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irenas's bib [120 articles]

Recent papers added to irenas's library classified by the tag bib. You can also see everyone's bib.
  • Information retrieval: an overview of system characteristics
    International Journal of Medical Informatics, Vol. 47, No. 1-2. (November 1997), pp. 5-26.
    by F Wiesman, Arie Hasman, HJ van den Herik
    posted to bib ir med new by irenas on 2006-01-10 19:13:39 as ** along with 1 group dbk-lab
  • Semantic similarity measures as tools for exploring the gene ontology.
    Pac Symp Biocomput (2003), pp. 601-612.
    by PW Lord, RD Stevens, A Brass, CA Goble
    posted to bib onto by irenas on 2005-06-06 18:22:28 as ** along with 8 people and 3 groups andytseng CitoJam ejmeij gaudan josemblazquez macavity1g sgoetz pmidford dbk-lab ilps LanguageModeling
  • Linking Experimental Results, Biological Networks and Sequence Analysis Methods Using Ontologies and Generalised Data Structures
    In Silico Biology, Vol. 5, No. 1. (January 2005), pp. 33-44.
    by Jacob Koehler, Chris Rawlings, Paul Verrier, Rowan Mitchell, Andre Skusa, Alexander Ruegg, Stephan Philippi
    posted to bib onto by irenas on 2005-06-04 13:38:21 as ** along with 1 group dbk-lab
  • Using the biological taxonomy to access biological literature with PathBinderH.
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2560-2562.
    by J Ding, K Viswanathan, D Berleant, L Hughes, ES Wurtele, D Ashlock, JA Dickerson, A Fulmer, PS Schnable
    posted to bib ir onto by irenas on 2005-05-18 11:09:48 as ** along with 1 group dbk-lab
  • The Unified Medical Language System (UMLS): integrating biomedical terminology.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by O Bodenreider
    posted to bib onto owg by irenas on 2005-05-14 19:22:08 as ** along with 7 people and 2 groups kuhn wnpx bundschu josepe kkaiser leechuck sgoetz dbk-lab IEG
  • Text-based knowledge discovery: search and mining of life-sciences documents.
    Drug Discov Today, Vol. 7, No. 11 Suppl. (1 June 2002)
    by R Mack, M Hehenberger
    posted to bib onto owg txtmining by irenas on 2005-05-14 19:01:30 as ** along with 1 person and 1 group daniel_schober dbk-lab
  • ABNER: an open source tool for automatically tagging genes, proteins, and other entity names in text.
    Bioinformatics (28 April 2005)
    by Burr Settles
    posted to bib ner by irenas on 2005-05-13 13:37:34 as ** along with 1 person and 1 group zlu dbk-lab
  • Enhancing a biomedical information extraction system with dictionary mining and context disambiguation
    IBM Journal of Research and Development, Vol. 48, No. 5/6. (2004), pp. 693-701.
    by S Mukherjea, Lv Subramaniam, G Chanda, S Sankararaman, R Kothari, V Batra, D Bhardwaj, B Srivastava
    posted to bib bio class ner by irenas on 2005-05-13 12:41:38 as ** along with 1 group dbk-lab
  • Comparison between tagged corpora for the named entity task
    (2000), pp. 20-26.
    by Chikashi Nobata, Nigel Collier, Junichi Tsujii
    edited by A Kilgarriff, T Berber
    posted to bib ner by irenas on 2005-05-13 12:09:58 as ** along with 1 group dbk-lab
  • Enhancing HMM-based biomedical named entity recognition by studying special phenomena.
    J Biomed Inform, Vol. 37, No. 6. (December 2004), pp. 411-422.
    by J Zhang, D Shen, G Zhou, J Su, CL Tan
    posted to bib genia hmm ner by irenas on 2005-05-13 10:32:45 as ** along with 2 people and 1 group bhaddow vlachmore dbk-lab
  • Using name-internal and contextual features to classify biological terms.
    J Biomed Inform, Vol. 37, No. 6. (December 2004), pp. 498-511.
    by M Torii, S Kamboj, K Vijay-Shanker
    posted to bib genia ner by irenas on 2005-05-12 19:38:47 as ** along with 2 people and 1 group yggdrasil johnkork dbk-lab
  • POSBIOTM-NER: a trainable biomedical named-entity recognition system.
    Bioinformatics (6 April 2005)
    by Yu Song, Eunju Kim, Gary Geunbae G Lee, Byoung-Kee K Yi
    posted to bib genia ner by irenas on 2005-05-12 19:30:56 as ** along with 1 person and 1 group yggdrasil dbk-lab
  • GENIA corpus--semantically annotated corpus for bio-textmining.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by JD Kim, T Ohta, Y Tateisi, J Tsujii
    posted to bib ml onto by irenas on 2005-05-12 19:02:12 as ** along with 6 people and 3 groups caporaso zlu jacky957 bundschu johnkork leechuck dbk-lab biomedical-nlp generif_paper
  • Creating an online dictionary of abbreviations from MEDLINE.
