Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor 2006-06 Association for Computational Linguistics New York, New York text conference publication ws-2006-hlt https://aclanthology.org/W06-3300/ The Semantics of a Definiendum Constrains both the Lexical Semantics and the Lexicosyntactic Patterns in the Definiens Hong Yu author Ying Wei author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication yu-wei-2006-semantics https://aclanthology.org/W06-3301/ 2006-06 1 8 Ontology-Based Natural Language Query Processing for the Biological Domain Jisheng Liang author Thien Nguyen author Krzysztof Koperski author Giovanni Marchisio author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication liang-etal-2006-ontology https://aclanthology.org/W06-3302/ 2006-06 9 16 Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction Alona Fyshe author Duane Szafron author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication fyshe-szafron-2006-term https://aclanthology.org/W06-3303/ 2006-06 17 24 Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity Antonio Sanfilippo author Christian Posse author Banu Gopalan author Stephen Tratz author Michelle Gregory author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication sanfilippo-etal-2006-integrating https://aclanthology.org/W06-3304/ 2006-06 25 32 A Priority Model for Named Entities Lorraine Tanabe author W John Wilbur author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication tanabe-wilbur-2006-priority https://aclanthology.org/W06-3305/ 2006-06 33 40 Human Gene Name Normalization using Text Matching with Automatically Extracted Synonym Dictionaries Haw-ren Fang author Kevin Murphy author Yang Jin author Jessica Kim author Peter White author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication fang-etal-2006-human https://aclanthology.org/W06-3306/ 2006-06 41 48 Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline Razvan Bunescu author Raymond Mooney author Arun Ramani author Edward Marcotte author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication bunescu-etal-2006-integrating https://aclanthology.org/W06-3307/ 2006-06 49 56 BIOSMILE: Adapting Semantic Role Labeling for Biomedical Verbs: Richard Tzong-Han Tsai author Wen-Chi Chou author Yu-Chun Lin author Cheng-Lung Sung author Wei Ku author Ying-Shan Su author Ting-Yi Sung author Wen-Lian Hsu author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication tsai-etal-2006-biosmile https://aclanthology.org/W06-3308/ 2006-06 57 64 Generative Content Models for Structural Analysis of Medical Abstracts Jimmy Lin author Damianos Karakos author Dina Demner-Fushman author Sanjeev Khudanpur author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication lin-etal-2006-generative https://aclanthology.org/W06-3309/ 2006-06 65 72 Exploring Text and Image Features to Classify Images in Bioscience Literature Barry Rafkind author Minsuk Lee author Shih-Fu Chang author Hong Yu author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication rafkind-etal-2006-exploring https://aclanthology.org/W06-3310/ 2006-06 73 80 Mining biomedical texts for disease-related pathways Andrey Rzhetsky author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication rzhetsky-2006-mining https://aclanthology.org/W06-3311/ 2006-06 81 Postnominal Prepositional Phrase Attachment in Proteomics Jonathan Schuman author Sabine Bergler author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication schuman-bergler-2006-postnominal https://aclanthology.org/W06-3312/ 2006-06 82 89 BioKI:Enzymes - an adaptable system to locate low-frequency information in full-text proteomics articles Sabine Bergler author Jonathan Schuman author Julien Dubuc author Alexandr Lebedev author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication bergler-etal-2006-bioki https://aclanthology.org/W06-3314/ 2006-06 91 92 A Graph-Search Framework for GeneId Ranking William Cohen author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication cohen-2006-graph https://aclanthology.org/W06-3315/ 2006-06 93 95 Semi-supervised anaphora resolution in biomedical texts Caroline Gasperin author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication gasperin-2006-semi https://aclanthology.org/W06-3316/ 2006-06 96 103 Using Dependency Parsing and Probabilistic Inference to Extract Relationships between Genes, Proteins and Malignancies Implicit Among Multiple Biomedical Research Abstracts Ben Goertzel author Hugo Pinto author Ari Heljakka author Michael Ross author Cassio Pennachin author Izabela Goertzel author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication goertzel-etal-2006-using https://aclanthology.org/W06-3317/ 2006-06 104 111 Recognizing Nested Named Entities in GENIA corpus Baohua Gu author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication gu-2006-recognizing https://aclanthology.org/W06-3318/ 2006-06 112 113 Biomedical Term Recognition with the Perceptron HMM Algorithm Sittichai Jiampojamarn author Grzegorz Kondrak author Colin Cherry author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication jiampojamarn-etal-2006-biomedical https://aclanthology.org/W06-3319/ 2006-06 114 115 Refactoring Corpora Helen L Johnson author William A Baumgartner Jr. author Martin Krallinger author K Bretonnel Cohen author Lawrence Hunter author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication johnson-etal-2006-refactoring https://aclanthology.org/W06-3320/ 2006-06 116 117 Rapid Adaptation of POS Tagging for Domain Specific Uses John E Miller author Michael Bloodgood author Manabu Torii author K Vijay-Shanker author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication miller-etal-2006-rapid https://aclanthology.org/W06-3321/ 2006-06 118 119 Extracting Protein-Protein interactions using simple contextual features Leif Arda Nielsen author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication nielsen-2006-extracting https://aclanthology.org/W06-3322/ 2006-06 120 121 Identifying Experimental Techniques in Biomedical Literature Meeta Oberoi author Craig A Struble author Sonia L Sugg author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication oberoi-etal-2006-identifying https://aclanthology.org/W06-3323/ 2006-06 122 123 A Pragmatic Approach to Summary Extraction in Clinical Trials Graciela Rosemblat author Laurel Graham author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication rosemblat-graham-2006-pragmatic https://aclanthology.org/W06-3324/ 2006-06 124 125 The Difficulties of Taxonomic Name Extraction and a Solution Guido Sautter author Klemens Böhm author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication sautter-bohm-2006-difficulties https://aclanthology.org/W06-3325/ 2006-06 126 133 Summarizing Key Concepts using Citation Sentences Ariel S Schwartz author Marti Hearst author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication schwartz-hearst-2006-summarizing https://aclanthology.org/W06-3326/ 2006-06 134 135 Subdomain adaptation of a POS tagger with a small corpus Yuka Tateisi author Yoshimasa Tsuruoka author Jun’ichi Tsujii author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication tateisi-etal-2006-subdomain https://aclanthology.org/W06-3327/ 2006-06 136 137 Bootstrapping and Evaluating Named Entity Recognition in the Biomedical Domain Andreas Vlachos author Caroline Gasperin author 2006-06 text Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology Karin Verspoor editor Kevin Bretonnel Cohen editor Ben Goertzel editor Inderjeet Mani editor Association for Computational Linguistics New York, New York conference publication vlachos-gasperin-2006-bootstrapping https://aclanthology.org/W06-3328/ 2006-06 138 145