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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. 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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 *** 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 *** 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. 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PubMed: 19758464 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. Epub 2009 Aug 4. PubMed: 19656727 PubMed-EX: A web browser extension to enhance PubMed search with text mining features Tsai RT, Dai HJ, Lai PT, Huang CH. Bioinformatics. 2009 Nov 15;25(22):3031-2. Epub 2009 Aug 4. 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 *** 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 *** Aug 11 2009 *** 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, Advance Access published online on August 4, 2009 DOI: 10.1093/bioinformatics/btp475 *** Jul 17 2009 *** Shanfeng Zhu, Jia Zeng, and Hiroshi Mamitsuka Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity Bioinformatics 2009 25: 1944-1951 DOI: 10.1093/bioinformatics/btp338. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/15/1944?etoc Yoshinobu Kano, William A. 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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 new evaluation methodology for literature-based discovery systems Meliha Yetisgen-Yildiz, Wanda Pratt Journal of Biomedical Informatics, Volume 42, Issue 4, Pages 633-643, 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. 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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. [Epub ahead of print] PubMed: 19520768 Interactive Text Mining with Pipeline Pilot: A Bibliographic Web-Based Tool for PubMed. Vellay SG, Latimer NE, Paillard G. 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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) Accelerating the annotation of sparse named entities by dynamic sentence selection Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou BMC Bioinformatics 2008, 9(Suppl 11):S8 (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 DOI: 10.1186/1471-2105-9-S11-S8 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, Agaugué 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, André P, Rabourdin-Combe C, Lotteau V. Mol Syst Biol. 2008;4:230. Epub 2008 Nov 4. PubMed: 18985028 *** 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. [Epub ahead of print] 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. [Epub ahead of print] 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. Epub 2008 Aug 20. 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. Epub 2008 Oct 24. 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 Inter-species normalization of gene mentions with GNAT. Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G. Bioinformatics. 2008 Aug 15;24(16):i126-132. PubMed: 1868981 Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining. Yu S, Van Vooren S, Tranchevent LC, De Moor B, Moreau Y. Bioinformatics. 2008 Aug 15;24(16):i119-25. PubMed: 18689812 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. Epub 2008 Jul 13. 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. Epub 2008 Jun 24. 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. Epub 2008 Sep 1. 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. Epub 2008 Sep 1. 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. Epub 2008 Sep 1. 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. Epub 2008 Sep 1. 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. Epub 2008 Sep 1. 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. Epub 2008 Sep 1. PubMed: 18834492 Mining physical protein-protein interactions from the literature. Huang M, Ding S, Wang H, Zhu X. Genome Biol. 2008;9 Suppl 2:S12. Epub 2008 Sep 1. 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. Epub 2008 Sep 1. 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 To appear in Proc ECCB'08, September 22-26, Italy Abstract: http://www.eccb08.org/?pageId=277#151 Inter-species normalization of gene mentions with GNAT Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder and Graciela Gonzalez To appear in Proc ECCB'08, September 22-26, Italy Abstract: http://www.eccb08.org/?pageId=277#174 *** 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, Anto³nio 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. Epub 2007 Dec 15. Review. 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 *** April 11 2008 *** *** 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 *** 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. Epub 2008 Mar 6. PubMed: 18328824 Manually structured digital abstracts: a scaffold for automatic text mining. Seringhaus M, Gerstein M. FEBS Lett. 2008 Apr 9;582(8):1170. Epub 2008 Mar 6. No abstract available. 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. Epub 2008 Mar 5. 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 *** 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 Analysis and Enhancement of Conditional Random Fields Gene Mention Taggers in BioCreative II Challenge Evaluation Yu-Ming Chang, Cheng-Ju Kuo, Han-Shen Huang, Yu-Shi Lin and Chun-Nan Hsu 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/Paper4.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. Table of contents - http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-319/Paper6.pdf Protein-protein interaction abstract identification with contextual bag of words Richard Tzong-Han Tsai, Hsieh-Chuan Hung, Hong-Jie Dai and Yi-Wen Lin 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/Paper7.pdf *** Dec 30 2007 *** Functional gene clustering via gene annotation sentences, MeSH and GO keywords from biomedical literature. Natarajan J, Ganapathy J. Bioinformation. 2007 Dec 30;2(5):185-93. PubMed: 18305827 *** Dec 14 2007 *** Automated Acquisition of Disease-Drug Knowledge from Biomedical and Clinical Documents: An Initial Study Elizabeth S. Chen, George Hripcsak, Hua Xu, Marianthi Markatou and Carol Friedman Journal of the American Medical Informatics Association, Volume 15, Issue 1, January-February 2008, Pages 87-98 Using the iHOP information resource to mine the biomedical literature on genes, proteins, and chemical compounds. Hoffmann R. Curr Protoc Bioinformatics. 2007 Dec;Chapter 1:Unit1.16. PubMed: 18428678 *** Dec 7 2007 *** Combining Gene Ontology and Argumentative Features for Automatic GeneRIF Extraction Julien Gobeill and Patrick Ruch Proc LBM 2007 Assessment of disease named entity recognition on a corpus of annotated sentences Antonio Jimeno, Ernesto Jimenez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga-Llavori and Dietrich Rebholz-Schuhmann Proc LBM 2007 and BMC Bioinformatics. 2008 Apr 11;9 Suppl 3:S3. PubMed: 18426548 New challenges for Text Mining: Mapping between text and manually curated pathways Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi and Jun'ichi Tsujii Proc LBM 2007 and BMC Bioinformatics. 2008 Apr 11;9 Suppl 3:S5. 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Watson and Fan Meng Bioinformatics Advance Access published online on September 6, 2007 DOI: 10.1093/bioinformatics/btm375 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm375 *** 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. 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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. 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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 *** 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 [Epub ahead of print] DOI: 10.1186/gb-2006-7-5-402 PMID: 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'tâ Stefan Schulz, Anand Kumarb and Thomas Bittner Journal of Biomedical Informatics, 39(3):350-361 DOI: 10.1016/j.jbi.2005.11.003 Abstract *** 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. 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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; [Epub ahead of print] 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 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 http://www.biomedcentral.com/1472-6947/5/35 *** 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 http://www.biomedcentral.com/1472-6947/5/35/abstract 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 http://www.biomedcentral.com/1472-6947/5/30/abstract *** 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 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 Séroussi, 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 *** 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 ----------------------------------------------------------- Other collections of BioNLP publications * BLIMP - Biomedical LIterature (and text) Mining Publications online search, browsing via 10 categories: background, IE, IR, reviews, ..
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
The Diploid Genome Sequence of an Individual Human Samuel Levy, Granger Sutton, Pauline C. Ng, Lars Feuk, Aaron L. Halpern, Brian P. Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F. Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R. MacDonald, Andy Wing Chun Pang, Mary Shago, Timothy B. Stockwell, Alexia Tsiamouri, Vineet Bafna, Vikas Bansal, Saul A. Kravitz, Dana A. Busam, Karen Y. Beeson, Tina C. McIntosh, Karin A. Remington, Josep F. Abril, John Gill, Jon Borman, Yu-Hui Rogers, Marvin E. Frazier, Stephen W. Scherer, Robert L. Strausberg, 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 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 http://www.biomedcentral.com/1471-2105/8/287/abstract
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
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 OBO to OWL: A Protege OWL Tab to Read/Save OBO Ontologies Dilvan A. Moreira and Mark A. Musen Bioinformatics published 12 May 2007, 10.1093/bioinformatics/btm258 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm258v1?papetoc 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
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
Numbers in square brackets reflect ISI impact factors, as of Nov 2007 (available only for life-science-oriented journals.)