Khelif, Michael Schroeder, and Thomas Waechter
BMC Bioinformatics, 10:28, 2009
Abstract: http://www.biomedcentral.com/1471-2105/10/28

Text mining
Andrew B. Clegg and Adrian J. Sheperd
Methods Mol Biol.2008; 453:471-91.
DOI: 10.1007/978-1-60327-429-6_25
PubMed: 18712320

*** Jan 17 2009 ***
MBA: a literature mining system for extracting biomedical abbreviations
Yun Xu , ZhiHao Wang , YiMing Lei , YuZhong Zhao and Yu Xue
BMC Bioinformatics 2009, 10:14
DOI: 10.1186/1471-2105-10-14
http://www.biomedcentral.com/1471-2105/10/14/

Porting a lexicalized-grammar parser to the biomedical domain.
Rimell L, Clark S.
J Biomed Inform. 2008 Dec 25
PubMed: 19141332

Exploiting the performance of dictionary-based bio-entity name recognition in biomedical literature
Zhihao Yang, Hongfei Lina and Yanpeng Li
Computational Biology and Chemistry, Volume 32, Issue 4, August 2008, Pages 287-291
DOI: 10.1016/j.compbiolchem.2008.03.008

A new evaluation methodology for literature-based discovery systems
Meliha Yetisgen-Yildiza and Wanda Pratt
Journal of Biomedical Informatics, Volume 42, Issue 4, Pages 633-643, 2009
DOI: 10.1016/j.jbi.2008.12.001

Automatically extracting cancer disease characteristics from pathology reports into a Disease Knowledge Representation Model
Anni Coden, Guergana Savova, Igor Sominsky, Michael Tanenblatt, James Masanz, Karin Schuler, James Cooper, Wei Guan, and Piet C. de Groen
Journal of Biomedical Informatics
Article in Press
DOI: 10.1016/j.jbi.2008.12.005

Improving accuracy for identifying related PubMed queries by an integrated approach
Zhiyong Lu and W. John Wilbu
Journal of Biomedical Informatics
Article in Press
DOI: 10.1016/j.jbi.2008.12.006

A Recent Advance in the Automatic Indexing of the Biomedical Literature
Aurelie Neveol, Sonya E. Shooshan, Susanne M. Humphrey, James G. Mork and Alan R. Aronson
Journal of Biomedical Informatics
Article in Press
DOI: 10.1016/j.jbi.2008.12.007

Towards role-based filtering of disease outbreak reports
Son Doan, Ai Kawazoe, Mike Conway and Nigel Collier
Journal of Biomedical Informatics
Article in Press
DOI: 10.1016/j.jbi.2008.12.009

Automatic summarization of MEDLINE citations for evidence-based medical treatment: A topic-oriented evaluation
Marcelo Fiszman, Dina Demner-Fushman, Halil Kilicoglu and Thomas C. Rindflesch
Journal of Biomedical Informatics
Article in Press
DOI: 10.1016/j.jbi.2008.10.002

*** Dec 14 2008 ***
Proceedings of the BioNLP 08 ACL Workshop: Themes in biomedical language processing
BMC Bioinformatics, 2009, Suppl 11
ToC: http://www.biomedcentral.com/1471-2105/9?issue=S11

Themes in biomedical natural language processing: BioNLP08
Dina Demner-Fushman, Sophia Ananiadou, K Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie Webber
BMC Bioinformatics 2008, 9(Suppl 11):S1 (19 November 2008)

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)

Mining clinical relationships from patient narratives
Angus Roberts, Robert Gaizauskas, Mark Hepple, Yikun Guo
BMC Bioinformatics 2008, 9(Suppl 11):S3 (19 November 2008)

Cascaded classifiers for confidence-based chemical named entity recognition
Peter Corbett, Ann Copestake
BMC Bioinformatics 2008, 9(Suppl 11):S4 (19 November 2008)

How to make the most of NE dictionaries in statistical NER
Yutaka Sasaki, Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou
BMC Bioinformatics 2008, 9(Suppl 11):S5 (19 November 2008)

Distinguishing the species of biomedical named entities for term identification.
Wang X, Matthews M.
BMC Bioinformatics. 2008 Nov 19;9 Suppl 11:S6
PubMed: 19025692
Full text: http://www.biomedcentral.com/1471-2105/9/S11/S6/
DOI: 10.1186/1471-2105-9-S11-S6

Disambiguation of biomedical text using diverse sources of information
Mark Stevenson, Yikun Guo, Robert Gaizauskas, David Martinez
BMC Bioinformatics 2008, 9(Suppl 11):S7 (19 November 2008)

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 Nov 19;9 Suppl 11:S9
PubMed: 19025695
Full text: http://www.biomedcentral.com/1471-2105/9/S11/S9/
DOI: 10.1186/1471-2105-9-S11-S9

Recognizing speculative language in biomedical research articles: a linguistically motivated perspective
Halil Kilicoglu, Sabine Bergler
BMC Bioinformatics 2008, 9(Suppl 11):S10 (19 November 2008)

Automatic inference of indexing rules for MEDLINE
Aurélie Névéol, Sonya E Shooshan, Vincent Claveau
BMC Bioinformatics 2008, 9(Suppl 11):S11 (19 November 2008)

Evaluating Contributions of Natural Language Parsers to Protein-Protein Interaction Extraction.
Miyao Y, Sagae K, Sætre R, Matsuzaki T, Tsujii J.
Bioinformatics, 2009, 25(3):394-400
http://bioinformatics.oxfordjournals.org/cgi/content/full/25/3/394
DOI: 10.1093/bioinformatics/btn631
PubMed: 19073593

*** Dec 9 2008 ***
Multi-label literature classification based on the Gene Ontology graph
Bo Jin, Brian Muller, Chengxiang Zhai, and Xinghua Lu
BMC Bioinformatics 2008, 9:525
DOI: 10.1186/1471-2105-9-525
Full text: http://www.biomedcentral.com/1471-2105/9/525/

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?
Rainer Winnenburg, Thomas Wächter, Conrad Plake, Andreas Doms and Michael Schroeder
Briefings in Bioinformatics, 2008
DOI: 10.1093/bib/bbn043
http://bib.oxfordjournals.org/cgi/content/full/bbn043

*** Nov 22 2008 ***
Word sense disambiguation across two domains: Biomedical literature and clinical notes
Guergana K. Savova, Anni R. Coden, Igor L. Sominsky, Rie Johnson, Philip V. Ogren, Piet C. de Groen, and Christopher G. Chute
Journal of Biomedical Informatics, Volume 41, Issue 6, December 2008, Pages 1088-1100
DOI: 10.1016/j.jbi.2008.02.003

Accelerating the annotation of sparse named entities by dynamic sentence selection
Yoshimasa Tsuruoka, Jun'ichi Tsujii and Sophia Ananiadou
BMC Bioinformatics 2008, 9(Suppl 11):S8, 19 November 2008
DOI: 10.1186/1471-2105-9-S11-S8
Paper: http://www.biomedcentral.com/1471-2105/9/S11/S8

Automatic DPC Code Selection from Electronic Medical Records.
Suzuki T, Yokoi H, Fujita S, Takabayashi K
Methods Inf Med. 2008 Nov 20;47(6):541-548
PubMed: 19023491

Discovering novel causal patterns from biomedical natural-language texts using Bayesian nets.
Atkinson J, Rivas A.
IEEE Trans Inf Technol Biomed. 2008 Nov;12(6):714-22.
PubMed: 19000950

Mapping Biomedical Literature with WNT Signaling Pathway.
Pena-Hernandez KE, Mahamaneerat WK, Kobayashi T, Shyu CR, Arthur GL, Caldwell CW.
AMIA Annu Symp Proc. 2008 Nov 6:1089.
PubMed: 18999226

SYRIAC: The SYstematic Review Information Automated Collection System A Data Warehouse for Facilitating Automated Biomedical Text Classification.
Yang JJ, Cohen A, McDonagh MS.
AMIA Annu Symp Proc. 2008 Nov 6:825-9.
PubMed: 18999194

A best-fit model for concept vectors in biomedical research grants.
Johnson CA, Lau W, Bhandari A, Hays T.
AMIA Annu Symp Proc. 2008 Nov 6:993.
PubMed: 18999112

A Fast Document Classification Algorithm for Gene Symbol Disambiguation in the BITOLA Literature-Based Discovery Support System.
Kastrin A, Hristovski D.
AMIA Annu Symp Proc. 2008 Nov 6:358-62.
PubMed: 18998999

*** Nov 4 2008 ***
Hepatitis C virus infection protein network.
de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, Agaugue S, Meiffren G, Pradezynski F, Faria BF, Chantier T, Le Breton M, Pellet J, Davoust N, Mangeot PE, Chaboud A, Penin F, Jacob Y, Vidalain PO, Vidal M, Andre P, Rabourdin-Combe C, Lotteau V.
Mol Syst Biol. 2008;4:230.
Paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2600670/?tool=pubmed
PubMed: 18985028
(ATM) (I) (N,S)

*** Oct 15 2008 ***
BioCaster: detecting public health rumors with a Web-based text mining system.
Collier N, Doan S, Kawazoe A, Goodwin RM, Conway M, Tateno Y, Ngo QH, Dien D, Kawtrakul A, Takeuchi K, Shigematsu M, Taniguchi K.
Bioinformatics. 2008 Oct 15
PubMed: 18922806

TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining.
Fang YC, Huang HC, Chen HH, Juan HF.
BMC Complement Altern Med. 2008 Oct 14;8:58.
PubMed: 18854039

BibGlimpse: the case for a light-weight reprint manager in distributed literature research.
Tüchler T, Velez G, Graf A, Kreil DP.
BMC Bioinformatics. 2008 Oct 1;9:406.
PubMed: 18828894