    J Am Med Inform Assoc, Vol. 9, No. 6. (c 2002), pp. 612-620.
    by JT Chang, H Schütze, RB Altman
    posted to acronym bib by irenas on 2005-05-12 18:52:55 as ** along with 2 people and 2 groups natsu helliontroy dbk-lab biomedical-nlp
  • A study of abbreviations in MEDLINE abstracts.
    Proc AMIA Symp (2002), pp. 464-468.
    by H Liu, AR Aronson, C Friedman
    posted to acronym bib by irenas on 2005-05-12 18:43:52 as ** along with 1 group dbk-lab
  • Text mining technology: Turning information into knowledge
    IBM White paper (1997)
    by D Tkach
    posted to bib txtmining by irenas on 2005-03-27 13:10:11 as ** along with 1 group dbk-lab
  • Generic summarization and keyphrase extraction using mutual reinforcement principle and sentence clustering
    (2002), pp. 113-120.
    by Hongyuan Zha
    posted to bib nemam term by irenas on 2005-03-27 13:06:38 as ** along with 1 person and 2 groups arthit dbk-lab automatic_summarization
  • Extraction of Keyphrases from Text: Evaluation of Four Algorithms
    (8 December 2002)
    by Peter D Turney
    posted to bib term by irenas on 2005-03-27 13:02:54 as ** along with 2 people and 2 groups arthit Phanix dbk-lab automatic_summarization
  • KEA: Practical Automatic Keyphrase Extraction
    (5 February 1999)
    by Ian H Witten, Gordon W Paynter, Eibe Frank, Carl Gutwin, Craig G Nevill-Manning
    posted to bib term by irenas on 2005-03-27 13:01:07 as ** along with 2 people and 2 groups aliku arthit dbk-lab automatic_summarization
  • Integration of text- and data-mining using ontologies successfully selects disease gene candidates.
    Nucleic Acids Res, Vol. 33, No. 5. (2005), pp. 1544-1552.
    by N Tiffin, JF Kelso, AR Powell, H Pan, VB Bajic, WA Hide
    posted to bib bio gene med nlp onto rel srb by irenas on 2005-03-25 17:08:07 as read along with 3 people and 2 groups yas benny fisherp dbk-lab T_lab
  • notes Use of keyword hierarchies to interpret gene expression patterns.
    Bioinformatics, Vol. 17, No. 4. (April 2001), pp. 319-326.
    by DR Masys, JB Welsh, J Lynn Fink, M Gribskov, I Klacansky, J Corbeil
    posted to bib bio data gene med medline nlp onto txtmining by irenas on 2005-03-25 17:05:04 as ** along with 2 people and 2 groups yas incovoma dbk-lab T_lab
  • MeSHmap: a text mining tool for MEDLINE.
    Proc AMIA Symp (2001), pp. 642-646.
    by P Srinivasan
    posted to bib bio ir med medline nlp tool by irenas on 2005-03-25 17:00:37 as read along with 2 people and 1 group meikipp guoziyi dbk-lab
  • notes GIS: a biomedical text-mining system for gene information discovery.
    Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 120-121.
    by JH Chiang, HC Yu, HJ Hsu
    posted to bib bio gene med nlp software tool txtmining by irenas on 2005-03-25 16:56:54 as read along with 1 person and 1 group jyuh dbk-lab
  • Identifying biological themes within lists of genes with EASE.
    Genome Biol, Vol. 4, No. 10. (2003)
    by DA Hosack, G Dennis, BT Sherman, HC Lane, RA Lempicki
    posted to bib bio gene nlp tool by irenas on 2005-03-25 16:54:00 as ** along with 2 people and 2 groups jeremymiller capitall dbk-lab GeschwindLab
  • notes Update on XplorMed: A web server for exploring scientific literature.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3866-3868.
    by C Perez-Iratxeta, AJ Pérez, P Bork, MA Andrade
    posted to bib bio ir med software tool by irenas on 2005-03-25 16:47:32 as read along with 2 people and 2 groups miguel yas dbk-lab T_lab
  • notes MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling.
    Biotechniques, Vol. 27, No. 6. (December 1999)
    by L Tanabe, U Scherf, LH Smith, JK Lee, L Hunter, JN Weinstein
    posted to bib bio gene nlp tool txtmining by irenas on 2005-03-25 16:37:06 as read along with 3 people and 2 groups Enro yas simmie dbk-lab T_lab
  • notes A literature network of human genes for high-throughput analysis of gene expression.
