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satre bionlp [40 articles]

Recent papers added to satre library classified by the tag bionlp. You can also see everyone's bionlp.
  • Task-oriented Evaluation of Syntactic Parsers and Their Representations
    (June 2008), pp. 46-54.
    by Yusuke Miyao, Rune Sætre, Kenji Sagae, Takuya Matsuzaki, Jun'ichi Tsujii
    posted to bionlp parsing ppi by satre on 2008-07-29 13:55:10 as read along with 1 person JeremyKahn
  • Literature mining for the biologist: from information retrieval to biological discovery
    Nature Reviews Genetics, Vol. 7, No. 2. (2006), pp. 119-129.
    by Lars J Jensen, Jasmin Saric, Peer Bork
    posted to annotation bionlp ner nlp pathway ppi review survey system-biology by satre on 2008-07-27 14:17:17 as ** along with 26 people and 3 groups yggdrasil Enro jyuh kuhn yas dullhunk hpiwowar dgront caporaso zlu jacky957 lynnefox jdiggans cjeans ghattem michaelmampaey dejori jandot mircea farzanehs larsjuhljensen adoms skumagai TheresaNiederberger akastrin ibuch T_lab biomedical-nlp ADMiRes
  • 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
  • Recent advances in natural language processing for biomedical applications.
    International Journal of Medical Informatics, Vol. 75, No. 6. (30 June 2006), pp. 413-417.
    by Nigel Collier, Adeline Nazarenko, Robert Baud, Patrick Ruch
    posted to biology bionlp medicalrecords review survey by satre on 2008-07-27 08:23:58 as ** along with 2 people and 1 group libah yas T_lab
  • Automatic classification of verbs in biomedical texts
    (2006), pp. 345-352.
    by Anna Korhonen, Yuval Krymolowski, Nigel Collier
    posted to bionlp corpus dictionary informationextraction nlp parsing rulebased by satre on 2008-07-27 04:03:29 as ** along with 1 person vlachmore
  • An open-source framework for large-scale, flexible evaluation of biomedical text mining systems
    Journal of Biomedical Discovery and Collaboration, Vol. 3 (29 January 2008), 1.
    by William A Baumgartner, Bretonnel K Cohen, Lawrence Hunter
    posted to bionlp nlp uima by satre on 2008-07-26 18:16:33 as ** along with 1 person jyuh
  • Developing a Robust Part-of-Speech Tagger for Biomedical Text
    Advances in Informatics (2005), pp. 382-392.
    by Yoshimasa Tsuruoka, Yuka Tateishi, Jin-Dong Kim, Tomoko Ohta, John Mcnaught, Sophia Ananiadou, Jun’ichi Tsujii
    posted to bionlp maximum-entropy-modeling ner parsing ppi textmining by satre on 2008-07-26 14:21:22 as **
  • APID: Agile Protein Interaction DataAnalyzer.
    Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006)
    by C Prieto, J De Las Rivas
    posted to bionlp database ppi ui-system by satre on 2008-07-26 14:17:43 as **
  • Mining MEDLINE: abstracts, sentences, or phrases?
    Pac Symp Biocomput (2002), pp. 326-337.
    by J Ding, D Berleant, D Nettleton, E Wurtele
    posted to annotation bionlp informationextraction ppi textmining by satre on 2008-07-24 14:39:52 as ** along with 4 people and 2 groups yas zlu bundschu ianturton T_lab generif_paper
  • Biomedical Language Processing: What's Beyond PubMed?
    Mol Cell, Vol. 21, No. 5. (3 March 2006), pp. 589-594.
    by L Hunter, KB Cohen
    posted to annotation bionlp corpus informationextraction ppi review textmining by satre on 2008-07-24 14:20:59 as ** along with 7 people and 3 groups irenas andytseng yas hpiwowar caporaso jacky957 TheresaNiederberger dbk-lab T_lab biomedical-nlp
  • BioRAT: extracting biological information from full-length papers.
