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yggdrasil's library [324 articles]

Recent papers added to yggdrasil's library.
  • OBO-Edit - An Ontology Editor for Biologists.
    Bioinformatics (1 June 2007)
    by John Day-Richter, Midori A A Harris, Melissa Haendel, Suzanna Lewis
    posted to no-tag by yggdrasil on 2008-10-10 10:44:52 as ** along with 8 people and 1 group leeleong jyuh dullhunk sebastien_vigneau leechuck sgoetz sobolevnrm niallhaslam baker-group
  • Gene mention normalization and interaction extraction with context models and sentence motifs
    Genome Biology, Vol. 9, No. Suppl 2. (2008)
    by Jorg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, Michael Schroeder
    posted to no-tag by yggdrasil on 2008-10-09 14:26:03 as **
  • Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
    Genome Biology, Vol. 9, No. Suppl 2. (2008)
    by Martin Krallinger, Alexander Morgan, Larry Smith, Florian Leitner, Lorraine Tanabe, John Wilbur, Lynette Hirschman, Alfonso Valencia
    posted to no-tag by yggdrasil on 2008-10-09 14:18:50 as **
  • Terminologies for text-mining; an experiment in the lipoprotein metabolism domain.
    BMC bioinformatics, Vol. 9 Suppl 4 (2008)
    by D Alexopoulou, T Wächter, L Pickersgill, C Eyre, M Schroeder
    posted to no-tag by yggdrasil on 2008-10-09 14:08:32 as ** along with 2 people jyuh mariakmejia
  • Overview of BioCreative II gene normalization
    Genome Biology, Vol. 9, No. Suppl 2. (2008)
    by Alexander Morgan, Zhiyong Lu, Xinglong Wang, Aaron Cohen, Juliane Fluck, Patrick Ruch, Anna Divoli, Katrin Fundel, Robert Leaman, Jorg Hakenberg, Chengjie Sun, Heng H Liu, Rafael Torres, Michael Krauthammer, William Lau, Hongfang Liu, Chun N Hsu, Martijn Schuemie, Bretonnel K Cohen, Lynette Hirschman
    posted to no-tag by yggdrasil on 2008-10-01 14:49:43 as **
  • A large-scale in situ screen provides molecular evidence for the induction of eye anterior segment structures by the developing lens.
    Developmental biology, Vol. 231, No. 1. (1 March 2001), pp. 63-76.
    by CJ Thut, RB Rountree, M Hwa, DM Kingsley
    posted to no-tag by yggdrasil on 2008-09-05 15:01:50 as **
  • Literature mining for the biologist: from information retrieval to biological discovery
    Nature Reviews Genetics, Vol. 7, No. 2., pp. 119-129.
    by Lars J Jensen, Jasmin Saric, Peer Bork
    posted to no-tag by yggdrasil on 2008-09-05 14:26:10 as ** along with 27 people and 3 groups dansullivanblk Enro jyuh kuhn yas dullhunk hpiwowar dgront caporaso zlu jacky957 lynnefox jdiggans cjeans ghattem michaelmampaey dejori jandot mircea farzanehs larsjuhljensen adoms skumagai TheresaNiederberger satre akastrin ibuch T_lab biomedical-nlp ADMiRes
  • Zea mays ontology--a database of international terms.
    Trends in plant science, Vol. 8, No. 11. (November 2003), pp. 517-520.
    by PL Vincent, EH Coe, ML Polacco
    posted to no-tag by yggdrasil on 2008-09-05 14:24:31 as **
  • Functional annotation of the Arabidopsis genome using controlled vocabularies.
    Plant Physiol, Vol. 135, No. 2. (June 2004), pp. 745-755.
    by TZ Berardini, S Mundodi, L Reiser, E Huala, M Garcia-Hernandez, P Zhang, LA Mueller, J Yoon, A Doyle, G Lander, N Moseyko, D Yoo, I Xu, B Zoeckler, M Montoya, N Miller, D Weems, SY Rhee
    posted to no-tag by yggdrasil on 2008-09-05 14:20:36 as ** along with 1 person dullhunk
  • An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature.