    Nat Genet, Vol. 28, No. 1. (May 2001), pp. 21-28.
    by TK Jenssen, A Laegreid, J Komorowski, E Hovig
    posted to bib bio gene nlp by irenas on 2005-03-25 16:33:23 as read along with 9 people and 4 groups TheresaNiederberger miguel okarsligil lfriedl yas balajis benny dullhunk adoms dbk-lab kdl Bioinformatics T_lab
  • Using BLAST for identifying gene and protein names in journal articles.
    Gene, Vol. 259, No. 1-2. (23 December 2000), pp. 245-252.
    by M Krauthammer, A Rzhetsky, P Morozov, C Friedman
    posted to bib bio gene med ner nlp protein term by irenas on 2005-03-25 15:20:31 as read along with 1 person and 2 groups bundschu dbk-lab generif_paper
  • Detecting Gene Symbols and Names in Biological Texts: A First Step toward Pertinent Information Extraction.
    Genome Inform Ser Workshop Genome Inform, Vol. 9 (1998), pp. 72-80.
    by D Proux, F Rechenmann, L Julliard, V Pillet, B Jacq
    posted to bib bio gene ie med ner nlp term by irenas on 2005-03-25 15:18:13 as read along with 1 person and 1 group yggdrasil dbk-lab
  • notes Generation of a large gene/protein lexicon by morphological pattern analysis.
    J Bioinform Comput Biol, Vol. 1, No. 4. (January 2004), pp. 611-626.
    by L Tanabe, WJ Wilbur
    posted to bib bio data gene med nemam ner nlp protein by irenas on 2005-03-25 14:58:20 as ** along with 1 group dbk-lab
  • A Probabilistic Model for Identifying Protein Names and their Name Boundaries
    (2003), pp. 251-259.
    by Kazuhiro Seki, Javed Mostafa
    posted to bib bio med ner protein stat term by irenas on 2005-03-25 14:56:05 as read along with 1 group dbk-lab
  • MedScan, a natural language processing engine for MEDLINE abstracts.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1699-1706.
    by S Novichkova, S Egorov, N Daraselia
    posted to bib bio med medline nlp sold tool by irenas on 2005-03-25 12:23:02 as ** along with 3 people and 2 groups yas natsu dullhunk dbk-lab T_lab
  • A simple and practical dictionary-based approach for identification of proteins in Medline abstracts.
    J Am Med Inform Assoc, Vol. 11, No. 3. (n 2004), pp. 174-178.
    by S Egorov, A Yuryev, N Daraselia
    posted to bib medline ner nlp protein term tool by irenas on 2005-03-25 12:21:35 as read along with 2 people and 1 group dullhunk gaudan dbk-lab
  • Extracting human protein interactions from MEDLINE using a full-sentence parser.
    Bioinformatics, Vol. 20, No. 5. (22 March 2004), pp. 604-611.
    by N Daraselia, A Yuryev, S Egorov, S Novichkova, A Nikitin, I Mazo
    posted to bib bio ie med medline nlp onto protein rel txtmining by irenas on 2005-03-25 12:20:09 as ** along with 5 people and 1 group satre Enro miguel natsu zlu dbk-lab
  • Practical Data Integration in Biopharmaceutical Research and Development
    PharmaGenomics (2003), pp. 22-35.
    by Roland Carel
    posted to bib bio db memo onto xml by irenas on 2005-03-24 15:16:25 as read along with 1 group dbk-lab
  • notes Rutabaga by any other name: extracting biological names.
    J Biomed Inform, Vol. 35, No. 4. (August 2002), pp. 247-259.
    by L Hirschman, AA Morgan, AS Yeh
    posted to bib bio ner nlp term by irenas on 2005-03-23 16:09:49 as ** along with 1 person and 1 group hpiwowar dbk-lab
  • An intelligent biological information management system.
    Bioinformatics, Vol. 18, No. 10. (October 2002), pp. 1283-1288.
    by M Palakal, S Mukhopadhyay, J Mostafa, R Raje, M N'Cho, S Mishra
    posted to bib bio nlp txtmining by irenas on 2005-03-23 16:08:13 as ***** along with 1 person and 1 group ibuch dbk-lab
  • Integrating query of relational and textual data in clinical databases: a case study.
    J Am Med Inform Assoc, Vol. 10, No. 1. (b 2003), pp. 21-38.
    by JM Fisk, P Mutalik, FW Levin, J Erdos, C Taylor, P Nadkarni
    posted to bib db ir med memo by irenas on 2005-03-23 16:01:48 as ** along with 1 group dbk-lab
  • notes MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations.