*** Oct 1 2008 ***
Ontology-centric integration and navigation of the dengue literature
Menaka Rajapakse, Rajaraman Kanagasabai, Wee Tiong Ang, Anitha Veeramani, Mark J. Schreiber and Christopher J.O. Baker
Journal of Biomedical Informatics, Volume 41, Issue 5, Pages 806-815
DOI: 10.1016/j.jbi.2008.04.004

Infrastructure for dynamic knowledge integration - Automated biomedical ontology extension using textual resources
Vit Novacek, Loredana Laera, Siegfried Handschuh and Brian Davis
Journal of Biomedical Informatics, Volume 41, Issue 5, Pages 816-828
DOI: 10.1016/j.jbi.2008.06.003

*** Sep 30 2008 ***
Abbreviation Definition Identification Based On Automatic Precision Estimates
Sunghwan Sohn, Donald C Comeau, Won Kim, and W John Wilbur
BMC Bioinformatics 2008, 9:402
DOI: 10.1186/1471-2105-9-402
PubMed: 18817555

*** Sep 29 2008 ***
Literature mining in support of drug discovery.
Agarwal P, Searls DB.
Brief Bioinform. 2008 Sep 27
PubMed: 18820304

Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users.
Shatkay H, Pan F, Rzhetsky A, Wilbur WJ.
Bioinformatics. 2008 Sep 15;24(18):2086-93
PubMed: 18718948

Textpresso for neuroscience: searching the full text of thousands of neuroscience research papers.
Möller HM, Rangarajan A, Teal TK, Sternberg PW.
Neuroinformatics. 2008 Sep;6(3):195-204
PubMed: 18949581

Text mining.
Clegg AB, Shepherd AJ.
Methods Mol Biol. 2008;453:471-91.
PubMed: 1871232

The @neurIST ontology of intracranial aneurysms: providing terminological services for an integrated IT infrastructure.
Boeker M, Stenzhorn H, Kumpf K, Bijlenga P, Schulz S, Hanser S.
AMIA Annu Symp Proc. 2007 Oct 11:56-60.
PubMed: 18693797

Integrating protein-protein interactions and text mining for protein function prediction.
Jaeger S, Gaudan S, Leser U, Rebholz-Schuhmann D.
BMC Bioinformatics. 2008 Jul 22;9 Suppl 8:S2.
PubMed: 18673526

Semantic reclassification of the UMLS concepts.
Fan JW, Friedman C.
Bioinformatics. 2008 Sep 1;24(17):1971-3
PubMed: 18625612

A comparative computational analysis of protein sequences and literature mining classify 'orphan' neurotransmitter transporters.
Panek J.
J Theor Biol. 2008 Sep 21;254(2):301-7
PubMed: 18621060

Integrating high dimensional bi-directional parsing models for gene mention tagging.
Hsu CN, Chang YM, Kuo CJ, Lin YS, Huang HS, Chung IF.
Bioinformatics. 2008 Jul 1;24(13):i286-94.
PubMed: 18586726

Identifying gene-disease associations using centrality on a literature mined gene-interaction network.
Ozgur A, Vu T, Erkan G, Radev DR.
Bioinformatics. 2008 Jul 1;24(13):i277-85.
PubMed: 1858672

Anni 2.0: a multipurpose text-mining tool for the life sciences.
Jelier R, Schuemie MJ, Veldhoven A, Dorssers LC, Jenster G, Kors JA.
Genome Biol. 2008;9(6):R96.
PubMed: 18549479

*** Sep 16 2008 ***
MPI-LIT: A literature-curated dataset of microbial binary protein-protein interactions
Seesandra V Rajagopala et al.
Bioinformatics Advance Access published online on September 11, 2008
DOI: 10.1093/bioinformatics/btn481
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn481

Database for exploration of functional context of genes implicated in ovarian cancer.
Kaur M, Radovanovic A, Essack M, Schaefer U, Maqungo M, Kibler T, Schmeier S, Christoffels A, Narasimhan K, Choolani M, Bajic VB.
Nucleic Acids Research Advance Access published online on September 12, 2008
DOI: 10.1093/nar/gkn593
Abstract: http://nar.oxfordjournals.org/cgi/content/abstract/gkn593

*** Sep 11 2008 ***
Identification and Analysis of Co-Occurrence Networks with NetCutter.
Müller H, Mancuso F.
PLoS ONE. 2008 Sep 10;3(9):e3178
Fulltext: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003178
DOI: 10.1371/journal.pone.0003178

FACTA: a text search engine for finding associated biomedical concepts
Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou
Bioinformatics Advance Access published online on September 4, 2008
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn469
DOI: 10.1093/bioinformatics/btn469

*** Sep 10 2008 ***
Nominalization and alternations in biomedical language.
Cohen KB, Palmer M, Hunter L.
PLoS ONE. 2008 Sep 9;3(9):e3158.
PubMed: 18779866

Literature mining method RaJoLink for uncovering relations between biomedical concepts.
Petric I, Urbancic T, Cestnik B, Macedoni-Luksic M
J Biomed Inform. 2009, 42(2):219-227.
PubMed: 18771753
DOI: 10.1016/j.jbi.2008.08.004

*** Sep 1 2008 ***
Genome Biology - Special Issue on The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge
http://genomebiology.com/supplements/9/S2
Research papers (named entity recognition, entity mention normalization, relation mining), summaries of BioCreative II tasks and results, review papers

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
PubMed: 18834500

Linking genes to literature: text mining, information extraction, and retrieval applications for biology.
Krallinger M, Valencia A, Hirschman L.
Genome Biol. 2008;9 Suppl 2:S8
PubMed: 18834499

Text mining for biology--the way forward: opinions from leading scientists.
Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A.
Genome Biol. 2008;9 Suppl 2:S7
PubMed: 18834498

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.
Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.
Genome Biol. 2008;9 Suppl 2:S5
PubMed: 18834496

Overview of the protein-protein interaction annotation extraction task of BioCreative II.
Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A.
Genome Biol. 2008;9 Suppl 2:S4
PubMed: 18834495

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
PubMed: 18834492
(NER) (NEN) (REL) (CTM)

Mining physical protein-protein interactions from the literature.
Huang M, Ding S, Wang H, Zhu X.
Genome Biol. 2008;9 Suppl 2:S12
PubMed: 18834490

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
PubMed: 18834487

Improving Subcellular Localization Prediction using Text Classification and the Gene Ontology
Alona Fyshe, Yifeng Liu, Duane Szafron, Russ Greiner and Paul Lu
Bioinformatics, Advance Access published online on August 26, 2008
DOI: 10.1093/bioinformatics/btn463

MULTI-DIMENSIONAL CLASSIFICATION of BIOMEDICAL TEXT: Toward Automated, Practical Provision of High-Utility Text to Diverse Users
Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky and W. John Wilbur
Bioinformatics Advance Access first published online on August 20, 2008
DOI: 10.1093/bioinformatics/btn381

*** July 30 2008 ***
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords.
Huang ZX, Tian HY, Hu ZF, Zhou YB, Zhao J, Yao KT.
BMC Bioinformatics. 2008 Jul 13;9:308.
PubMed: 18620599

Seeking a new biology through text mining.
Rzhetsky A, Seringhaus M, Gerstein M.
Cell. 2008 Jul 11;134(1):9-13.
PubMed: 18614002

PuReD-MCL: a graph-based PubMed document clustering methodology.
Theodosiou T, Darzentas N, Angelis L, Ouzounis CA.
Bioinformatics. 2008 Sep 1;24(17):1935-41.
PubMed: 1859371

Discovering biomedical knowledge from the literature.
Saric J, Engelken H, Reyle U.
Methods Mol Biol. 2008;484:415-33.
PubMed: 1859219

*** June 18 2008 ***
Semantic Role Labeling for Protein Transport Predicates
Steven Bethard, Zhiyong Lu, James H Martin and Lawrence Hunter
BMC Bioinformatics 2008, 9:277
DOI: 10.1186/1471-2105-9-277
http://www.biomedcentral.com/1471-2105/9/277/

*** June 7 2008 ***
PageRank without hyperlinks: reranking with PubMed related article networks for biomedical text retrieval
Jimmy Lin
BMC Bioinformatics 2008, 9:270
DOI: 10.1186/1471-2105-9-270
http://www.biomedcentral.com/1471-2105/9/270/

*** May 29 2008 ***
PIE: an online prediction system for protein-protein interactions from text.
Kim S, Shin SY, Lee IH, Kim SJ, Sriram R, Zhang BT
Nucl Acid Res, 2008, epub ahead of print
http://nar.oxfordjournals.org/cgi/content/abstract/gkn281
DOI: 10.1093/nar/gkn281

*** May 25 2008 ***
Gene Regulation Ontology (GRO): Design Principles and Use Cases.
Beisswanger E, Lee V, Kim JJ, Rebholz-Schuhmann D, Splendiani A, Dameron O, Schulz S, Hahn U
Stud Health Technol Inform. 2008;136:9-14

*** May 16 2008 ***
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.
Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS
Nucleic Acids Res. 2008 May 16
http://nar.oxfordjournals.org/cgi/content/abstract/gkn296
DOI: 10.1093/nar/gkn296

E3Miner: a text mining tool for ubiquitin-protein ligases.
Lee H, Yi GS, Park JC
Nucleic Acids Res. 2008 May 15
http://nar.oxfordjournals.org/cgi/content/abstract/gkn286
DOI: 10.1093/nar/gkn286

*** May 12 2008 ***
Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining
Shi Yu, Steven Van Vooren, Leon-Charles Tranchevent, Bart De Moor and Yves Moreau
In Proc ECCB'08, September 22-26, Italy
Abstract: http://www.eccb08.org/?pageId=277#151
Bioinformatics. 2008 Aug 15;24(16):i119-25.
PubMed: 18689812