    Mechanisms of development, Vol. 74, No. 1-2. (June 1998), pp. 111-120.
    by JL Bard, MH Kaufman, C Dubreuil, RM Brune, A Burger, RA Baldock, DR Davidson
    posted to no-tag by yggdrasil on 2008-09-05 14:10:48 as **
  • 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 no-tag by yggdrasil on 2008-07-29 10:07:08 as ** along with 6 people and 4 groups irenas yas hpiwowar kkaiser vlachmore TheresaNiederberger dbk-lab T_lab IEG dbmi-nlp
  • An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by EB Camon, DG Barrell, EC Dimmer, V Lee, M Magrane, J Maslen, D Binns, R Apweiler
    posted to no-tag by yggdrasil on 2008-05-26 17:37:43 as ** along with 4 people and 2 groups yas helliontroy CitoJam adoms T_lab biomedical-nlp
  • TREC 2005 Genomics Track Overview
    (2005)
    by W Hersh, A Cohen, J Yang, RT Bhupatiraju, P Roberts, M Hearst
    posted to no-tag by yggdrasil on 2008-05-26 14:06:45 as ** along with 1 person and 1 group helliontroy biomedical-nlp
  • Assisted Curation: Does Text Mining Really Help?
    (January 2008)
    by Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjov, Ewan Klein, Michael Matthews, Stuart Roebuck, Richard Tobin, Xinglong Wang
    posted to no-tag by yggdrasil on 2008-05-26 10:28:13 as ** along with 1 person and 1 group bhaddow Text Analytics
  • Assessing the accuracy of prediction algorithms for classification: an overview.
    Bioinformatics, Vol. 16, No. 5. (2000), pp. 412-24.
    by P Baldi, S Brunak, Y Chauvin, CA Andersen, H Nielsen
    posted to no-tag by yggdrasil on 2008-05-24 14:14:55 as ** along with 1 person elfar
  • Semantically linking and browsing PubMed abstracts with gene ontology
    BMC Genomics, Vol. 9, No. Suppl 1. (2008)
    by Bhanu Vanteru, Jahangheer Shaik, Mohammed Yeasin
    posted to no-tag by yggdrasil on 2008-05-22 09:02:37 as ** along with 3 people A_Hoogendam adoms jyuh
  • Learning statistical models for annotating proteins with function information using biomedical text.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by S Ray, M Craven
    posted to no-tag by yggdrasil on 2008-05-21 10:54:26 as ** along with 3 people and 2 groups irenas helliontroy bhaddow dbk-lab biomedical-nlp
  • Mining protein function from text using term-based support vector machines.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by SB Rice, G Nenadic, BJ Stapley
    posted to no-tag by yggdrasil on 2008-05-20 21:27:14 as ** along with 1 person and 1 group helliontroy biomedical-nlp
  • Protein annotation as term categorization in the gene ontology using word proximity networks.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by K Verspoor, J Cohn, C Joslyn, S Mniszewski, A Rechtsteiner, LM Rocha, T Simas
    posted to no-tag by yggdrasil on 2008-05-20 21:26:14 as ** along with 2 people and 1 group helliontroy gaudan biomedical-nlp
  • Automatic recognition of multi-word terms:. the C-value/NC-value method
    International Journal on Digital Libraries, Vol. V3, No. 2. (2000), pp. 115-130.
    by Katerina Frantzi, Sophia Ananiadou, Hideki Mima
    posted to no-tag by yggdrasil on 2008-05-20 21:11:15 as ** along with 4 people katychuang florianleitner leechuck bross
  • A sentence sliding window approach to extract protein annotations from biomedical articles.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by M Krallinger, M Padron, A Valencia
    posted to no-tag by yggdrasil on 2008-05-20 19:26:41 as ** along with 1 person and 1 group helliontroy biomedical-nlp
  • Evaluation of BioCreAtIvE assessment of task 2.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by C Blaschke, EA Leon, M Krallinger, A Valencia
    posted to no-tag by yggdrasil on 2008-05-20 19:02:35 as ** along with 4 people and 2 groups leechuck yas helliontroy zlu T_lab biomedical-nlp
  • Data-poor categorization and passage retrieval for Gene Ontology annotation in Swiss-Prot.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by F Ehrler, A Geissbühler, A Jimeno, P Ruch
    posted to no-tag by yggdrasil on 2008-05-20 18:59:12 as ** along with 2 people and 2 groups irenas helliontroy dbk-lab biomedical-nlp
  • Extracting functional annotations of proteins based on hybrid text mining approaches.
