%0 Conference Proceedings %T Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %E Verspoor, Karin %E Cohen, Kevin Bretonnel %E Goertzel, Ben %E Mani, Inderjeet %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F ws-2006-hlt %U https://aclanthology.org/W06-3300 %0 Conference Proceedings %T The Semantics of a Definiendum Constrains both the Lexical Semantics and the Lexicosyntactic Patterns in the Definiens %A Yu, Hong %A Wei, Ying %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F yu-wei-2006-semantics %U https://aclanthology.org/W06-3301 %P 1-8 %0 Conference Proceedings %T Ontology-Based Natural Language Query Processing for the Biological Domain %A Liang, Jisheng %A Nguyen, Thien %A Koperski, Krzysztof %A Marchisio, Giovanni %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F liang-etal-2006-ontology %U https://aclanthology.org/W06-3302 %P 9-16 %0 Conference Proceedings %T Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction %A Fyshe, Alona %A Szafron, Duane %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F fyshe-szafron-2006-term %U https://aclanthology.org/W06-3303 %P 17-24 %0 Conference Proceedings %T Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity %A Sanfilippo, Antonio %A Posse, Christian %A Gopalan, Banu %A Tratz, Stephen %A Gregory, Michelle %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F sanfilippo-etal-2006-integrating %U https://aclanthology.org/W06-3304 %P 25-32 %0 Conference Proceedings %T A Priority Model for Named Entities %A Tanabe, Lorraine %A Wilbur, W. John %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F tanabe-wilbur-2006-priority %U https://aclanthology.org/W06-3305 %P 33-40 %0 Conference Proceedings %T Human Gene Name Normalization using Text Matching with Automatically Extracted Synonym Dictionaries %A Fang, Haw-ren %A Murphy, Kevin %A Jin, Yang %A Kim, Jessica %A White, Peter %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F fang-etal-2006-human %U https://aclanthology.org/W06-3306 %P 41-48 %0 Conference Proceedings %T Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline %A Bunescu, Razvan %A Mooney, Raymond %A Ramani, Arun %A Marcotte, Edward %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F bunescu-etal-2006-integrating %U https://aclanthology.org/W06-3307 %P 49-56 %0 Conference Proceedings %T BIOSMILE: Adapting Semantic Role Labeling for Biomedical Verbs: %A Tsai, Richard Tzong-Han %A Chou, Wen-Chi %A Lin, Yu-Chun %A Sung, Cheng-Lung %A Ku, Wei %A Su, Ying-Shan %A Sung, Ting-Yi %A Hsu, Wen-Lian %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F tsai-etal-2006-biosmile %U https://aclanthology.org/W06-3308 %P 57-64 %0 Conference Proceedings %T Generative Content Models for Structural Analysis of Medical Abstracts %A Lin, Jimmy %A Karakos, Damianos %A Demner-Fushman, Dina %A Khudanpur, Sanjeev %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F lin-etal-2006-generative %U https://aclanthology.org/W06-3309 %P 65-72 %0 Conference Proceedings %T Exploring Text and Image Features to Classify Images in Bioscience Literature %A Rafkind, Barry %A Lee, Minsuk %A Chang, Shih-Fu %A Yu, Hong %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F rafkind-etal-2006-exploring %U https://aclanthology.org/W06-3310 %P 73-80 %0 Conference Proceedings %T Mining biomedical texts for disease-related pathways %A Rzhetsky, Andrey %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F rzhetsky-2006-mining %U https://aclanthology.org/W06-3311 %P 81 %0 Conference Proceedings %T Postnominal Prepositional Phrase Attachment in Proteomics %A Schuman, Jonathan %A Bergler, Sabine %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F schuman-bergler-2006-postnominal %U https://aclanthology.org/W06-3312 %P 82-89 %0 Conference Proceedings %T BioKI:Enzymes - an adaptable system to locate low-frequency information in full-text proteomics articles %A Bergler, Sabine %A Schuman, Jonathan %A Dubuc, Julien %A Lebedev, Alexandr %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F bergler-etal-2006-bioki %U