Inter-species normalization of gene mentions with GNAT
Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder and Graciela Gonzalez
In Proc ECCB'08, September 22-26, Italy
Abstract: http://www.eccb08.org/?pageId=277#174
Bioinformatics. 2008 Aug 15;24(16):i126-132.
PubMed: 1868981
(CTM) (NER) (NEN) (T)

*** May 5 2008 ***
Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology
Mikel Egana Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens
BMC Bioinformatics 2008, 9(Suppl 5):S1
http://www.biomedcentral.com/1471-2105/9/S5/S1

Gene Ontology annotations: what they mean and where they come from
David P Hill, Barry Smith, Monica S McAndrews-Hill, Judith A Blake
BMC Bioinformatics 2008, 9(Suppl 5):S2
http://www.biomedcentral.com/1471-2105/9/S5/S2

Mapping proteins to disease terminologies: from UniProt to MeSH
Anaïs Mottaz, Yum L Yip, Patrick Ruch, Anne-Lise Veuthey
BMC Bioinformatics 2008, 9(Suppl 5):S3
DOI: 10.1186/1471-2105-9-S5-S3
http://www.biomedcentral.com/1471-2105/9/S5/S3

Metrics for GO based protein semantic similarity: a systematic evaluation
Catia Pesquita, Daniel Faria, Hugo Bastos, Anto�nio EN Ferreira, André O Falcão, Francisco M Couto
BMC Bioinformatics 2008, 9(Suppl 5):S4
http://www.biomedcentral.com/1471-2105/9/S5/S4

Facilitating the development of controlled vocabularies for metabolomics technologies with text mining
Irena Spasic, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B Kell, Norman W Paton
BMC Bioinformatics 2008, 9(Suppl 5):S5
http://www.biomedcentral.com/1471-2105/9/S5/S5

*** April 25 2008 ***
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining.
Spasic I, Schober D, Sansone SA, Rebholz-Schuhmann D, Kell DB, Paton NW.
BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S5.
PubMed: 18460187

Terminologies for text-mining; an experiment in the lipoprotein metabolism domain.
Alexopoulou D, Wächter T, Pickersgill L, Eyre C, Schroeder M.
BMC Bioinformatics. 2008 Apr 25;9 Suppl 4:S2.
PubMed: 1846017

Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model.
Zhou D, He Y, Kwoh CK.
Int J Bioinform Res Appl. 2008;4(1):64-80.
PubMed: 18283029

Extracting interactions between proteins from the literature.
Zhou D, He Y.
J Biomed Inform. 2008 Apr;41(2):393-407
PubMed: 1820746

*** April 23 2008 ***
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.
PubMed: 18433469
DOI: 10.1186/1471-2105-9-207
Paper: http://www.biomedcentral.com/1471-2105/9/207
(OA) (REL) (ML)

*** April 11 2008 ***
Identification of transcription factor contexts in literature using machine learning approaches.
Yang H, Nenadic G, Keane JA.
BMC Bioinformatics. 2008 Apr 11;9 Suppl 3:S11.
PubMed: 18426546

Gene Tree Labeling Using Nonnegative Matrix Factorization on Biomedical Literature
Kevin E. Heinrich, Michael W. Berry, and Ramin Homayouni
Comput Intell Neurosci. 2008; 276535
DOI: 10.1155/2008/276535

A text-mining perspective on the requirements for electronically annotated abstracts.
Leitner F, Valencia A.
FEBS Lett. 2008 Apr 9;582(8):1178-81
PubMed: 18328824

Manually structured digital abstracts: a scaffold for automatic text mining.
Seringhaus M, Gerstein M.
FEBS Lett. 2008 Apr 9;582(8):1170
PubMed: 18328823

*** March 17 2008 ***
Discovering gene annotations in biomedical text databases
Ali Cakmak and Gultekin Ozsoyoglu
BMC Bioinformatics 2008, 9:143
DOI: 10.1186/1471-2105-9-143

*** March 12 2008 ***
e-LiSe - an online tool for finding needles in the "(Medline) haystack"
Arek Gladki, Pawel Siedlecki, Szymon Kaczanowski, and Piotr Zielenkiewicz
Bioinformatics. 2008 Apr 15;24(8):1115-7
DOI: 10.1093/bioinformatics/btn086
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn086
PubMed: 18321884

MiSearch Adaptive PubMed Search Tool
David J. States, Alex S. Ade, Zachary C. Wright, Aaron V. Bookvich, and Brian D. Athey
Bioinformatics Advance Access first published online on March 6, 2008
DOI: 10.1093/bioinformatics/btn033
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn033

*** Feb 20 2008 ***
PDTD: a web-accessible protein database for drug target identification
Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang and Hualiang Jiang
BMC Bioinformatics 2008, 9:104
DOI: 10.1186/1471-2105-9-104

MScanner: a classifier for retrieving Medline citations
Graham L Poulter, Daniel L Rubin, Russ B Altman and Cathal Seoighe
BMC Bioinformatics 2008, 9:108
DOI: 10.1186/1471-2105-9-108

*** Feb 14 2008 ***
Text-mining assisted regulatory annotation
Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L Griffith, Paco Hulpiau, Steven JM Jones, Stephen B Montgomery, Casey M Bergman and The Open Regulatory Annotation Consortium
Genome Biology 2008, 9:R31
DOI: 10.1186/gb-2008-9-2-r31

*** Feb 5 2008 ***
OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature
Laura I Furlong, Holger Dach, Martin Hofmann-Apitius, and Ferran Sanz
BMC Bioinformatics 2008, 9:84
DOI: 10.1186/1471-2105-9-84

*** Feb 5 2008 ***
OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression
Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner Jr., Helen L Johnson, Philip V Ogren, and K Bretonnel Cohen
BMC Bioinformatics 2008, 9:78
DOI: 10.1186/1471-2105-9-78

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.
PubMed: 18230184

Intrinsic evaluation of text mining tools may not predict performance on realistic tasks.
Caporaso JG, Deshpande N, Fink JL, Bourne PE, Cohen KB, Hunter L.
Pac Symp Biocomput. 2008:640-51.
PubMed: 18229722

Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example.
Kano Y, Nguyen N, Saetre R, Yoshida K, Miyao Y, Tsuruoka Y, Matsubayashi Y, Ananiadou S, Tsujii J.
Pac Symp Biocomput. 2008:616-27.
PubMed: 18229720

Information needs and the role of text mining in drug development.
Roberts PM, Hayes WS.
Pac Symp Biocomput. 2008:592-603.
PubMed: 18229718

Enabling integrative genomic analysis of high-impact human diseases through text mining.
Dudley J, Butte AJ.
Pac Symp Biocomput. 2008:580-91.
PubMed: 18229717

Getting started in text mining
Kevin Bretonnel Cohen and Lawrence Hunter
PLoS Comput Biol, 4(1):e20, 2008
DOI: 10.1371/journal.pcbi.0040020
PubMed: 18225946
(R)

*** Jan 30 2008 ***
Exploring hedge identification in biomedical literature
Ben Medlock
Journal of Biomedical Informatics, Volume 41, Issue 4, Pages 636-654
DOI: 10.1016/j.jbi.2008.01.001

The strength of co-authorship in gene name disambiguation
Farkas R
BMC Bioinformatics, 2008 9:69 (29 January 2008)
http://www.biomedcentral.com/1471-2105/9/69/abstract

*** Jan 18 2008 ***
Decentralised Clinical Guidelines Modelling with Lightweight Coordination Calculus
Bo Hu, Srinandan Dasmahapatra, Dave Robertson and Paul Lewis
Proc 2nd International Symposium on Languages in Biology and Medicine (LBM 2007), Singapore, December 6-7, 2007.
Table of contents - http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-319/Paper1.pdf

Recognition of Multi-sentence n-ary Subcellular Localization Mentions in Biomedical Abstracts
Gabor Melli, Martin Ester and Anoop Sarkar
Proc 2nd International Symposium on Languages in Biology and Medicine (LBM 2007), Singapore, December 6-7, 2007.
Table of contents - http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-319/Paper2.pdf

The Integration of Multiple Feature Representations for Protein Protein Interaction Classification Task
Man Lan and Chew Lim Tan
Proc 2nd International Symposium on Languages in Biology and Medicine (LBM 2007), Singapore, December 6-7, 2007.
Table of contents - http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-319/Paper3.pdf

Classifier ensemble for biomedical document retrieval
Manabu Torii and Hongfang Liu
Proc 2nd International Symposium on Languages in Biology and Medicine (LBM 2007), Singapore, December 6-7, 2007.
Table of contents - http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-319/Paper5.pdf

Syntactic features for protein-protein interaction extraction
Rune Saetre, Kenji Sagae and Jun'ichi Tsujii
Proc 2nd International Symposium on Languages in Biology and Medicine (LBM 2007), Singapore, December 6-7, 2007.
http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-319/ - http://sunsite.informatik.rwth-aachen.de/Pub
lications/CEUR-WS/Vol-319/Paper6.pdf

*** Dec 6 2007 ***
Deja vu - A Study of Duplicate Citations in Medline
Mounir Errami, Justin M. Hicks, Wayne Fisher, David Trusty, Jonathan D. Wren, Tara C. Long, and Harold R. Garner
Bioinformatics published 1 December 2007,
10.1093/bioinformatics/btm574
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm574v1?papetoc

*** Nov 26 2007 ***
Mining experimental evidence of molecular function claims from the literature
Colleen E. Crangle, J. Michael Cherry, Eurie L. Hong, and Alex Zbyslaw
Bioinformatics 2007 23: 3232-3240.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/23/3232?etoc