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 3206-3213.
    by DP Corney, BF Buxton, WB Langdon, DT Jones
    posted to bionlp fulltext ie informationextraction pos by satre on 2008-07-24 14:16:43 as ** along with 9 people and 5 groups camster snuppepuppan irenas Enro jyuh A_Olympia helliontroy massivemayhem sobolevnrm Philosophy_of_Information dbk-lab Blog_and_Wiki_Research biomedical-nlp baker-group
  • Literature mining and database annotation of protein phosphorylation using a rule-based system
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2759-2765.
    by Z Hu, M Narayanaswamy, K Ravikumar, K Vijay-Shanker, C Wu
    posted to annotation bionlp phosphorylation rulebased textmining by satre on 2008-07-24 14:14:05 as *** along with 3 people benny zlu jacky957
  • Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example
    No. 13. (2008), pp. 616-627.
    by Yoshinobu Kano, Ngan Nguyen, Rune Saetre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiro Matsubayashi, Sophia Ananiadou, Jun'ichi Tsujii
    posted to aimed bionlp corpus dictionary ner parsing ppi svm textmining uima by satre on 2008-07-23 11:52:33 as read along with 1 group dbmi-nlp
  • ALIBABA: PubMed as a graph
    Bioinformatics, Vol. 22, No. 19. (1 October 2006), pp. 2444-2445.
    by Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jorg Hakenberg, Ulf Leser
    posted to bionlp ppi textmining by satre on 2008-07-22 22:43:17 as ** along with 5 people and 2 groups jyuh ianturton avivagabriel dagmar A_Hoogendam dIEMoSIRIS compneur
  • 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
  • Discovering patterns to extract protein-protein interactions from the literature: Part II.
    Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3294-3300.
    by Y Hao, X Zhu, M Huang, M Li
    posted to biocreative bionlp corpus parsing ppi textmining by satre on 2008-07-22 22:21:54 as *** along with 2 people davidandrzej natsu
  • 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
  • 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
  • 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
  • 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 bionlp parsing ppi textmining by satre on 2008-07-22 18:59:46 as *** along with 5 people and 1 group irenas Enro miguel natsu zlu dbk-lab
  • A text-mining perspective on the requirements for electronically annotated abstracts.
    FEBS letters, Vol. 582, No. 8. (9 April 2008), pp. 1178-1181.
    by F Leitner, A Valencia
    posted to annotation biocreative bionlp ppi textmining by satre on 2008-07-22 16:27:49 as *** along with 2 people ianturton 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
  • PIE: an online prediction system for protein-protein interactions from text
    Nucl. Acids Res. (28 May 2008), gkn281.
    by Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, Byoung-Tak Zhang
    posted to bionlp ppi textmining by satre on 2008-07-22 14:40:56 as ** along with 3 people neils tharris jyuh
  • Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.
    BMC Bioinformatics, Vol. 6, No. 1. (7 June 2005)
    by James W Cooper, Aaron Kershenbaum
    posted to bionlp ibm ppi rulebased svm textmining by satre on 2008-07-22 12:46:44 as *** along with 3 people snuppepuppan pggm chad_davis
  • Automatic extraction of biological information from scientific text: protein-protein interactions.
    Proc Int Conf Intell Syst Mol Biol (1999), pp. 60-67.
    by C Blaschke, MA Andrade, C Ouzounis, A Valencia
    posted to bionlp ner ppi textmining by satre on 2008-07-22 11:57:46 as *** along with 6 people and 3 groups Enro miguel yas helliontroy bundschu TheresaNiederberger T_lab biomedical-nlp generif_paper
  • Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts.
    Genome informatics. Workshop on Genome Informatics, Vol. 9 (1998), pp. 62-71.
    by T Sekimizu, HS Park, J Tsujii
    posted to bionlp parsing ppi rulebased textmining by satre on 2008-07-22 08:25:43 as **
  • Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model.
