Tag bionlp [160 articles] Export

Recent papers classified by the tag bionlp.

	Challenges for automatically extracting molecular interactions from full-text articles [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 311. by Tara McIntosh, James Curran posted to nlp ie bionlp biomed by erikv on 2009-10-26 08:11:16 as along with 4 people and 1 group robert85 lmichan daforerog cisevol BergmanLab
	Bioinformatics applications of information extraction from scientific journal articles [My Copy] Journal of Information Science, Vol. 26, No. 2. (1 April 2000), pp. 75-85. by Kevin Humphreys, George Demetriou, Robert Gaizauskas posted to information_extraction_technology bionlp by vlachmore on 2009-10-04 23:11:57 as
	Benchmarking natural-language parsers for biological applications using dependency graphs [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (25 January 2007), 24. by Andrew Clegg, Adrian Shepherd posted to parsing bionlp by vlachmore on 2009-10-02 11:48:41 as along with 7 people and 1 group andrewclegg henk-cul aclegg operon bhaddow kemo TheresaNiederberger dbmi-nlp
	BioInfer: a corpus for information extraction in the biomedical domain [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007), 50. by Sampo Pyysalo, Filip Ginter, Juho Heimonen, et al.Jari Bjorne, Jorma Boberg, Jouni Jarvinen, Tapio Salakoski posted to ppi corpus bionlp by satre on 2009-08-30 13:12:55 as along with 10 people and 1 group arafalov farzanehs sacebro yas lynnefox bhaddow johnkork balex kemo mircea T_lab
	Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge [My Copy] Genome Biology, Vol. 9, No. Suppl 2. (2008) by Martin Krallinger, Alexander Morgan, Larry Smith, et al.Florian Leitner, Lorraine Tanabe, John Wilbur, Lynette Hirschman, Alfonso Valencia posted to biocreative bionlp ie ppi review by satre on 2009-04-20 03:19:55 as along with 3 people yas bouncingbudha yggdrasil
	Task-oriented Evaluation of Syntactic Parsers and Their Representations [My Copy] In Proceedings of ACL-08: HLT (June 2008), pp. 46-54. by Yusuke Miyao, Rune S\aetre, Kenji Sagae, Takuya Matsuzaki, Jun'ichi Tsujii posted to bionlp evaluation interaction parsing protein-protein by vlachmore on 2009-04-08 01:17:24 as along with 3 people and 1 group henk-cul JeremyKahn satre dbmi-nlp
	Challenges in Mapping of Syntactic Representations for Framework- Independent Parser Evaluation [My Copy] by Kenji Sagae, Yusuke Miyao, Takuya Matsuzaki posted to bionlp evaluation interaction parsing protein-protein by vlachmore on 2009-04-08 01:15:56 as
	Empirical distributional semantics: methods and biomedical applications. [My Copy] Journal of biomedical informatics, Vol. 42, No. 2. (13 April 2009), pp. 390-405. by Trevor Cohen, Dominic Widdows posted to bionlp distributional semantics by vlachmore on 2009-03-24 13:21:11 as along with 4 people and 1 group henk-cul briordan mitko dullhunk dbmi-nlp
	The role of syntactic features in protein interaction extraction [My Copy] In DTMBIO '08: Proceeding of the 2nd international workshop on Data and text mining in bioinformatics (2008), pp. 61-68. by Timur Fayruzov, Martine De Cock, Chris Cornelis, Veronique Hoste posted to aimed bionlp corpus informationextraction nlp parsing ppi review by satre on 2009-03-24 08:42:42 as
	BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features [My Copy] BMC Bioinformatics, Vol. 8 (01 September 2007), 325. by Richard T. Tsai, Wen-Chi Chou, Ying-Shan Su, et al.Yu-Chun Lin, Cheng-Lung Sung, Hong-Jie Dai, Irene T. Yeh, Wei Ku, Ting-Yi Sung, Wen-Lian Hsu posted to biomedical bionlp labelling role semantic by vlachmore on 2009-02-11 15:35:22 as along with 6 people and 2 groups Effie yas mircea Barend guhjy irenas NaCTeM T_lab