*** Nov 15 2007 ***
Kernel approaches for genic interaction extraction
Seonho Kim, Juntae Yoon, and Jihoon Yang
Bioinformatics published 14 November 2007
10.1093/bioinformatics/btm544
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm544v1?papetoc

*** Nov 12 2007 ***
Frontiers of biomedical text mining: current progress
Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, and Kevin B. Cohen
Brief Bioinform 2007 8:358-375.
http://bib.oxfordjournals.org/cgi/content/abstract/8/5/358?etoc

*** Nov 9 2007 ***
PubMed related articles: a probabilistic topic-based model for content similarity.
Lin J, Wilbur WJ.
BMC Bioinformatics. 2007 Oct 30;8(1):423
http://www.biomedcentral.com/1471-2105/8/423

Mining biological networks for unknown pathways
Ali Cakmak and Gultekin Ozsoyoglu
Bioinformatics 2007 23: 2775-2783.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/20/2775?etoc

*** Oct 15 2007 ***
Leveraging Biological Identifier Relationships and Related Documents to Enhance Information Retrieval for Proteomics
Andrew Smith, Kei Cheung, Michael Krauthammer, Martin Schultz, and Mark Gerstein
Bioinformatics published 7 October 2007, 10.1093/bioinformatics/btm452
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm452v1?papetoc

*** Oct 10 2007 ***
Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies
Hoehndorf R, Loebe F, Kelso J, Herre H
BMC Bioinformatics, 2007 8:377 (9 October 2007)
http://www.biomedcentral.com/1471-2105/8/377/abstract

*** Sep 17 2007 ***
Medline search engine for finding genetic markers with biological significance
Weijian Xuan, Pinglang Wang, Stanley J. Watson and Fan Meng
Bioinformatics 2007 23(18):2477-2484
DOI: 10.1093/bioinformatics/btm375
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/18/2477

Literature-based concept profiles for gene annotation: The issue of weighting
International Journal of Medical Informatics, In Press, Corrected Proof, Available online 10 September 2007
Rob Jelier, Martijn J. Schuemie, Peter-Jan Roes, Erik M. van Mulligen and Jan A. Kors
DOI: 10.1016/j.ijmedinf.2007.07.004

Functional profiling of microarray experiments using text-mining derived
bioentities
Pablo Minguez, Fatima Al-Shahrour, David Montaner, and Joaquin Dopazo
Bioinformatics published 13 September 2007,
DOI: 10.1093/bioinformatics/btm445 Open Access
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm445v1?papetoc

*** Sep 14 2007 ***
BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features
Richard Tzong-Han Tsai and Wen-Chi Chou and Ying-Shan Su and Yu-Chun Lin and Cheng-Lung Sung and Hong-Jie Dai and Irene Tzu-Hsuan Yeh and Wei Ku and Ting-Yi Sung and Wen-Lian Hsu
BMC Bioinformatics, 8:325, 2007, doi:10.1186/1471-2105-8-325
http://www.biomedcentral.com/1471-2105/8/325

*** Sep 06 2007 ***
Judging the Frequency of English Words
J. Charles Alderson
Applied Linguistics 2007 28:383-409.
http://applij.oxfordjournals.org/cgi/content/abstract/28/3/383?etoc

BioText Search Engine: beyond abstract search
Marti A. Hearst, Anna Divoli, Harendra Guturu, Alex Ksikes, Preslav Nakov, Michael A. Wooldridge, and Jerry Ye
Bioinformatics 2007 23: 2196-2197.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/16/2196?etoc

OBO-Edit an ontology editor for biologists
John Day-Richter, Midori A. Harris, Melissa Haendel, The Gene Ontology
OBO-Edit Working Group, and Suzanna Lewis
Bioinformatics 2007 23: 2198-2200.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/16/2198?etoc

*** Aug 31 2007 ***
Global mapping of gene/protein interactions in PubMed abstracts: A framework and an experiment with P53 interactions
Xin Li, Hsinchun Chen, Zan Huang, Hua Su and Jesse D. Martinez
Journal of Biomedical Informatics, Volume 40, Issue 5, 453-464, 2007
Full text

*** Aug 15 2007 ***
Clustering microarray-derived gene lists through implicit literature relationships
F. Burkart, Jonathan D. Wren, Jason I. Herschkowitz, Charles M. Perou, and Harold R. Garner
Bioinformatics 2007 23: 1995-2003.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/15/1995?etoc

*** Aug 13 2007 ***
Learning string similarity measures for gene/protein name dictionary look-up using logistic regression
Yoshimasa Tsuruoka, John McNaught, Jun'ichi Tsujii, and Sophia Ananiadou
Bioinformatics, 23(20):2768-2774
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/20/2768?etoc

*** Aug 8 2007 ***
OBO to OWL: a protege OWL tab to read/save OBO ontologies
Dilvan A. Moreira and Mark A. Musen
Bioinformatics 2007 23: 1868-1870.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/14/1868?etoc

MutationFinder: a high-performance system for extracting point mutation mentions from text
J. Gregory Caporaso, William A. Baumgartner, Jr, David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter
Bioinformatics 2007 23: 1862-1865.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/14/1862?etoc

*** Aug 7 2007 ***
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
Rodriguez-Penagos C, Salgado H, Martinez-Flores I, Collado-Vides J
BMC Bioinformatics, 2007 8:293 (7 August 2007)
http://www.biomedcentral.com/1471-2105/8/293/abstract

*** Aug 1 2007 ***
PepBank - a database of peptides based on sequence text mining and public peptide data sources
Shtatland T, Guettler D, Kossodo M, Pivovarov M, Weissleder R
BMC Bioinformatics, 2007 8:280 (1 August 2007)
http://www.biomedcentral.com/1471-2105/8/280/abstract

*** Jul 24 2007 ***
Using contextual and lexical features to restructure and validate the classification of biomedical concepts
Fan J, Xu H, Friedman C
BMC Bioinformatics, 2007 8:264 (24 July 2007)
http://www.biomedcentral.com/1471-2105/8/264/abstract

False positive reduction in protein-protein interaction predictions using gene ontology annotations
Mahdavi M, Lin Y
BMC Bioinformatics, 2007 8:262 (23 July 2007)
http://www.biomedcentral.com/1471-2105/8/262/abstract

*** Jul 23 2007 ***
Learning to extract relations for protein annotation
Jee-Hyub Kim, Alex Mitchell, Teresa K. Attwood, and Melanie Hilario
Bioinformatics 2007 23: i256-i263.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i256?etoc

Identification of new drug classification terms in textual resources
Corinna Kolarik, Martin Hofmann-Apitius, Marc Zimmermann, and Juliane Fluck
Bioinformatics 2007 23: i264-i272.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i264?etoc

Negation of protein protein interactions: analysis and extraction
Olivia Sanchez-Graillet and Massimo Poesio
Bioinformatics 2007 23: i424-i432.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i424?etoc

*** July 10 2007 ***
Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks
Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I
BMC Bioinformatics, 2007 8:243 (10 July 2007)
http://www.biomedcentral.com/1471-2105/8/243/abstract

*** June 30 2007 ***
Natural language processing and visualization in the molecular imaging domain
P. Karina Tulipano, Ying Tao, William S. Millar, Pat Zanzonico, Katherine Kolbert, Hua Xu, Hong Yu, Lifeng Chen, Yves A. Lussier and Carol Friedman
Journal of Biomedical Informatics, Volume 40, Issue 3, June 2007, Pages 270-281
DOI: 10.1016/j.jbi.2006.08.002

Measures of semantic similarity and relatedness in the biomedical domain
Ted Pedersen, Serguei V.S. Pakhomov, Siddharth Patwardhan and Christopher G. Chute
Journal of Biomedical Informatics, Volume 40, Issue 3, June 2007, Pages 288-299
DOI: 10.1016/j.jbi.2006.06.004

Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification
Martijn J. Schuemie, Barend Mons, Marc Weeber and Jan A. Kors
Journal of Biomedical Informatics, Volume 40, Issue 3, June 2007, Pages 316-324
DOI: 10.1016/j.jbi.2006.09.002

Relemed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles.
Mir S Siadaty, Jianfen Shu, and William A Knaus
BMC Medical Informatics and Decision Making 2007, 7:1
DOI: 10.1186/1472-6947-7-1
http://www.biomedcentral.com/1472-6947/7/1
PubMed: 17214888

Deafness mutation mining using regular expression based pattern matching
Christopher M Frenz
BMC Medical Informatics and Decision Making 2007, 7:32
DOI: 10.1186/1472-6947-7-32
http://www.biomedcentral.com/1472-6947/7/32

Creating a medical dictionary using word alignment: The influence of sources and resources
Mikael Nyström, Magnus Merkel, Håkan Petersson, and Hans Åhlfeldt
BMC Medical Informatics and Decision Making 2007, 7:37
DOI: 10.1186/1472-6947-7-37
http://www.biomedcentral.com/1472-6947/7/37

*** June 21 2007 ***
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
Hagit Shatkay, Annette Hoglund, Scott Brady, Torsten Blum, Pierre Donnes, and Oliver Kohlbacher
Bioinformatics 2007 23: 1410-1417.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1410?etoc

uBioRSS: Tracking taxonomic literature using RSS
Patrick R. Leary, David P. Remsen, Catherine N. Norton, David J. Patterson, and Indra Neil Sarkar
Bioinformatics 2007 23: 1434-1436.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1434?etoc

*** May 16 2007 ***

Validating discovery in literature-based discovery
Ronald N. Kostoff
Journal of Biomedical Informatics
Volume 40, Issue 4, August 2007, pp. 448-450
DOI: 10.1016/j.jbi.2007.05.001
Comment on [YetisgenYildiz 2006], response see [Pratt 2007]