https://aclanthology.org/W06-3314 %P 91-92 %0 Conference Proceedings %T A Graph-Search Framework for GeneId Ranking %A Cohen, William %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F cohen-2006-graph %U https://aclanthology.org/W06-3315 %P 93-95 %0 Conference Proceedings %T Semi-supervised anaphora resolution in biomedical texts %A Gasperin, Caroline %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F gasperin-2006-semi %U https://aclanthology.org/W06-3316 %P 96-103 %0 Conference Proceedings %T Using Dependency Parsing and Probabilistic Inference to Extract Relationships between Genes, Proteins and Malignancies Implicit Among Multiple Biomedical Research Abstracts %A Goertzel, Ben %A Pinto, Hugo %A Heljakka, Ari %A Ross, Michael %A Pennachin, Cassio %A Goertzel, Izabela %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F goertzel-etal-2006-using %U https://aclanthology.org/W06-3317 %P 104-111 %0 Conference Proceedings %T Recognizing Nested Named Entities in GENIA corpus %A Gu, Baohua %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F gu-2006-recognizing %U https://aclanthology.org/W06-3318 %P 112-113 %0 Conference Proceedings %T Biomedical Term Recognition with the Perceptron HMM Algorithm %A Jiampojamarn, Sittichai %A Kondrak, Grzegorz %A Cherry, Colin %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F jiampojamarn-etal-2006-biomedical %U https://aclanthology.org/W06-3319 %P 114-115 %0 Conference Proceedings %T Refactoring Corpora %A Johnson, Helen L. %A Baumgartner Jr., William A. %A Krallinger, Martin %A Cohen, K. Bretonnel %A Hunter, Lawrence %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F johnson-etal-2006-refactoring %U https://aclanthology.org/W06-3320 %P 116-117 %0 Conference Proceedings %T Rapid Adaptation of POS Tagging for Domain Specific Uses %A Miller, John E. %A Bloodgood, Michael %A Torii, Manabu %A Vijay-Shanker, K. %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F miller-etal-2006-rapid %U https://aclanthology.org/W06-3321 %P 118-119 %0 Conference Proceedings %T Extracting Protein-Protein interactions using simple contextual features %A Nielsen, Leif Arda %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F nielsen-2006-extracting %U https://aclanthology.org/W06-3322 %P 120-121 %0 Conference Proceedings %T Identifying Experimental Techniques in Biomedical Literature %A Oberoi, Meeta %A Struble, Craig A. %A Sugg, Sonia L. %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F oberoi-etal-2006-identifying %U https://aclanthology.org/W06-3323 %P 122-123 %0 Conference Proceedings %T A Pragmatic Approach to Summary Extraction in Clinical Trials %A Rosemblat, Graciela %A Graham, Laurel %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F rosemblat-graham-2006-pragmatic %U https://aclanthology.org/W06-3324 %P 124-125 %0 Conference Proceedings %T The Difficulties of Taxonomic Name Extraction and a Solution %A Sautter, Guido %A Böhm, Klemens %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F sautter-bohm-2006-difficulties %U https://aclanthology.org/W06-3325 %P 126-133 %0 Conference Proceedings %T Summarizing Key Concepts using Citation Sentences %A Schwartz, Ariel S. %A Hearst, Marti %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F schwartz-hearst-2006-summarizing %U https://aclanthology.org/W06-3326 %P 134-135 %0 Conference Proceedings %T Subdomain adaptation of a POS tagger with a small corpus %A Tateisi, Yuka %A Tsuruoka, Yoshimasa %A Tsujii, Jun’ichi %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F tateisi-etal-2006-subdomain %U https://aclanthology.org/W06-3327 %P 136-137 %0 Conference Proceedings %T Bootstrapping and Evaluating Named Entity Recognition in the Biomedical Domain %A Vlachos, Andreas %A Gasperin, Caroline %Y Verspoor, Karin %Y Cohen, Kevin Bretonnel %Y Goertzel, Ben %Y Mani, Inderjeet %S Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology %D 2006 %8 June %I Association for Computational Linguistics %C New York, New York %F vlachos-gasperin-2006-bootstrapping %U https://aclanthology.org/W06-3328 %P 138-145