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Tag ner [153 articles]

Recent papers classified by the tag ner.
  • Using BLAST for identifying gene and protein names in journal articles
    Gene, Vol. 259, No. 1-2. (23 December 2000), pp. 245-252.
    by Michael Krauthammer, Andrey Rzhetsky, Pavel Morozov, Carol Friedman
    posted to alignment ner sequence by yggdrasil on 2008-05-15 10:49:16 as ** along with 4 people and 1 group yas bhaddow klo vlachmore T_lab
  • Automated extraction of information on protein-protein interactions from the biological literature.
    Bioinformatics, Vol. 17, No. 2. (February 2001), pp. 155-161.
    by T Ono, H Hishigaki, A Tanigami, T Takagi
    posted to ner by yggdrasil on 2008-05-09 12:32:13 as ** along with 7 people and 3 groups irenas yas blackbart helliontroy zlu bundschu satre T_lab biomedical-nlp generif_paper
  • Distributed modules for text annotation and IE applied to the biomedical domain
    International Journal of Medical Informatics, Vol. In Press, Corrected Proof
    by Harald Kirsch, Sylvain Gaudan, Dietrich Rebholz-Schuhmann
    posted to component ie java module ner textmining by yggdrasil on 2008-04-23 10:30:26 as ** along with 3 people and 2 groups irenas yas gaudan dbk-lab T_lab
  • GAPSCORE: finding gene and protein names one word at a time.
    Bioinformatics, Vol. 20, No. 2. (22 January 2004), pp. 216-225.
    by JT Chang, H Schütze, RB Altman
    posted to ner by yas on 2006-01-15 17:18:49 as ** along with 1 group T_lab
  • Gene name ambiguity of eukaryotic nomenclatures.
    Bioinformatics, Vol. 21, No. 2. (15 January 2005), pp. 248-256.
    by L Chen, H Liu, C Friedman
    posted to ner by yas on 2006-01-11 15:57:04 as ** along with 3 people and 3 groups cisevol snuppepuppan irenas BergmanLab dbk-lab T_lab
  • BioThesaurus: a web-based thesaurus of protein and gene names.
    Bioinformatics (2 November 2005)
    by Hongfang Liu, Zhang-Zhi Z Hu, Jian Zhang, Cathy Wu
    posted to ner by yas on 2006-01-03 15:03:29 as ** along with 2 people and 1 group jyuh jacky957 T_lab
  • Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification.
    J Biomed Inform, Vol. 40, No. 3. (June 2007), pp. 316-324.
    by MJ Schuemie, B Mons, M Weeber, JA Kors
    posted to ner by yas on 2008-06-09 08:11:20 as ** along with 1 person Barend
  • Biology's name game.
    Nature, Vol. 411, No. 6838. (7 June 2001), pp. 631-632.
    by H Pearson
    posted to ner by yas on 2006-01-11 16:00:56 as ** along with 2 people and 2 groups irenas dullhunk dbk-lab T_lab
  • What makes a gene name? Named entity recognition in the biomedical literature
    Briefings in Bioinformatics, Vol. 6, No. 4. (December 2005), pp. 357-369.
    by Leser, Ulf, Hakenberg, Jorg
    posted to ner review by yas on 2006-01-09 04:41:02 as ** along with 1 group T_lab
  • High-recall protein entity recognition using a dictionary.
    Bioinformatics, Vol. 21 Suppl 1 (1 June 2005)
    by Z Kou, WW Cohen, RF Murphy
    posted to ner by yas on 2005-11-28 07:56:31 as ** along with 2 people and 1 group bhaddow gaudan T_lab
  • Biomedical named entity recognition using two-phase model based on SVMs.
    J Biomed Inform, Vol. 37, No. 6. (December 2004), pp. 436-447.
    by KJ Lee, YS Hwang, S Kim, HC Rim
    posted to ner by yas on 2006-10-04 04:41:34 as ** along with 1 person and 1 group bhaddow T_lab
  • Two-phase biomedical NE recognition based on SVMs
    (2003), pp. 33-40.
    by Ki-Joong Lee, Young-Sook Hwang, Hae-Chang Rim
    posted to ner by yas on 2006-10-04 04:37:52 as ** along with 1 group T_lab
  • Term identification in the biomedical literature.