Response to "Validating discovery in literature-based discovery"
Wanda Pratt, Meliha Yetisgen-Yildiz
Journal of Biomedical Informatics
Volume 40, Issue 4, August 2007, Pages 450-452
DOI: 10.1016/j.jbi.2007.07.002
Response to [Kostoff 2007], also see original article [YetisgenYildiz 2006]

*** April 26 2007 ***
A quantitative model for linking two disparate sets of articles in MEDLINE
Vetle I. Torvik and Neil R. Smalheiser
Bioinformatics 2007 23: 1658-1665.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/1658?etoc

*** March 7 2007 ***
A new method to measure the semantic similarity of GO terms
James Z. Wang, Zhidian Du, Rapeeporn Payattakool, Philip S. Yu, and Chin-Fu Chen
Bioinformatics 2007 23: 1274-1281.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/10/1274?etoc

*** Feb 20 2007 ***
Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL
Mikel Egana Aranguren, Sean Bechoffer, Phillip Lord, Ulrike Sattler and Robert Stevens
BMC Bioinformatics 2007, 8:57
DOI: 10.1186/1471-2105-8-57
http://www.biomedcentral.com/1471-2105/8/57/abstract

*** Oct 1 2006 ***
AliBaba: PubMed as a graph
Conrad Plake, Torsten Schiemann, Markus Pankalla, Jörg Hakenberg, Ulf Leser
Bioinformatics. 2006 Oct 1;22(19):2444-5.
DOI: 10.1093/bioinformatics/btl408
Paper: http://bioinformatics.oxfordjournals.org/cgi/content/full/22/19/2444
PubMed: 16870931
(T) (OA) (NA) (NS) (REL) (IR)

*** Jul 5 2006 ***
Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues
Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu and Carol Friedman
BMC Bioinformatics 2006, 7:334
DOI: 10.1186/1471-2105-7-334
http://www.biomedcentral.com/1471-2105/7/334

*** May 29 2006 ***
A New Algorithm for Pattern Optimization in Protein-Protein Interaction Extraction System
Yu Hao, Xiaoyan Zhu, and Ming Li
In: Pattern Recognition and Image Analysis: Second Iberian Conference, IbPRIA 2005, Estoril, Portugal, June 7-9, 2005, Proceedings, Part II; Springer LNCS - Volume 3523/2005, ISBN: 3-540-26154-0, doi: 10.1007/b136831; pp. 397ff
DOI: 10.1007/11492542_49
http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/11492542_49

Machine Learning for Information Extraction in Genomics - State of the art and perspectives
Claire Nedellec
In: Text Mining and its Applications: Results of the NEMIS Launch Conference Series: Studies in Fuzziness and Soft Computing, Sirmakessis, Spiros (Ed.), Springer Verlag, 2004.
Dagstuhl Seminar: Machine Learning for the Semantic Web (Dagstuhl-MLSW), 13-18 February 2005
PDF - http://www.smi.ucd.ie/Dagstuhl-MLSW/

*** May 22 2006 ***
The success (or not) of HUGO nomenclature
Javier Tamames and Alfonso Valencia
Genome Biol. 2006 May 15;7(5):402
DOI: 10.1186/gb-2006-7-5-402
PubMed: 16707004
Abstract - http://genomebiology.com/2006/7/5/402

*** May 09 2006 ***
Biomedical Ontologies: Special Issue
Journal of Biomedical Informatics, Vol. 39, Issue 3, June 2006
Table of Contents

Biomedical ontologies: What part-of is and isn't
Stefan Schulz, Anand Kumarb and Thomas Bittner
Journal of Biomedical Informatics, 39(3):350-361
DOI: 10.1016/j.jbi.2005.11.003
Abstract
(ONT)

*** April 25 2006 ***
Quality control for terms and definitions in ontologies and taxonomies
Jacob Köhler, Katherine Munn, Alexander Ruegg, Andre Skusa and Barry Smith
BMC Bioinformatics 2006, 7:212
DOI: 10.1186/1471-2105-7-212
http://www.biomedcentral.com/1471-2105/7/212/abstract

*** April 3 2006 ***
Automatic pathway building in biological association networks
Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia and Ilya Mazo
BMC Bioinformatics 2006, 7:171
DOI: 10.1186/1471-2105-7-171
http://www.biomedcentral.com/1471-2105/7/171/abstract/

Exploring supervised and unsupervised methods to detect topics in biomedical text
Minsuk Lee, Weiqing Wang and Hong Yu
BMC Bioinformatics 2006, 7:140
DOI: 10.1186/1471-2105-7-140
http://www.biomedcentral.com/1471-2105/7/140/abstract

*** March 20 2006 ***
LSAT: learning about alternative transcripts in MEDLINE
Parantu K. Shah and Peer Bork
Bioinformatics 2006 22(7):857-865
DOI: 10.1093/bioinformatics/btk044
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/7/857?etoc

Biomedical Language Processing: What's Beyond PubMed?
Lawrence Hunter and K. Bretonnel Cohen
Molecular Cell 21, 589-594, March 3, 2006

*** March 10 2006 ***
Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005)
Udo Hahn and Alfonso Valencia
Bioinformatics 2006 22: 643-644.
http://bioinformatics.oxfordjournals.org/cgi/content/full/22/6/643?etoc

Extraction of regulatory gene/protein networks from Medline
Jasmin Saric, Lars Juhl Jensen, Rossitza Ouzounova, Isabel Rojas, and Peer Bork
Bioinformatics 2006 22: 645-650.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/6/645?etoc

Automatic term list generation for entity tagging
Ted Sandler, Andrew I. Schein, and Lyle H. Ungar
Bioinformatics 2006 22: 651-657.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/6/651?etoc

Automatic assignment of biomedical categories: toward a generic approach
Patrick Ruch
Bioinformatics 2006 22: 658-664.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/6/658?etoc

Automatic extension of Gene Ontology with flexible identification of candidate terms
Jin-Bok Lee, Jung-jae Kim, and Jong C. Park
Bioinformatics 2006 22: 665-670.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/6/665?etoc

Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data
Zuyi Wang, Yue Wang, Jianhua Xuan, Yibin Dong, Marina Bakay, Yuanjian Feng, Robert Clarke, and Eric P. Hoffman
Bioinformatics 2006 22: 755-761.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/6/755?etoc

SUSPECTS: enabling fast and effective prioritization of positional candidates
E. A. Adie, R. R. Adams, K. L. Evans, D. J. Porteous, and B. S. Pickard
Bioinformatics 2006 22: 773-774.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/6/773?etoc

*** March 2 2006 ***
Text Mining for Biology and Biomedicine
Sophia Ananiadou and John McNaught, Editors
ISBN 1-58053-984-X, 302 pages
http://www.artechhouse.com/Default.asp?Frame=Book.asp&Book=1-58053-984-X

*** February 28 2006 ***
A text-mining analysis of the human phenome
Marc A van Driel, Jorn Bruggeman, Gert Vriend, Han G Brunner and Jack A M Leunissen
European Journal of Human Genetics, advance online publication, 22 February 2006
DOI: 10.1038/sj.ejhg.5201585
http://www.nature.com/ejhg/journal/vaop/ncurrent/abs/5201585a.html

*** February 22 2006 ***
BioContrasts: Extracting and exploiting protein-protein contrastive relations from biomedical literature
Jung-jae Kim, Zhuo Zhang, Jong C. Park, and See-Kiong Ng
Bioinformatics 2006 22(5):597-605
DOI: 10.1093/bioinformatics/btk016
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/5/597?etoc

*** Jan 31 2006 ***
Word sense disambiguation by selecting the best semantic type based on Journal Descriptor Indexing: Preliminary experiment.
S.M. Humphreys et al.
J Am Soc Inf Sci Tech, 57:96--113, 2006
http://portal.acm.org/citation.cfm?id=1107442.1107452

*** January 25 2006 ***
A hybrid method for relation extraction from biomedical literature
Huang M, Zhu X, Li M
Int J Med Inform. 2005 Aug 8
DOI: 10.1016/j.ijmedinf.2005.06.010 PubMed:16095962
Full text

*** January 19 2006 ***
Knowledge-based computational search for genes associated with the metabolic syndrome
Tsutomu Matsunaga and Masa-aki Muramatsu
Bioinformatics 2005 21(14):3146-3154
DOI: 10.1093/bioinformatics/bti484 PubMed:15886278
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/14/3146

*** Jan 4 2006 ***

Using statistical and knowledge-based approaches for literature-based discovery
Meliha Yetisgen-Yildiz and Wanda Pratt
Journal of Biomedical Informatics
Volume 39, Issue 6, December 2006, Pages 600-611
DOI: 10.1016/j.jbi.2005.11.010
See comment in [Kostoff 2007] and reponse in [Pratt 2007]

*** January 3 2006 ***
BioThesaurus: a web-based thesaurus of protein and gene names
Hongfang Liu, Zhang-Zhi Hu, Jian Zhang, and Cathy Wu
Bioinformatics 2006 22(1):103-105
DOI: 10.1093/bioinformatics/bti749
http://bioinformatics.oxfordjournals.org/cgi/content/short/bti749

Distributed modules for text annotation and IE applied to the biomedical domain
Harald Kirsch, Sylvain Gaudan, and Dietrich Rebholz-Schuhmann
International Journal of Medical Informatics 2005 Aug 4; advance access online
Article

*** December 13 2005 ***
Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists
Vladimir B. Bajic, Merlin Veronika, Pardha Sarathi Veladandi, Archana Meka, Mok-Wei Heng, Kanagasabai Rajaraman, Hong Pan and Sanjay Swarup
Plant Physiology 2005 Aug; 138(4):1914-25
http://www.plantphysiol.org/cgi/content/abstract/138/4/1914