	Semantic Role Labeling for Protein Transport Predicates [My Copy] BMC Bioinformatics, Vol. 9 (11 June 2008), 277. by Steven Bethard, Zhiyong Lu, James H. Martin, Lawrence Hunter posted to bionlp labelling role semantic by vlachmore on 2009-02-10 16:45:04 as along with 1 person and 1 group Effie NaCTeM
	The Role of Nominalizations in Prepositional Phrase Attachment in GENIA [My Copy] Advances in Artificial Intelligence (2008), pp. 271-282. by Jonathan Schuman, Sabine Bergler posted to attachment bionlp genia nominalizations phrase prepositional by vlachmore on 2009-02-10 13:27:36 as
	Linking entries in protein interaction database to structured text: The FEBS Letters experiment. [My Copy] FEBS Lett (6 March 2008) by Arnaud Ceol, Andrew Chatr-Aryamontri, Luana Licata, Gianni Cesareni posted to bionlp interaction protein by vlachmore on 2009-02-05 14:49:31 as along with 1 person guhjy
	Exploring hedge identification in biomedical literature. [My Copy] Journal of biomedical informatics, Vol. 41, No. 4. (11 August 2008), pp. 636-654. by B. Medlock posted to bionlp hedge speculative by vlachmore on 2009-01-27 14:55:44 as along with 4 people and 1 group henk-cul farzanehs dullhunk hpiwowar dbmi-nlp
	Zone analysis in biology articles as a basis for information extraction [My Copy] International Journal of Medical Informatics, Vol. 75, No. 6. (17 June 2006), pp. 468-487. by Y. Mizuta, A. Korhonen, T. Mullen, N. Collier posted to analysis bionlp extraction information zone by vlachmore on 2009-01-26 10:53:00 as along with 4 people and 3 groups Effie robert85 yas helliontroy NaCTeM T_lab biomedical-nlp
	Extraction of CYP Chemical Interactions from Biomedical Literature Using Natural Language Processing Methods. [My Copy] Journal of chemical information and modeling (21 January 2009) by Dazhi Jiao, David J J. Wild posted to bionlp dependency-parsing lexical-features machine-learning maxent named-entity-recognition parsing pos-tagging relation-extraction syntactic-features by henk-cul on 2009-01-23 14:55:14 as along with 2 people and 1 group sobolevnrm zimbo1 baker-group
	Event extraction from biomedical papers using a full parser. [My Copy] Pac Symp Biocomput (2001), pp. 408-419. by A. Yakushiji, Y. Tateisi, Y. Miyao, J. Tsujii posted to bionlp event extraction by vlachmore on 2009-01-23 13:14:07 as along with 3 people and 2 groups henk-cul helliontroy yggdrasil dbmi-nlp biomedical-nlp
	Unsupervised Event Extraction from Biomedical Text Based on Event and Pattern Information [My Copy] Computational Linguistics and Intelligent Text Processing (2004), pp. 533-536. by Hong-Woo Chun, Young-Sook Hwang, Hae-Chang Rim posted to bionlp even extraction by vlachmore on 2009-01-23 13:12:27 as
	All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. [My Copy] BMC bioinformatics, Vol. 9 Suppl 11 (2008) by A. Airola, S. Pyysalo, J. Björne, T. Pahikkala, F. Ginter, T. Salakoski posted to bionlp graph_kernel interaction protein-protein by vlachmore on 2009-01-21 14:25:26 as along with 1 person mhamada
	Linking genes to literature: text mining, information extraction, and retrieval applications for biology [My Copy] Genome Biology, Vol. 9, No. Suppl 2. (2008), S8. by Martin Krallinger, Alfonso Valencia, Lynette Hirschman posted to bionlp review by henk-cul to the group dbmi-nlp on 2009-01-21 00:53:22 as along with 13 people artaban421 druvus satre daforerog mitko liblab lmichan aberamanda Alois guhjy dullhunk bouncingbudha goettl
	Evaluation of biomedical text-mining systems: lessons learned from information retrieval. [My Copy] Briefings in bioinformatics, Vol. 6, No. 4. (December 2005), pp. 344-356. by William Hersh posted to biomedical bionlp review by henk-cul on 2009-01-06 23:41:58 as along with 6 people and 1 group artaban421 daforerog lmichan svozil aheilbut hpiwowar Bioinformatics