    International journal of bioinformatics research and applications, Vol. 4, No. 1. (2008), pp. 64-80.
    by D Zhou, Y He, CK Kwoh
    posted to bionlp ppi svm textmining by satre on 2008-07-22 07:58:17 as **
  • Extracting Protein-Protein Interactions from the Literature Using the Hidden Vector State Model
    Computational Science – ICCS 2006 (2006), pp. 718-725.
    by Deyu Zhou, Yulan He, Chee Kwoh
    posted to bionlp ppi svm textmining by satre on 2008-07-22 03:07:27 as ***
  • Extracting Protein-Protein Interaction Information from Biomedical Text with SVM
    IEICE - Trans. Inf. Syst., Vol. E89-D, No. 8. (2006), pp. 2464-2466.
    by Tomohiro Mitsumori, Masaki Murata, Yasushi Fukuda, Kouichi Doi, Hirohumi Doi
    posted to bionlp ppi svm textmining by satre on 2008-07-22 03:03:44 as ** along with 1 person farzanehs
  • Accomplishments and challenges in literature data mining for biology.
    Bioinformatics, Vol. 18, No. 12. (December 2002), pp. 1553-1561.
    by L Hirschman, JC Park, J Tsujii, L Wong, CH Wu
    posted to bionlp textmining by satre on 2008-07-21 15:11:32 as ** along with 7 people and 6 groups irenas Enro yas benny kehan caporaso vlachmore dbk-lab biodiversity_conservation Bioinformatics T_lab biomedical-nlp GrassBase
  • 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
  • Assisted curation: does text mining really help?
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 556-567.
    by B Alex, C Grover, B Haddow, M Kabadjov, E Klein, M Matthews, S Roebuck, R Tobin, X Wang
    posted to bionlp ner ppi by satre on 2008-07-20 11:40:07 as *** along with 1 person and 1 group henk-cul dbmi-nlp
  • 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 **
  • RelExRelation extraction using dependency parse trees
    Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 365-371.
    by Fundel, Katrin, Kuffner, Robert, Zimmer, Ralf
    posted to bionlp parsing ppi textmining by satre on 2008-07-19 07:12:54 as ** along with 5 people chad_davis bhaddow vlachmore TheresaNiederberger gilesc
  • Learning Relations from Biomedical Corpora Using Dependency Trees
    Knowledge Discovery and Emergent Complexity in Bioinformatics (2007), pp. 61-80.
    by Sophia Katrenko, Pieter Adriaans
    posted to aimed bionlp ppi textmining by satre on 2008-07-19 07:01:10 as read
  • New challenges for text mining: mapping between text and manually curated pathways.
    BMC bioinformatics, Vol. 9 Suppl 3 (2008)
    by K Oda, JD Kim, T Ohta, D Okanohara, T Matsuzaki, Y Tateisi, J Tsujii
    posted to bionlp pathtext ppi textmining by satre on 2008-07-19 04:18:01 as read along with 2 people mariakmejia maralena
  • A survey of current work in biomedical text mining.
    Brief Bioinform, Vol. 6, No. 1. (March 2005), pp. 57-71.
    by AM Cohen, WR Hersh
    posted to bionlp review textmining by satre on 2008-07-18 17:59:15 as *** along with 17 people and 7 groups irenas carlblesius route145 yas natsu t11 hpiwowar fisherp biblio24 bhaddow johnkork c061978 kkaiser benfqt farzanehs lillejul TheresaNiederberger dbk-lab Blog_and_Wiki_Research mgh-lcs hst-bmi T_lab Evidence-based-medicine IEG
  • PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine.
    BMC Bioinformatics, Vol. 4 (27 March 2003)
    by I Donaldson, J Martin, B de Bruijn, C Wolting, V Lay, B Tuekam, S Zhang, B Baskin, GD Bader, K Michalickova, T Pawson, CW Hogue
    posted to bionlp ppi svm ui-system by satre on 2008-07-18 17:52:28 as *** along with 3 people chad_davis blackbart bouncingbudha
  • 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 bionlp dictionary ppi rulebased by satre on 2008-07-18 14:30:36 as ** along with 7 people and 3 groups irenas yas blackbart helliontroy zlu bundschu yggdrasil T_lab biomedical-nlp generif_paper
  • A critical review of PASBio's argument structures for biomedical verbs
    BMC Bioinformatics, Vol. 7, No. Suppl 3. (2006)
    by Bretonnel K Cohen, Lawrence Hunter
    posted to bionlp corpus pasbio by satre on 2008-06-02 07:49:10 as *** along with 1 person yas
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