Recent advances in natural language processing for biomedical applications
Nigel Collier, Adeline Nazarenko, Robert Baud and Patrick Ruch
International Journal of Medical Informatics 2005
DOI: 10.1016/j.ijmedinf.2005.06.008
Abstract

A System for Identifying Named Entities in Biomedical Text: how Results From two Evaluations Reflect on Both the System and the Evaluations.
Dingare S, Nissim M, Finkel J, Manning C, Grover C.
Comp Funct Genomics. 2005;6(1-2):77-85.
PubMed: 18629295

Critical assessment of information extraction systems in biology.
Blaschke C, Hirschman L, Yeh A, Valencia A.
Comp Funct Genomics. 2003;4(6):674-7.
PubMed: 18629031

*** December 6 2005 ***
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome
Arun K. Ramani, Razvan C. Bunescu, Raymond J. Mooney, and Edward M. Marcotte
Genome Biology 2005, 6:R40
DOI: 10.1186/gb-2005-6-5-r40
http://genomebiology.com/2005/6/5/R40

*** November 29 2005 ***
What Makes a Gene Name? Named Entity Recognition in the Biomedical Literature
Ulf Leser, Jörg Hakenberg
Briefings in Bioinformatics, 6(4):357-369, December 2005
PubMed:16420734
http://www.ingentaconnect.com/content/hsp/bib/2005/00000006/00000004/art00005

Evaluation of Biomedical Text Mining Systems: Lessons Learned from Information Retrieval
William Hersh
Briefings in Bioinformatics, 6(4):344-356, December 2005
PubMed:16420733
http://www.ingentaconnect.com/content/hsp/bib/2005/00000006/00000004/art00004

*** November 17 2005 ***
Advances in text analytics for drug discovery
Roberts, P.M., Hayes, W.S
Current Opinion in Drug Discovery and Development 2005, 8(3):323-328

Systems literature analysis
Persidis, A., Deftereos, S., Persidis, A.
Pharmacogenomics 2004, 5(7):943-947
DOI: 10.1517/14622416.5.7.943
http://www.futuremedicine.com/doi/abs/10.1517/14622416.5.7.943

Do you do text?
C. Blaschke, A. Yeh, E. Camon, M. Colosimo, R. Apweiler, L. Hirschman, and A. Valencia
Bioinformatics 2005, advance access September 29
DOI: 10.1093/bioinformatics/bti695
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bti695

*** November 4 2005 ***
METIS: multiple extraction techniques for informative sentences
A. L. Mitchell, A. Divoli, J.-H. Kim, M. Hilario, I. Selimas, and T. K. Attwood
Bioinformatics 2005 21(22):4196-4197
DOI: 10.1093/bioinformatics/bti675
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/22/4196?etoc

*** October 24 2005 ****
Markov model recognition and classification of DNA/protein sequences within large text databases
Jonathan D. Wren, William H. Hildebrand, Sreedevi Chandrasekaran, and Ulrich Melcher
Bioinformatics 2005 21: 4046-4053.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/21/4046?etoc

*** October 18 2005 ***
Automatic extraction of candidate nomenclature terms using the doublet method
Jules J Berman
BMC Medical Informatics and Decision Making 2005, 5:35
DOI: 10.1186/1472-6947-5-35
Paper: http://www.biomedcentral.com/1472-6947/5/35

Automation of a problem list using natural language processing
Stephane Meystre and Peter J. Haug
BMC Medical Informatics and Decision Making 2005, 5:30
DOI: 10.1186/1472-6947-5-30
Paper: http://www.biomedcentral.com/1472-6947/5/30

*** October 6 2005 ***
Hairpins in bookstacks: Information retrieval from biomedical text
Hagit Shatkay
Briefings in Bioinformatics, 6(3), 222-238, Sep 2005
Abstract

Text mining and ontologies in biomedicine: Making sense of raw text
Irena Spasic, Sophia Ananiadou, John McNaught, Anand Kumar
Briefings in Bioinformatics, 6(3), 239-251, Sep 2005
Abstract

Information retrieval and knowledge discovery utilising a biomedical Semantic Web
Sougata Mukherjea
Briefings in Bioinformatics, 6(3), 252-262, Sep 2005
Abstract

Extraction of biological interaction networks from scientific literature
Andre Skusa, Alexander Rüegg, Jacob Köhler
Briefings in Bioinformatics, 6(3), 263-276, Sep 2005
Abstract

Online tools to support literature-based discovery in the life sciences
Marc Weeber, Jan A. Kors, Barend Mons
Briefings in Bioinformatics, 6(3), 277-286, Sep 2005
Abstract

The next generation of literature analysis: Integration of genomic analysis into text mining
Matthias Scherf, Anton Epple, Thomas Werner
Briefings in Bioinformatics, 6(3), 287-297, Sep 2005
Abstract

Get ready to GO! A biologist's guide to the Gene Ontology
[No authors listed]
Briefings in Bioinformatics, 6(3), 298-304, Sep 2005
Abstract

*** October 5 2005 ***
Proceedings of ECCB/JBI 2005 (4 papers):
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, and Hiroshi Mamitsuka
Bioinformatics 2005 21: ii245-ii251
Abstract

Implementing the iHOP concept for navigation of biomedical literature
Robert Hoffmann and Alfonso Valencia
Bioinformatics 2005 21: ii252-ii258
Abstract

Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts
Robert Kuffner, Katrin Fundel, and Ralf Zimmer
Bioinformatics 2005 21: ii259-ii267
Abstract

Web servicing the biological office
Martin Szugat, Daniel Guttler, Katrin Fundel, Florian Sohler, and Ralf Zimmer
Bioinformatics 2005 21: ii268-ii269
Abstract

*** September 21 2005 ***
Extracting Genetic Pathways From Text and Grounding at the Spatio-Temporal Level
Gail Sinclair, Bonnie Webber, Duncan Davidson
Proceedings of BioSysBio: Bioinformatics and Systems Biology Conference
BMC Bioinformatics 2005, 6(Suppl 3):P26
DOI: 10.1186/1471-2105-6-S3-P26
http://www.biomedcentral.com/1471-2105/6/S3/P26/abstract

*** August 22 2005 ***
Applying GIFT, a Gene Interactions Finder in Text, to fly literature
Nu'ria Domedel-Puig and Lorenz Wernisch
Bioinformatics 2005 21(17):3582-3583
DOI: 10.1093/bioinformatics/bti578
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/17/3582?etoc

Proceedings of the
First International Symposium on Semantic Mining in Biomedicine (SMBM)
are now online at CEUR-WS:
http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS//Vol-148/

*** August 8 2005 ***
Resolving abbreviations to their senses in Medline.
S. Gaudan, H. Kirsch, D. Rebholz-Schuhmann
Bioinformatics 2005 21(18):3658-3664.
DOI: 10.1093/bioinformatics/bti586
http://bioinformatics.oxfordjournals.org/cgi/content/short/21/18/3658

A controlled trial of automated classification of negation from clinical note
Peter L. Elkin, Steven H. Brown, Brent A. Bauer, Casey S. Husser, William Carruth, Larry R. Bergstrom, and Dietlind L. Wahner-Roedler
BMC Medical Informatics and Decision Making 2005, 5:13
DOI: 10.1186/1472-6947-5-13
http://www.biomedcentral.com/1472-6947/5/13

*** July 22 2005 ***
PubNet: a flexible system for visualizing literature derived networks
Shawn M. Douglas, Gaetano T. Montelione, Mark Gerstein
Genome Biology 2005, 6:R80
DOI: 10.1186/gb-2005-6-9-r80
http://genomebiology.com/2005/6/9/R80/abstractb

*** July 15 2005 ***
Discovering patterns to extract protein-protein interactions from the literature: Part II
Yu Hao, Xiaoyan Zhu, Minlie Huang, and Ming Li
Bioinformatics 2005 21: 3294-3300
DOI: 10.1093/bioinformatics/bti493
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/15/3294?etoc

*** July 1 2005 ***
Evaluating and integrating treebank parsers on a biomedical corpus
Andrew B. Clegg and Adrian J. Shepherd
Proceedings of the Association for Computational Linguistics Workshop on Software 2005
http://textmining.cryst.bbk.ac.uk/acl05/

MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms
Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, and John Quackenbush
Bioinformatics 2005 21: 3324-3326
DOI: 10.1093/bioinformatics/bti503
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/15/3324?etoc

*** June 30 2005 ***
ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text
Burr Settles
Bioinformatics 2005 21: 3191-3192
DOI: 10.1093/bioinformatics/bti475
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/14/3191?etoc

Text-mining and information-retrieval services for molecular biology
Martin Krallinger, Alfonso Valencia
Genome Biology 2005, 6:224
DOI: 10.1186/gb-2005-6-7-224
http://genomebiology.com/2005/6/7/224/abstract

Knowledge discovery and system biology in molecular medicine: an application on neurodegenerative diseases
Matteo Fattore and Patrizio Arrigo
In Silico Biology 2005; 5(2):199-208
http://www.bioinfo.de/isb/2004050019/

*** June 24 2005 ***
Extraction of Transcript Diversity from Scientific Literature
Parantu K. Shah, Lars J. Jensen, Stephanie Boue, Peer Bork
PLoS Comp Biol 1(1): e10
DOI: 10.1371/journal.pcbi.0010010
Paper

Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation
Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni Jarvinen and Tapio Salakoski
BMC Bioinformatics 2005, 6:157
DOI: 10.1186/1471-2105-6-157
http://www.biomedcentral.com/1471-2105/6/157

Thesaurus-based disambiguation of gene symbols
Bob J A Schijvenaars, Barend Mons, Marc Weeber, Martijn J Schuemie, Erik M van Mulligen, Hester M Wain and Jan A Kors
BMC Bioinformatics 2005, 6:149
DOI: 10.1186/1471-2105-6-149
http://www.biomedcentral.com/1471-2105/6/149/abstract