	Facts from text-is text mining ready to deliver? [My Copy] PLoS Biol, Vol. 3, No. 2. (February 2005) by D. Rebholz-Schuhmann, H. Kirsch, F. Couto posted to biomedical bionlp review by henk-cul on 2009-01-06 23:41:01 as along with 16 people and 3 groups arafalov raiyar snuppepuppan irenas yas dullhunk t11 onca dgront caporaso shimah78us daniel_schober dejori adoms jfr hpiwowar dbk-lab T_lab biomedical-nlp
	Status of text-mining techniques applied to biomedical text [My Copy] Drug Discovery Today, Vol. 11, No. 7-8. (April 2006), pp. 315-325. by R. Erhardt, R. Schneider, C. Blaschke posted to biomedical bionlp review by henk-cul on 2009-01-06 23:40:07 as along with 18 people and 2 groups holopoj mitko fisherp liblab svozil Zephyrus ogenex lesikv bqchinh Enro guhjy hpiwowar ibuch mroos TheresaNiederberger akastrin aliekens irenas Bioinformatics AID
	Mining the biomedical literature in the genomic era: an overview. [My Copy] J Comput Biol, Vol. 10, No. 6. (2003), pp. 821-855. by H. Shatkay, R. Feldman posted to biomedical bionlp review by henk-cul on 2009-01-06 23:38:40 as along with 12 people and 3 groups artaban421 mitko lmichan cisevol irenas Enro miguel yas benny balex adoms aheilbut BergmanLab dbk-lab T_lab
	Frontiers of biomedical text mining: current progress [My Copy] Brief Bioinform (30 October 2007), bbm045. by Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, Kevin B. Cohen posted to bionlp review by henk-cul on 2008-12-24 20:19:37 as along with 20 people and 3 groups artaban421 Effie svozil eitanla1 junehlee Keywan arafalov Waderoad vkwn farzanehs bqchinh cisevol guhjy yas dullhunk hpiwowar wchapman yggdrasil TheresaNiederberger irenas Bioinformatics BergmanLab dbmi-nlp
	Text mining and its potential applications in systems biology. [My Copy] Trends Biotechnol (11 October 2006) by Sophia Ananiadou, Douglas B B. Kell, Jun-Ichi I. Tsujii posted to bionlp review by henk-cul on 2008-12-24 20:18:31 as along with 17 people and 3 groups artaban421 eesruiz liblab guhjy irenas jfr yas dullhunk fisherp jacky957 daniel_schober dejori pablomendes pmendes TheresaNiederberger alanrw satre ImagCom - Biomedical Text Computing dbk-lab T_lab
	Hairpins in bookstacks: Information retrieval from biomedical text [My Copy] Brief Bioinform, Vol. 6, No. 3. (1 January 2005), pp. 222-238. by Hagit Shatkay posted to bionlp ir review by henk-cul to the group dbmi-nlp on 2008-12-24 20:16:38 as along with 7 people and 3 groups artaban421 mitko eesruiz svozil guhjy yas hpiwowar ImagCom - Biomedical Text Computing Bioinformatics T_lab
	Getting started in text mining. [My Copy] PLoS computational biology, Vol. 4, No. 1. (1 January 2008), e20. by K. Bretonnel Cohen, Lawrence Hunter posted to biomedical bionlp review by henk-cul on 2008-12-24 20:14:28 as along with 23 people and 2 groups artaban421 daforerog ajholanda lmichan eesruiz ogenex robert85 jarek lesikv guhjy y4su0 yas dullhunk hpiwowar sebastien_vigneau shigepong cjeans wchapman sci91078 jfr TheresaNiederberger ulmer quianominorleo ImagCom - Biomedical Text Computing dbmi-nlp
	Nominalization and alternations in biomedical language. [My Copy] PLoS ONE, Vol. 3, No. 9. (2008) by K. B. Cohen, M. Palmer, L. Hunter posted to alternations bionlp nominalizations by vlachmore on 2008-12-23 12:03:10 as along with 3 people and 2 groups Effie henk-cul yas NaCTeM dbmi-nlp