    Bioinformatics, Vol. 21, No. 5. (1 March 2005), pp. 694-695.
    by J Ding, D Berleant
    posted to bib bio medline nlp software tool txtmining by irenas on 2005-03-23 15:43:37 as ** along with 2 people and 1 group Enro jyuh dbk-lab
  • notes MedPost: a part-of-speech tagger for bioMedical text.
    Bioinformatics, Vol. 20, No. 14. (22 September 2004), pp. 2320-2321.
    by L Smith, T Rindflesch, WJ Wilbur
    posted to bib nlp software tool by irenas on 2005-03-23 15:37:46 as ** along with 6 people and 4 groups yggdrasil TheresaNiederberger yas hpiwowar kkaiser vlachmore dbk-lab T_lab IEG dbmi-nlp
  • notes Biomedical ontologies.
    Pac Symp Biocomput (2005), pp. 76-78.
    by O Bodenreider, JA Mitchell, AT McCray
    posted to bib bio onto by irenas on 2005-03-23 11:45:07 as ** along with 1 group dbk-lab
  • notes Biological nomenclatures: a source of lexical knowledge and ambiguity.
    Pac Symp Biocomput (2004), pp. 238-249.
    by O Tuason, L Chen, H Liu, JA Blake, C Friedman
    posted to ambig bib bio ner nlp term var by irenas on 2005-03-23 11:42:35 as ** along with 1 person and 1 group t11 dbk-lab
  • Evaluating UMLS strings for natural language processing.
    Proc AMIA Symp (2001), pp. 448-452.
    by AT McCray, O Bodenreider, JD Malley, AC Browne
    posted to bib nemam nlp onto umls by irenas on 2005-03-23 11:42:14 as ** along with 1 person and 2 groups kkaiser dbk-lab IEG
  • Protein structures and information extraction from biological texts: the PASTA system.
    Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 135-143.
    by R Gaizauskas, G Demetriou, PJ Artymiuk, P Willett
    posted to bib bio ie nlp protein tool by irenas on 2005-03-23 11:41:03 as ** along with 3 people and 2 groups yggdrasil caporaso vlachmore dbk-lab biomedical-nlp
  • EDGAR: extraction of drugs, genes and relations from the biomedical literature.
    Pac Symp Biocomput (2000), pp. 517-528.
    by TC Rindflesch, L Tanabe, JN Weinstein, L Hunter
    posted to bib class gene ie ner nlp term tool by irenas on 2005-03-23 11:39:30 as ** along with 2 people and 1 group zlu ibuch dbk-lab
  • The UMLS project: making the conceptual connection between users and the information they need.
    Bull Med Libr Assoc, Vol. 81, No. 2. (April 1993), pp. 170-177.
    by BL Humphreys, DA Lindberg
    posted to bib bio med onto umls by irenas on 2005-03-23 11:36:17 as ** along with 2 people and 4 groups wcrosbie kkaiser dbk-lab Wikipedia CoP_CMS IEG
  • NLP techniques associated with the OpenGALEN ontology for semi-automatic textual extraction of medical knowledge: abstracting and mapping equivalent linguistic and logical constructs.
    Proc AMIA Symp (2000), pp. 76-80.
    by MB do Amaral, A Roberts, AL Rector
    posted to bib med nlp onto txtmining by irenas on 2005-03-23 11:35:30 as ** along with 1 person and 1 group daniel_schober dbk-lab
  • notes Integrating a hypernymic proposition interpreter into a semantic processor for biomedical texts.
    AMIA Annu Symp Proc (2003), pp. 239-243.
    by M Fiszman, TC Rindflesch, H Kilicoglu
    posted to bib bio ie med nlp by irenas on 2005-03-23 11:32:53 as ** along with 2 people and 2 groups ville helliontroy dbk-lab biomedical-nlp
  • notes Biomedical literature mining: challenges and solutions in the 'omics' era.
    Am J Pharmacogenomics, Vol. 4, No. 6. (2004), pp. 383-393.
    by D Chaussabel
    posted to bib bio med nemam nlp omics txtmining by irenas on 2005-03-23 11:32:20 as ** along with 4 people and 1 group Enro andytseng qfwills daniel_schober dbk-lab
  • notes Meeting medical terminology needs--the Ontology-Enhanced Medical Concept Mapper.
    IEEE Trans Inf Technol Biomed, Vol. 5, No. 4. (December 2001), pp. 261-270.
    by G Leroy, H Chen
    posted to bib med onto term by irenas on 2005-03-23 11:31:52 as ** along with 1 group dbk-lab
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