    J Biomed Inform, Vol. 37, No. 6. (December 2004), pp. 512-526.
    by M Krauthammer, G Nenadic
    posted to abbreviation-resolution ner review by yas on 2005-09-25 03:39:36 as ** along with 7 people and 4 groups cisevol irenas kslibrarian bourne bhaddow kkaiser akastrin BergmanLab dbk-lab T_lab IEG
  • Automatic term list generation for entity tagging.
    Bioinformatics (25 October 2005)
    by Ted Sandler, Andrew I I Schein, Lyle H H Ungar
    posted to clustering ner by yas on 2005-11-28 06:16:41 as ** along with 1 group T_lab
  • Instance Filtering for entity recognition
    SIGKDD Explor. Newsl., Vol. 7, No. 1. (June 2005), pp. 11-18.
    by Alfio M Gliozzo, Claudio Giuliano, Raffaella Rinaldi
    posted to ner by yas on 2005-10-06 13:37:43 as ** along with 2 people and 1 group arafalov professeur T_lab
  • A simple approach for protein name identification: prospects and limits.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by K Fundel, D Güttler, R Zimmer, J Apostolakis
    posted to ner by yas on 2006-01-24 12:41:39 as ** along with 6 people and 1 group apostola chad_davis bhaddow gaudan incovoma TheresaNiederberger T_lab
  • Various criteria in the evaluation of biomedical named entity recognition.
    BMC Bioinformatics, Vol. 7, No. 1. (24 February 2006)
    by Tzong-Han H Tsai, Shih-Hung H Wu, Wen-Chi C Chou, Yu-Chun C Lin, Ding He, Jieh Hsiang, Ting-Yi Y Sung, Wen-Lian L Hsu
    posted to ner by yas on 2006-03-14 04:31:12 as ** along with 1 person and 2 groups bundschu T_lab generif_paper
  • Identifying gene and protein mentions in text using conditional random fields.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by R McDonald, F Pereira
    posted to ner by yas on 2008-01-07 09:27:56 as ** along with 4 people and 1 group bundschu bhaddow johnkork gmonce generif_paper
  • ProMiner: rule-based protein and gene entity recognition.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by D Hanisch, K Fundel, HT Mevissen, R Zimmer, J Fluck
    posted to ner by yas on 2006-01-24 12:43:07 as ** along with 4 people and 1 group chad_davis zlu incovoma TheresaNiederberger T_lab
  • Gene name identification and normalization using a model organism database
    J. of Biomedical Informatics, Vol. 37, No. 6. (December 2004), pp. 396-410.
    by Alexander A Morgan, Lynette Hirschman, Marc Colosimo, Alexander S Yeh, Jeff B Colombe
    posted to ner by yas on 2007-07-20 12:37:31 as ** along with 4 people and 2 groups helliontroy bhaddow johnkork vlachmore T_lab biomedical-nlp
  • Text Chunking using Regularized Winnow
    (2001), pp. 539-546.
    by Tong Zhang, Fred Damerau, David Johnson
    posted to learning ner sequential by wcohen on 2005-11-09 18:54:02 as ** along with 2 people and 1 group yoavg petrijooste NLP
  • Unsupervised models for named entity classification
    (1999)
    by M Collins, Y Singer
    posted to ner by wcohen on 2005-10-31 23:43:21 as read along with 4 people buescher76 johnkork monster vlachmore
  • 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 bionlp entity hmm named ner recognition by vlachmore on 2007-12-17 17:46:22 as read along with 2 people and 1 group irenas bhaddow dbk-lab
  • Protein names precisely peeled off free text.