	Text mining for biology - the way forward: opinions from leading scientists [My Copy] Genome Biology, Vol. 9, No. Suppl 2. (2008), S7. by Russ Altman, Casey Bergman, Judith Blake, et al.Christian Blaschke, Aaron Cohen, Frank Gannon, Les Grivell, Udo Hahn, William Hersh, Lynette Hirschman, Lars Jensen, Martin Krallinger, Barend Mons, Sean O'Donoghue, Manuel Peitsch, Dietrich R. Schuhmann, Hagit Shatkay, Alfonso Valencia posted to biomedical bionlp review by henk-cul to the group dbmi-nlp on 2008-12-02 21:45:48 as along with 13 people lmichan artaban421 abhishek_tiwari daforerog kiekyon liblab fisherp hpiwowar guhjy barriot imrchen fgibson dullhunk
	Text Mining [My Copy] Bioinformatics (2008), pp. 471-491. by Andrew B. Clegg, Adrian J. Shepherd posted to biomedical bionlp review by henk-cul to the group dbmi-nlp on 2008-11-24 18:58:22 as along with 5 people lyss artaban421 q_w_e_r_t_y piobyz zimbo1
	Semantic Annotation of Biomedical Literature Using Google [My Copy] Computational Science and Its Applications – ICCSA 2005 (2005), pp. 327-337. by Rune Sætre, Amund Tveit, Tonje S. Steigedal, Astrid Lægreid posted to bioinformatics bionlp textmining by mircea on 2008-11-05 21:51:29 as
	Computational biology resources lack persistence and usability. [My Copy] PLoS computational biology, Vol. 4, No. 7. (July 2008) by S. Veretnik, J. L. Fink, P. E. Bourne posted to nsf09 bionlp empiricism science usability by spinaltap526 on 2008-10-27 18:57:25 as along with 9 people and 1 group wangbo vkwn jfr xjlibod dullhunk hpiwowar nuin fgibson maximilianh BergmanLab
	FACTA: a text search engine for finding associated biomedical concepts. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 21. (1 November 2008), pp. 2559-2560. by Y. Tsuruoka, J. Tsujii, S. Ananiadou posted to annotation bionlp ie informationextraction informationretrieval pathtext pathway ppi textmining by satre on 2008-10-27 05:57:02 as along with 11 people and 2 groups artaban421 idonaldson Effie sobolevnrm ajaymalik henk-cul Gaetan wisdom_love dullhunk nuin guhjy NaCTeM baker-group
	Biomedical Language Processing: Perspective What's Beyond PubMed? [My Copy] Molecular Cell, Vol. 21, No. 5. (03 March 2006), pp. 589-594. by Lawrence Hunter, Bretonnel K. Cohen posted to bionlp survey by farzanehs on 2008-10-17 15:13:48 as along with 16 people and 3 groups billhao Gaetan artaban421 robert85 lmichan gavinhoran ogenex henk-cul irenas andytseng yas hpiwowar caporaso jacky957 TheresaNiederberger satre dbk-lab T_lab biomedical-nlp
	Automating curation using a natural language processing pipeline [My Copy] Genome Biology, Vol. 9, No. Suppl 2. (2008) by Beatrice Alex, Claire Grover, Barry Haddow, et al.Mijail Kabadjov, Ewan Klein, Michael Matthews, Richard Tobin, Xinglong Wang posted to bc2 bionlp curation ner relation-extraction term text-mining by bhaddow on 2008-09-12 17:40:32 as along with 1 person arafalov
	Protein names precisely peeled off free text. [My Copy] 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 2 people and 1 group eesruiz t11 ImagCom - Biomedical Text Computing
	Literature mining for the biologist: from information retrieval to biological discovery [My Copy] Nature Reviews Genetics, Vol. 7, No. 2. (01 February 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 46 people and 4 groups MARCOUNAM eudominguezmartin sm-rush LEONRANGEL artaban421 rocling bertelsen virolog dipenps druvus Zephyrus fgibson psique lmichan cisevol ilyashl henk-cul daforerog isimpson dansullivanblk yggdrasil Enro guhjy kuhn yas dullhunk hpiwowar dgront caporaso zlu jacky957 lynnefox jdiggans cjeans ghattem michaelmampaey dejori jandot mircea farzanehs larsjuhljensen adoms skumagai TheresaNiederberger akastrin ibuch BergmanLab T_lab biomedical-nlp ADMiRes
	Recent advances in natural language processing for biomedical applications. [My Copy] 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 [My Copy] In ACL '06: Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the ACL (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 [My Copy] 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 2 people and 1 group henk-cul guhjy dbmi-nlp
