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