    Bioinformatics, Vol. 20 Suppl 1 (4 August 2004)
    by S Mika, B Rost
    posted to bionlp entity named ner protein recognition svms by vlachmore on 2008-08-04 16:32:09 as ** along with 1 person t11
  • 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 bionlp entity named ner recognition by vlachmore on 2007-10-04 18:44:43 as ** along with 3 people and 2 groups irenas caporaso yggdrasil dbk-lab biomedical-nlp
  • Introduction to the CoNLL-2003 shared task: language-independent named entity recognition
    (2003), pp. 142-147.
    by Erik, Fien De Meulder
    posted to entity named ner recognition by vlachmore on 2007-10-04 18:59:44 as read
  • Automatically annotating documents with normalized gene lists.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by J Crim, R McDonald, F Pereira
    posted to bionlp entity named ner recognition by vlachmore on 2007-10-04 19:09:42 as ** along with 2 people and 1 group oannes zlu Regulomics_UCHSC
  • Ranking algorithms for named-entity extraction: boosting and the voted perceptron
    (2001), pp. 489-496.
    by Michael Collins
    posted to boosting entity named ner perceptron ranking recognition by vlachmore on 2007-10-04 18:42:11 as read
  • Multi-criteria-based active learning for named entity recognition
    (2004)
    by Dan Shen, Jie Zhang, Jian Su, Guodong Zhou, Chew-Lim Tan
    posted to active clustering entity learning named ner recognition active_learning by vlachmore on 2007-10-08 13:46:00 as read
  • Rutabaga by any other name: extracting biological names
    Journal of Biomedical Informatics, Vol. 35, No. 4. (August 2002), pp. 247-259.
    by Lynette Hirschman, Alexander A Morgan, Alexander S Yeh
    posted to bionlp bootstrapping entity named ner recognition by vlachmore on 2007-12-17 17:31:51 as **
  • Gene name extraction using FlyBase resources
    (2003), pp. 1-8.
    by Alex Morgan, Lynette Hirschman, Alexander Yeh, Marc Colosimo
    posted to bootstrapping entity flybase gene named ner recognition by vlachmore on 2007-10-04 18:49:40 as read along with 1 person and 1 group helliontroy biomedical-nlp
  • Early results for named entity recognition with conditional random fields
    (2003)
    by A Mccallum, W Li
    posted to conditional crf entity feature fields induction named ner random recognition by vlachmore on 2008-01-21 11:34:34 as ** along with 2 people and 1 group bundschu rstata generif_paper
  • Incorporating non-local information into information extraction systems by Gibbs sampling
    (2005), pp. 363-370.
    by Jenny R Finkel, Trond Grenager, Christopher Manning
    posted to conditional crf fields ner random skip-chain by vlachmore on 2008-05-15 15:39:54 as ** along with 5 people julianpan bhaddow rsantana eegilbert markusd
  • Named entity recognition through classifier combination
    (2003), pp. 168-171.
    by Radu Florian, Abe Ittycheriah, Hongyan Jing, Tong Zhang
    posted to classifier ensemble entity named ner recognition by vlachmore on 2007-10-04 18:55:04 as **
  • Progress on Multi-lingual Named Entity Annotation Guidelines using RDF(S)
    by Nigel Collier, Koichi Takeuchi, Chikashi Nobatal, Junichi Fukumoto, Norihiro Ogata
    posted to entity guidelines named ner recognition by vlachmore on 2007-10-04 18:39:01 as **
  • BANNER: an executable survey of advances in biomedical named entity recognition.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 652-663.
    by R Leaman, G Gonzalez
    posted to bionlp crf entity gene name named ner recognition by vlachmore on 2008-05-09 14:25:32 as ** along with 1 person graciela
  • ATP-dependent chromatin remodeling factors and DNA damage repair
    Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 618, No. 1-2. (1 May 2007), pp. 65-80.
    by Mary A Osley, Toyoko Tsukuda, Jac A Nickoloff
    posted to chromatin damage dna dsb ner repair review by skoch3 on 2008-04-16 07:04:35 as ***** along with 1 group Koch_Lab
  • Unsupervised Named-Entity Recognition: Generating Gazetteers and Resolving Ambiguity
    Advances in Artificial Intelligence (2006), pp. 266-277.