	Developing a Robust Part-of-Speech Tagger for Biomedical Text [My Copy] Advances in Informatics (2005), pp. 382-392. by Yoshimasa Tsuruoka, Yuka Tateishi, Jin-Dong Kim, et al.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 along with 1 person farzanehs
	APID: Agile Protein Interaction DataAnalyzer. [My Copy] 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 along with 1 person chad_davis
	Mining MEDLINE: abstracts, sentences, or phrases? [My Copy] 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
	BioRAT: extracting biological information from full-length papers [My Copy] Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 3206-3213. by David P. A. Corney, Bernard F. Buxton, William B. Langdon, David T. Jones posted to bionlp fulltext ie informationextraction pos by satre on 2008-07-24 14:16:43 as along with 13 people and 7 groups robert85 svozil cisevol arafalov camster snuppepuppan irenas Enro guhjy A_Olympia helliontroy massivemayhem sobolevnrm Bioinformatics BergmanLab 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 [My Copy] 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
	AliBaba: PubMed as a graph. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 19. (1 October 2006), pp. 2444-2445. by C. Plake, T. Schiemann, M. Pankalla, J. Hakenberg, U. Leser posted to bionlp ppi textmining by satre on 2008-07-22 22:43:17 as along with 7 people and 2 groups daforerog Scis0000002 guhjy ianturton avivagabriel dagmar A_Hoogendam dIEMoSIRIS compneur
	Finding the evidence for protein-protein interactions from PubMed abstracts. [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006) by H. Jang, J. Lim, J. H. Lim, S. J. Park, K. C. Lee, S. H. Park posted to bionlp ner ppi by satre on 2008-07-22 22:30:50 as along with 1 person guhjy
	Discovering patterns to extract protein-protein interactions from the literature: Part II. [My Copy] 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 3 people arafalov davidandrzej natsu
	Detecting gene relations from Medline abstracts. [My Copy] 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 2 people and 2 groups henk-cul yas dbmi-nlp T_lab

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ner	38
ppi	32
textmining	29
review	21
corpus	15
parsing	15
entity	13
named	12
recognition	12
gene	11
annotation	10
bioinformatics	10
biomedical	10
nlp	10
article1	7
extraction	7
normalization	7
rulebased	7
svm	7
dictionary	6
informationextraction	6
relation-extraction	6
interaction	5
nsf09	5
pathway	5
term	5
bc1	4
biocreative	4
crf	4
genia	4
hmm	4
ie	4
information	4
protein-protein	4
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adaptation	3
aimed	3
biology	3
clustering	3
curation	3
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mining	3
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pathtext	3
retrieval	3
search	3
semantic	3
shared	3
survey	3
task	3
text-mining	3
ui-system	3
bootstrapping	2
cathywu	2
corpora	2
distributional	2
evaluation	2
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labelling	2
maxent	2
nominalizations	2
ontology	2
pos-tagging	2
protein	2
pubmed	2
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svms	2
system-biology	2
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tagging	2
text	2
uima	2
verb	2
algorithm	1
bioinfer	1
biomed	1
biomedicine	1
blast	1
classification	1
figures	1
gene_ontology	1
graph	1
graph_kernel	1
hedge	1
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information-extraction	1
latent	1
machines	1
pas	1
pasbio	1
phrase	1
semantics	1
tokenisation	1
top5	1
vector	1
zone	1

Tag bionlp [160 articles] Export

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