*** June 13 2005 ***
Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information
James W. Cooper and Aaron Kershenbaum
BMC Bioinformatics 2005, 6:143
DOI: 10.1186/1471-2105-6-143
http://www.biomedcentral.com/1471-2105/6/143/abstract

Which gene did you mean?
Barend Mons
BMC Bioinformatics 2005, 6:142
DOI: 10.1186/1471-2105-6-142
http://www.biomedcentral.com/1471-2105/6/142/abstract

Overview of BioCreAtIvE: critical assessment of information extraction for biology
Lynette Hirschman, Alexander Yeh, Christian Blaschke, and Alfonso Valencia
from "A critical assessment of text mining methods in molecular biology" Granada, Spain, March 28-31, 2004
BMC Bioinformatics 2005, 6(Suppl 1):S1
DOI: 10.1186/1471-2105-6-S1-S1
http://www.biomedcentral.com/1471-2105/6/S1/S1
Links to 18 papers and summaries on NER (gene/protein names), EMN (gene names), and automated GO annotation

*** May 26 2005 ***
Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks
Robert Hoffmann, Martin Krallinger, Eduardo Andres, Javier Tamames, Christian Blaschke, and Alfonso Valencia
Sci. STKE, Vol. 2005, Issue 283, pp. pe21
DOI: 10.1126/stke.2832005pe21
http://stke.sciencemag.org/cgi/content/abstract/2005/283/pe21

*** May 23 2005 ***
MaSTerClass: a case-based reasoning system for the classification of biomedical terms
Irena Spasic, Sophia Ananiadou, and Junichi Tsujii
Bioinformatics 2005 21:2748-2758.
DOI: 10.1093/bioinformatics/bti338
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/11/2748?etoc

Literature mining and database annotation of protein phosphorylation using a rule-based system
Z. Z. Hu, M. Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, and C. H. Wu
Bioinformatics 2005 21:2759-2765.
DOI: 10.1093/bioinformatics/bti390
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/11/2759?etoc

POSBIOTM--NER: a trainable biomedical named-entity recognition system
Yu Song, Eunju Kim, Gary Geunbae Lee, and Byoung-kee Yi
Bioinformatics 2005 21:2794-2796.
DOI: 10.1093/bioinformatics/bti414
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/11/2794?etoc

A survey of current work in biomedical text mining
Aaron M. Cohen and William R. Hersh
Briefings in Bioinformatics, March 2005, vol. 6, no. 1, pp. 57-71(15)
http://www.ingentaconnect.com/content/hsp/bib/2005/00000006/00000001/art00006

*** May 16 2005 ***
Using the biological taxonomy to access biological literature with PathBinderH
J. Ding, K. Viswanathan, D. Berleant, L. Hughes, E. S. Wurtele, D. Ashlock, J. A. Dickerson, A. Fulmer, and P. S. Schnable
Bioinformatics 2005 21: 2560-2562.
DOI: 10.1093/bioinformatics/bti381
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/10/2560?etoc

*** May 10 2005 ***
Integration of the Gene Ontology into an object-oriented architecture
Daniel Shegogue, W. JIM Zheng
BMC Bioinformatics 2005, 6:113
DOI: 10.1186/1471-2105-6-113
http://www.biomedcentral.com/1471-2105/6/113/abstract

*** 2 May 2005 ***
Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes
R. Jelier, G. Jenster, L. C. J. Dorssers, C. C. van der Eijk, E. M. van Mulligen, B. Mons, and J. A. Kors
Bioinformatics 2005, 21(9):2049-2058.
DOI: 10.1093/bioinformatics/bti268
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/9/2049?etoc

Concept-based annotation of enzyme classes
Oliver Hofmann and Dietmar Schomburg
Bioinformatics 2005, 21(9):2059-2066.
DOI: 10.1093/bioinformatics/bti284
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/9/2059?etoc

BioIE: extracting informative sentences from the biomedical literature
Anna Divoli and Teresa K. Attwood
Bioinformatics 2005, 21(9):2138-2139.
DOI: 10.1093/bioinformatics/bti296
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/9/2138?etoc

*** 28 April 2005 ***
Knowledge discovery in biology and biotechnology texts: a review of techniques, evaluation strategies, and applications
Natarajan J, Berrar D, Hack CJ, and Dubitzky W
Critical Reviews in Biotechnology 2005 Jan-Jun; 25(1-2):31-52
PubMed

Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts
Aaron M Cohen, William R Hersh, Christopher Dubay and Kent Spackman
BMC Bioinformatics 2005, 6:103
DOI: 10.1186/1471-2105-6-103
http://www.biomedcentral.com/1471-2105/6/103/abstract

Domain-specific language models and lexicons for tagging
Anni R. Coden, Serguei V. Pakhomov, Rie K. Ando, Patrick H. Duffy and Christopher G. Chute
Journal of Biomedical Informatics 2005, 38(6):422-430
DOI: 10.1016/j.jbi.2005.02.009
Summary

Extracting information on pneumonia in infants using natural language processing of radiology reports
Eneida A. Mendonça, Janet Haas, Lyudmila Shagina, Elaine Larson and Carol Friedman
Journal of Biomedical Informatics, in Press, Corrected Proof, Available online 30 March 2005
DOI: 10.1016/j.jbi.2005.02.003
Summary

Assessment of approximate string matching in a biomedical text retrieval problem
J.F. Wang, Z.R. Li, C.Z. Cai, and Y.Z. Chen
Computers in Biology and Medicine, 2005, Article in Press, Corrected Proof, Available online 6 August 2004
DOI: 10.1016/j.compbiomed.2004.06.002
Summary

A graphic tool for curating molecular interaction networks from the literature
Changsu Lee, Jinah Park, and Jong C. Park
Computers in Biology and Medicine, Volume 35, Issue 7, October 2005, Pages 555-564
DOI: 10.1016/j.compbiomed.2004.04.005
Summary

ISO reference terminology models for nursing: Applicability for natural language processing of nursing narratives
Suzanne Bakken, Sookyung Hyun, Carol Friedman and Stephen B. Johnson
International Journal of Medical Informatics, Article in Press, Corrected Proof , Available online 7 April 2005
DOI: 10.1016/j.ijmedinf.2005.01.002
Summary

Extending the GEM model to support knowledge extraction from textual guidelines
Gersende Georg, Brigitte S�roussi, and Jacques Bouaud
International Journal of Medical Informatics, Volume 74, Issues 2-4, March 2005, Pages 79-87
DOI: 10.1016/j.ijmedinf.2004.07.006
Summary

UMLF: a unified medical lexicon for French
Pierre Zweigenbaum, Robert Baud, Anita Burgun, Fiammetta Namer, Èric Jarrousse, Natalia Grabar, Patrick Ruch, Franck Le Duff, Jean-Franiçois Forget, Magaly Douyáre, and Stèfan Darmoni
International Journal of Medical Informatics, Volume 74, Issues 2-4, March 2005, Pages 119-124
DOI: 10.1016/j.ijmedinf.2004.03.010
Summary

Using literature-based discovery to identify disease candidate genes
Dimitar Hristovski, Borut Peterlin, Joyce A. Mitchell, and Susanne M. Humphrey
International Journal of Medical Informatics, Volume 74, Issues 2-4, March 2005, Pages 289-298
DOI: 10.1016/j.ijmedinf.2004.04.024
Summary

Assisting medical annotation in Swiss-Prot using statistical classifiers
Pavel B. Dobrokhotov, Cyril Goutte, Anne-Lise Veuthey, and Eric Gaussier
International Journal of Medical Informatics, Volume 74, Issues 2-4, March 2005, Pages 317-324
DOI: 10.1016/j.ijmedinf.2004.04.017
Summary

*** 15 April 2005 ***
Summarization from Medical Documents: A Survey
Stergos D. Afantenos, Vangelis Karkaletsis, Panagiotis Stamatopoulos
Artificial Intelligence in Medicine, Volume 33, Issue 2, February 2005, Pages 157-177.
DOI: 10.1016/j.artmed.2004.07.017
http://arXiv.org/abs/cs/0504061

*** 13 April 2005 ***
Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction
Carlos Santos, Daniela Eggle, and David. J. States
Bioinformatics 2005 21: 1653-1658.
DOI: 10.1093/bioinformatics/bti165
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/8/1653?etoc

Visualizing information across multidimensional post-genomic structured and textual databases
Ying Tao, Carol Friedman, and Yves A. Lussier
Bioinformatics 2005 21: 1659-1667.
DOI: 10.1093/bioinformatics/bti210
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/8/1659?etoc

GPSDB: a new database for synonyms expansion of gene and protein names
Violaine Pillet, Marc Zehnder, Alexander K. Seewald, Anne-Lise Veuthey, and Johann Petrak
Bioinformatics 2005 21: 1743-1744.
DOI: 10.1093/bioinformatics/bti235
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/8/1743?etoc

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures
Norihiro Kikuchi, Akihiko Kameyama, Shuuichi Nakaya, Hiromi Ito, Takashi Sato, Toshihide Shikanai, Yoriko Takahashi, and Hisashi Narimatsu
Bioinformatics 2005 21: 1717-1718.
DOI: 10.1093/bioinformatics/bti152
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/8/1717?etoc

*** 8 April 2005 ***
Building a protein name dictionary from full text: a machine learning term extraction approach
Lei Shi, Fabien Campagne
BMC Bioinformatics 2005, 6:88 (7 April 2005)
DOI: 10.1186/1471-2105-6-88
http://www.biomedcentral.com/1471-2105/6/88/abstract