    by David Nadeau, Peter Turney, Stan Matwin
    posted to ner by sids on 2007-08-09 13:37:32 as read along with 3 people and 1 group topher AlisonBabeu brightbyte oktave-labs
  • A document retrieval system for man-machine interaction
    (1964)
    by G Salton
    posted to informationextraction informationretrieval ner nlp textmining by satre on 2008-07-27 11:49:55 as ***
  • BIND--The Biomolecular Interaction Network Database.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 242-245.
    by GD Bader, I Donaldson, C Wolting, BF Ouellette, T Pawson, CW Hogue
    posted to database ner pathway ppi by satre on 2008-07-26 13:52:22 as *** along with 4 people wnpx blackbart ruvido carlk
  • Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data
    (2001), pp. 282-289.
    by John D Lafferty, Andrew Mccallum, Fernando CN Pereira
    posted to crf machinelearning ner pos by satre on 2008-07-26 12:54:24 as *** along with 2 people bsilverthorn dsha
  • Bidirectional inference with the easiest-first strategy for tagging sequence data
    (2005), pp. 467-474.
    by Yoshimasa Tsuruoka, Jun'ichi Tsujii
    posted to machinelearning ner pos by satre on 2008-07-26 12:55:39 as ***
  • Finding the evidence for protein-protein interactions from PubMed abstracts.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by H Jang, J Lim, JH Lim, SJ Park, KC Lee, SH Park
    posted to bionlp ner ppi by satre on 2008-07-22 22:30:50 as ** along with 1 person jyuh
  • OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression
    BMC Bioinformatics, Vol. 9 (31 January 2008), 78.
    by Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner, Helen L Johnson, Philip V Ogren, Bretonnel K Cohen
    posted to biocreative bionlp ner ppi textmining uima by satre on 2008-07-22 14:54:31 as ** along with 4 people and 1 group sobolevnrm thomaskelder jyuh yas baker-group
  • Language independent NER using a maximum entropy tagger
    (2003), pp. 164-167.
    by James R Curran, Stephen Clark
    posted to bionlp memm ner by satre on 2008-07-19 10:53:16 as **
  • Detecting gene relations from Medline abstracts.
    Pac Symp Biocomput (2001), pp. 483-495.
    by M Stephens, M Palakal, S Mukhopadhyay, R Raje, J Mostafa
    posted to bionlp ner ppi textmining by satre on 2008-07-22 21:53:55 as ** along with 1 person and 1 group yas T_lab
  • Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts.
    Genome informatics. Workshop on Genome Informatics, Vol. 10 (1999), pp. 104-112.
    by SK Ng, M Wong
    posted to bionlp dictionary ner pathtext ppi textmining ui-system by satre on 2008-07-21 15:09:46 as read
  • Normalizing biomedical terms by minimizing ambiguity and variability
    BMC Bioinformatics, Vol. 9, No. Suppl 3. (2008)
    by Yoshimasa Tsuruoka, John Mcnaught, Sophia Ananiadou
    posted to bionlp dictionary ner textmining by satre on 2008-07-22 19:05:53 as ** along with 3 people dullhunk vlachmore jyuh
  • Text mining and its potential applications in systems biology.
    Trends in Biotechnology (11 October 2006)
    by Sophia Ananiadou, Douglas B Kell, Junichi Tsujii
    posted to bionlp ner system-biology textmining by satre on 2008-07-27 13:52:18 as *** along with 12 people and 2 groups irenas jfr yas dullhunk fisherp jacky957 daniel_schober dejori pablomendes pmendes TheresaNiederberger alanrw dbk-lab T_lab
  • Learning string similarity measures for gene/protein name dictionary look-up using logistic regression.
    Bioinformatics (12 August 2007)
    by Yoshimasa Tsuruoka, John McNaught, Jun'ichi Tsujii, Sophia Ananiadou
    posted to bionlp dictionary ner rulebased textmining by satre on 2008-07-22 19:04:25 as ** along with 4 people jyuh dullhunk bhaddow vlachmore
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