    (2004)
    by Jung H Chiang, Hsu C Yu
    posted to no-tag by yggdrasil on 2008-05-20 16:45:21 as ** along with 1 person and 1 group caporaso biomedical-nlp
  • GOAnnotator: linking protein GO annotations to evidence text
    Journal of Biomedical Discovery and Collaboration, Vol. 1 (20 December 2006), 19.
    by Francisco M Couto, Mario J Silva, Vivian Lee, Emily Dimmer, Evelyn Camon, Rolf Apweiler, Harald Kirsch, Dietrich Rebholz-Schuhmann
    posted to no-tag by yggdrasil on 2008-05-20 09:50:44 as ** along with 2 people dullhunk clockett
  • Overview of BioCreAtIvE: critical assessment of information extraction for biology.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by L Hirschman, A Yeh, C Blaschke, A Valencia
    posted to benchmark by yggdrasil on 2008-05-19 17:59:31 as ** along with 7 people and 2 groups yas helliontroy bhaddow johnkork leechuck vlachmore satre T_lab biomedical-nlp
  • Finding genomic ontology terms in text using evidence content.
    BMC Bioinformatics, Vol. 6 Suppl 1 (2005)
    by FM Couto, MJ Silva, PM Coutinho
    posted to concept_recognition go by yggdrasil on 2008-05-19 17:55:34 as ** along with 4 people and 3 groups irenas oannes helliontroy josepe dbk-lab biomedical-nlp Regulomics_UCHSC
  • A Maximum Entropy Approach to Natural Language Processing
    Computational Linguistics, Vol. 22, No. 1. (1996), pp. 39-71.
    by Adam L Berger, Stephen D Della Pietra, Vincent JD Della Pietra
    posted to me by yggdrasil on 2008-05-16 15:50:35 as ** along with 9 people dmolla mafwood anoopsarkar halacsy erikv whym rayzhang ananthrk FabianNe
  • A stochastic parts program and noun phrase parser for unrestricted text
    (1988), pp. 136-143.
    by Kenneth W Church
    posted to no-tag by yggdrasil on 2008-05-16 13:42:34 as ** along with 1 person and 1 group yoavg NLP
  • Internal and external evidence in the identification and semantic categorization of proper names
    (1996), pp. 21-39.
    by David D Mcdonald
    posted to ner rules by yggdrasil on 2008-05-16 12:56:41 as **
  • 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 machine-learing rules by yggdrasil on 2008-05-16 11:09:42 as ** along with 3 people and 2 groups irenas caporaso vlachmore dbk-lab biomedical-nlp
  • 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 no-tag by yggdrasil on 2008-05-16 10:19:12 as ** along with 1 person and 1 group irenas dbk-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 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
  • BioIE: retargetable information extraction and ontological annotation of biological interactions from the literature.
    J Bioinform Comput Biol, Vol. 2, No. 3. (September 2004), pp. 551-568.
    by JJ Kim, JC Park
    posted to no-tag by yggdrasil on 2008-05-15 10:10:16 as ** along with 1 person and 1 group irenas dbk-lab
  • Genescene: An ontology-enhanced integration of linguistic and co-occurrence based relations in biomedical texts: Research Articles
    J. Am. Soc. Inf. Sci. Technol., Vol. 56, No. 5. (March 2005), pp. 457-468.
    by Gondy Leroy, Hsinchun Chen
    posted to concept recognition by yggdrasil on 2008-05-15 09:08:42 as ***** along with 2 people and 2 groups irenas helliontroy dbk-lab biomedical-nlp
  • Text mining and ontologies in biomedicine: making sense of raw text.