*** 6 April 2005 ***
Systematic Association of Genes to Phenotypes by Genome and Literature Mining
Jan O. Korbel, Tobias Doerks, Lars J. Jensen, Carolina Perez-Iratxeta, Szymon Kaczanowski, Sean D. Hooper, Miguel A. Andrade, Peer Bork
PLoS Biology, April 5, 2005
DOI: 10.1371/journal.pbio.0030166
Full - http://dx.doi.org/10.1371/journal.pbio.0030166

Ranking the whole MEDLINE database according to a large training set using text indexing
Brian P Suomela, Miguel A Andrade
BMC Bioinformatics 2005 6:75
DOI: 10.1186/1471-2105-6-75
http://www.biomedcentral.com/1471-2105/6/75/abstract

A Taxonomic Search Engine: Federating taxonomic databases using web services
Roderic DM Page
BMC Bioinformatics 2005 6:48
DOI: 10.1186/1471-2105-6-48
http://www.biomedcentral.com/1471-2105/6/48/abstract

CoPub Mapper: mining MEDLINE based on search term co-publication
Blaise T.F. Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman, Guido Jenster
BMC Bioinformatics 2005 6:51
DOI: 10.1186/1471-2105-6-51
http://www.biomedcentral.com/1471-2105/6/51/abstract

Automatic extraction of gene/protein biological functions from biomedical text
Asako Koike, Yoshiki Niwa, and Toshihisa Takagi
Bioinformatics 2005 21(7):1227-1236
DOI: 10.1093/bioinformatics/bti084
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/7/1227

Inferring pathways from gene lists using a literature-derived network of biological relationships
Dilip Rajagopalan and Pankaj Agarwal
Bioinformatics 2005 21(6):788-793
DOI: 10.1093/bioinformatics/bti069
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/6/788

*** Sep 2004 ***
Extracting and characterizing gene-drug relationships from the literature.
Chang, Jeffrey T; Altman, Russ B
Pharmacogenetics. 2004 Sep;14(9):577-86.
PubMed: 15475731

*** August 2004 ***
Gene name ambiguity of eukaryotic nomenclatures
Lifeng Chen, Hongfang Liu, and Carol Friedman
Bioinformatics 2005 21(2):248-256
DOI: 10.1093/bioinformatics/bth496
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/2/248

Gene clustering by Latent Semantic Indexing of MEDLINE abstracts
Ramin Homayouni, Kevin Heinrich, Lai Wei, and Michael W. Berry
Bioinformatics 2004 21(1):104-115
DOI: 10.1093/bioinformatics/bth464
http://bioinformatics.oupjournals.org/cgi/content/abstract/21/1/104

*** July 2004 ***
Discovering patterns to extract protein-protein interactions from full texts
Minlie Huang, Xiaoyan Zhu, Yu Hao, Donald G. Payan, Kunbin Qu, and Ming Li
Bioinformatics 2004 20(18):3604-3612
DOI: 10.1093/bioinformatics/bth451
http://bioinformatics.oupjournals.org/cgi/content/abstract/20/18/3604

Ontology-assisted database integration to support natural language processing and biomedical data-mining
Jean-Luc Verschelde, Marianna Casella Dos Santos, Tom Deray, Barry Smith, and Werner Ceusters
JIB - The Integrative Bioinformatics Journal, 2004:1
Summary - http://www-bm.ipk-gatersleben.de/stable/php/journal/articles/pdf/jib-1.pdf

A web tool for finding gene candidates associated with experimentally induced arthritis in the rat
Lars Andersson, Greta Petersen, Per Johnson, and Fredrik Stahl
Arthritis Res Ther. 2005; 7(3): R485-R492
DOI: 10.1186/ar1700
Abstract

Extraction of protein interaction information from unstructured text using a context-free grammar
Joshua M. Temkin and Mark R. Gilder
Bioinformatics 19(16):2046-2053, 2003
DOI: 10.1093/bioinformatics/btg279
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/16/2046

Unsupervised monolingual and bilingual word-sense disambiguation of medical documents using UMLS
Dominic Widdows, Stanley Peters, Scott Cederberg, Chiu-Ki Chan, Diana Steffen, Paul Buitelaar
Proc ACL Workshop on Nat Lang Proc in Biomed, 2003, 9--16, Sapporo, Japan, July
2003
http://citeseer.ist.psu.edu/584877.html

ISMB 2003 Text Mining SIG Meeting Report.
Blaschke C, Yeh A, Hirschman L, Valencia A.
Comp Funct Genomics. 2003;4(6):667-73. No abstract available.
PubMed: 18629019

By topic - [BioNLP by date]

Mining and using mutations
Next-generation sequencing: techniques, algorithms, applications
Pharmacogenetics and -genomics: basics, text-mining

Other collections of publications

BioNLP
- BLIMP - Biomedical LIterature (and text) Mining Publications online search, browsing via 10 categories: background, IE, IR, reviews, ..
Natural language processing
- Statistical Natural Language Processing Reading List by F. Peng
  A large collection of references to various topics in NLP and ML. Slightly, but not completely, outdated.

Machine Learning

Semi-Supervised Learning Literature Survey
Xiaojin Zhu
Computer Sciences TR 1530, University of Wisconsin Madison, Dec 14 2007
http://pages.cs.wisc.edu/~jerryzhu/research/ssl/semireview.html

A review of feature selection techniques in bioinformatics
Yvan Saeys, Inaki Inza, and Pedro Larranaga
Bioinformatics published 24 August 2007, 10.1093/bioinformatics/btm344
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm344v1?papetoc

Support Vector Machines

Learning with Kernels
SVM^light: Provides links to papers (bottom of page)

Boosting

Boosting: Robert Schapire's own collection of papers and tutorials on boosting.

Biology / Bioinformatics / Life sciences

The Diploid Genome Sequence of an Individual Human
Samuel Levy, Granger Sutton, Pauline C. Ng, Lars Feuk, Aaron L. Halpern, ... and J. Craig Venter
Comparison of the DNA sequence of an individual human from the reference sequence reveals a surprising amount of difference.
PLoS Biol 5(10): e254 doi:10.1371/journal.pbio.0050254
http://lists.plos.org/lt.php?id=eklUBw1SUgBSGggFBldJCwMHUVEM

Human Variation Database: An open source database template for genomic discovery
Anthony P. Fejes, Alireza Hadj Khodabakhshi, Inanc Birol, and Steven J.M. Jones
Bioinformatics published 2 March 2011
DOI: 10.1093/bioinformatics/btr100
Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btr100v1?papetoc

Tools for Visually Exploring Biological Networks
Matthew Suderman and Michael Hallett
Bioinformatics published 25 August 2007, 10.1093/bioinformatics/btm401
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm401v1?papetoc

Current progress in bioinformatics 2007
Russ B. Altman
Brief Bioinform published 27 August 2007, 10.1093/bib/bbm041
http://bib.oxfordjournals.org/cgi/content/extract/bbm041v1?papetoc

OReFiL: an online resource finder for life sciences
Yasunori Yamamoto and Toshihisa Takagi
BMC Bioinformatics 2007, 8:287
DOI: 10.1186/1471-2105-8-287
PubMed: 17683589
http://www.biomedcentral.com/1471-2105/8/287/abstract

Databases curating info on relationships between different types of compounds etc

TTD: Therapeutic Target Database --- drug / (protein)-target / disease
http://xin.cz3.nus.edu.sg/group/ttd/ttd.asp

DITOP: drug-induced toxicity related protein database
Jing-Xian Zhang, Wei-Juan Huang, Jing-Hua Zeng, Wen-Hui Huang, Yi Wang, Rui Zhao, Bu-Cong Han, Qing-Feng Liu, Yu-Zong Chen, and Zhi-Liang Ji
Bioinformatics Advance Access published on July 1, 2007
DOI 10.1093/bioinformatics/btm139.
Bioinformatics 23: 1710-1712
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/1710?etoc

Ontologies in the life sciences

Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community
Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW
BMC Bioinformatics 2011, 12:32 (24 January 2011)
Abstract: http://www.biomedcentral.com/1471-2105/12/32/abstract
(ONT)

Biomedical Ontologies: Special Issue
Journal of Biomedical Informatics, Vol. 39, Issue 3, June 2006
Table of Contents
(ONT) (R)

Biomedical ontologies: What part-of is and isn't
Stefan Schulz, Anand Kumarb and Thomas Bittner
Journal of Biomedical Informatics, 39(3):350-361
DOI: 10.1016/j.jbi.2005.11.003
Abstract
(ONT)

An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology
Shobhit Jain and Gary D Bader
BMC Bioinformatics 2010, 11:562
DOI: 10.1186/1471-2105-11-562
Paper: http://www.biomedcentral.com/1471-2105/11/562/
(ONT) (PPI)

OBO Explorer: An Editor for Open Biomedical Ontologies in OWL
Stuart Aitken, Yin Chen, and Jonathan Bard
Bioinformatics published 1 December 2007, 
10.1093/bioinformatics/btm593
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm593v1?papetoc
(ONT)

Enrichment of OBO ontologies
Michael Bada and Lawrence Hunter
Journal of Biomedical Informatics, Volume 40, Issue 3, June 2007, Pages 300-315
DOI: 10.1016/j.jbi.2006.07.003 
(ONT)

Data integration in the life sciences

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
Bare J, Shannon P, Schmid A, Baliga N
BMC Bioinformatics, 2007 8:456 (19 November 2007)
http://www.biomedcentral.com/1471-2105/8/456/abstract

Anatomy of data integration
Olga Brazhnik and John F. Jones
Journal of Biomedical Informatics, Volume 40, Issue 3, June 2007, Pages 252-269
DOI: 10.1016/j.jbi.2006.09.001

An efficient strategy for extensive integration of diverse biological data for protein function prediction
Hon Nian Chua, Wing-Kin Sung, and Limsoon Wong
Bioinformatics 2007 23: 3364-3373. 
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/24/3364?etoc