    Brief Bioinform, Vol. 6, No. 3. (September 2005), pp. 239-251.
    by I Spasic, S Ananiadou, J McNaught, A Kumar
    posted to no-tag by yggdrasil on 2008-05-15 08:35:55 as ** along with 7 people and 3 groups irenas andytseng yas hpiwowar helliontroy johnkork daniel_schober dbk-lab T_lab biomedical-nlp
  • UIMA: an architectural approach to unstructured information processing in the corporate research environment
    Nat. Lang. Eng., Vol. 10, No. 3-4. (2004), pp. 327-348.
    by David Ferrucci, Adam Lally
    posted to no-tag by yggdrasil on 2008-05-12 13:55:42 as ** along with 1 person zlu
  • Question Answering in Biomedicine
    (2003)
    by Pierre Zweigenbaum
    posted to file-import-08-05-12 question_answering by yggdrasil on 2008-05-12 13:25:22 as **
  • Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data
    (2006), pp. 16-27.
    by Annette Höglund, Torsten Blum, Scott Brady, Pierre Dönnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay
    posted to file-import-08-05-12 by yggdrasil on 2008-05-12 13:09:25 as **
  • Predicting Gene Functions from Text Using a Cross-Species Approach
    (2006), pp. 88-99.
    by Emilia Stoica, Marti A Hearst
    posted to recognition term by yggdrasil on 2008-05-12 13:04:44 as *****
  • Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature.
    (2007), pp. 292-303.
    by Aurélie Névéol, Sonya E Shooshan, Susanne M Humphrey, Thomas C Rindflesch, Alan R Aronson
    edited by Russ B Altman, Keith A Dunker, Lawrence Hunter, Tiffany Murray, Teri E Klein
    posted to recognition summarization term by yggdrasil on 2008-05-12 12:48:38 as ** along with 1 person bundschu
  • Frontiers of biomedical text mining: current progress
    Brief Bioinform (30 October 2007), bbm045.
    by Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, Kevin B Cohen
    posted to survey textming by yggdrasil on 2008-05-12 12:22:22 as read along with 8 people and 2 groups cisevol jyuh yas dullhunk hpiwowar wchapman TheresaNiederberger irenas BergmanLab dbmi-nlp
  • Event extraction from biomedical papers using a full parser.
    Pac Symp Biocomput (2001), pp. 408-419.
    by A Yakushiji, Y Tateisi, Y Miyao, J Tsujii
    posted to no-tag by yggdrasil on 2008-05-10 17:32:33 as ** along with 1 person and 1 group helliontroy biomedical-nlp
  • Recognizing noun phrases in biomedical text: an evaluation of lab prototypes and commercial chunkers
    BMC Bioinformatics, Vol. 7, No. 1. (4 April 2005)
    by J Wermter, J Fluck, J Stroetgen, S Geißler, U Hahn
    edited by U Hahn, A Valencia
    posted to chunking survey by yggdrasil on 2008-05-10 13:28:02 as ** along with 5 people and 4 groups irenas yas dullhunk caporaso kkaiser dbk-lab T_lab biomedical-nlp IEG
  • Text Chunking Using Transformation-Based Learning
    (1995), pp. 82-94.
    by Lance Ramshaw, Mitch Marcus
    edited by David Yarovsky, Kenneth Church
    posted to no-tag by yggdrasil on 2008-05-10 13:11:11 as ** along with 2 people and 1 group yoavg vlachmore NLP
  • 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 recognition term by yggdrasil on 2008-05-09 16:52:42 as ** along with 2 people and 1 group irenas johnkork dbk-lab
  • Automatic extraction of acronym-meaning pairs from MEDLINE databases.
    Medinfo, Vol. 10, No. Pt 1. (2001), pp. 371-375.
    by J Pustejovsky, J Castaño, B Cochran, M Kotecki, M Morrell
    posted to no-tag by yggdrasil on 2008-05-09 16:46:14 as ** along with 1 person natsu
  • 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 no-tag by yggdrasil on 2008-05-09 12:46:12 as ** along with 1 person and 1 group irenas dbk-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
  • Unsupervised Multilingual Sentence Boundary Detection
    Comput. Linguist., Vol. 32, No. 4. (December 2006), pp. 485-525.
    by Tibor Kiss, Jan Strunk
    posted to segmentation sentence by yggdrasil on 2008-05-08 09:29:48 as ** along with 1 person spinaltap526
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