@proceedings{ws-2009-bionlp,
    title = "Proceedings of the {B}io{NLP} 2009 Workshop",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1300/"
}
@inproceedings{pyysalo-etal-2009-static,
    title = "Static Relations: a Piece in the Biomedical Information Extraction Puzzle",
    author = "Pyysalo, Sampo  and
      Ohta, Tomoko  and
      Kim, Jin-Dong  and
      Tsujii, Jun{'}ichi",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1301/",
    pages = "1--9"
}
@inproceedings{mowery-etal-2009-distinguishing,
    title = "Distinguishing Historical from Current Problems in Clinical Reports {--} Which Textual Features Help?",
    author = "Mowery, Danielle  and
      Harkema, Henk  and
      Dowling, John  and
      Lustgarten, Jonathan  and
      Chapman, Wendy",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1302/",
    pages = "10--18"
}
@inproceedings{christensen-etal-2009-onyx,
    title = "{ONYX}: A System for the Semantic Analysis of Clinical Text",
    author = "Christensen, Lee  and
      Harkema, Henk  and
      Haug, Peter  and
      Irwin, Jeannie  and
      Chapman, Wendy",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1303/",
    pages = "19--27"
}
@inproceedings{morante-daelemans-2009-learning,
    title = "Learning the Scope of Hedge Cues in Biomedical Texts",
    author = "Morante, Roser  and
      Daelemans, Walter",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1304/",
    pages = "28--36"
}
@inproceedings{hahn-etal-2009-feasible,
    title = "How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions",
    author = "Hahn, Udo  and
      Tomanek, Katrin  and
      Buyko, Ekaterina  and
      Kim, Jung-jae  and
      Rebholz-Schuhmann, Dietrich",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1305/",
    pages = "37--45"
}
@inproceedings{wong-etal-2009-extraction,
    title = "Extraction of Named Entities from Tables in Gene Mutation Literature",
    author = "Wong, Wern  and
      Martinez, David  and
      Cavedon, Lawrence",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1306/",
    pages = "46--54"
}
@inproceedings{tan-lambrix-2009-selecting,
    title = "Selecting an Ontology for Biomedical Text Mining",
    author = "Tan, He  and
      Lambrix, Patrick",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1307/",
    pages = "55--62"
}
@inproceedings{xu-etal-2009-investigation,
    title = "Investigation of Unsupervised Pattern Learning Techniques for Bootstrap Construction of a Medical Treatment Lexicon",
    author = "Xu, Rong  and
      Morgan, Alexander A.  and
      Das, Amar  and
      Garber, Alan",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1308/",
    pages = "63--70"
}
@inproceedings{stevenson-etal-2009-disambiguation,
    title = "Disambiguation of Biomedical Abbreviations",
    author = "Stevenson, Mark  and
      Guo, Yikun  and
      Alamri, Abdulaziz  and
      Gaizauskas, Robert",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1309/",
    pages = "71--79"
}
@inproceedings{kappeler-etal-2009-tx,
    title = "{TX} Task: Automatic Detection of Focus Organisms in Biomedical Publications",
    author = "Kappeler, Thomas  and
      Kaljurand, Kaarel  and
      Rinaldi, Fabio",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1310/",
    pages = "80--88"
}
@inproceedings{hamon-grabar-2009-exploring,
    title = "Exploring Graph Structure for Detection of Reliability Zones within Synonym Resources: Experiment with the Gene Ontology",
    author = "Hamon, Thierry  and
      Grabar, Natalia",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1311/",
    pages = "89--96"
}
@inproceedings{jin-etal-2009-towards,
    title = "Towards Automatic Generation of Gene Summary",
    author = "Jin, Feng  and
      Huang, Minlie  and
      Lu, Zhiyong  and
      Zhu, Xiaoyan",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1312/",
    pages = "97--105"
}
@inproceedings{ohta-etal-2009-incorporating,
    title = "Incorporating {GENETAG}-style annotation to {GENIA} corpus",
    author = "Ohta, Tomoko  and
      Kim, Jin-Dong  and
      Pyysalo, Sampo  and
      Wang, Yue  and
      Tsujii, Jun{'}ichi",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1313/",
    pages = "106--107"
}
@inproceedings{sun-etal-2009-user,
    title = "User-Driven Development of Text Mining Resources for Cancer Risk Assessment",
    author = "Sun, Lin  and
      Korhonen, Anna  and
      Silins, Ilona  and
      Stenius, Ulla",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1314/",
    pages = "108--116"
}
@inproceedings{erdem-yeniterzi-2009-transforming,
    title = "Transforming Controlled Natural Language Biomedical Queries into Answer Set Programs",
    author = "Erdem, Esra  and
      Yeniterzi, Reyyan",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1315/",
    pages = "117--124"
}
@inproceedings{bashyam-taira-2009-incorporating,
    title = "Incorporating Syntactic Dependency Information towards Improved Coding of Lengthy Medical Concepts in Clinical Reports",
    author = "Bashyam, Vijayaraghavan  and
      Taira, Ricky K",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1316/",
    pages = "125--132"
}
@inproceedings{liu-etal-2009-identifying,
    title = "Identifying Interaction Sentences from Biological Literature Using Automatically Extracted Patterns",
    author = "Liu, Haibin  and
      Blouin, Christian  and
      Ke{\v{s}}elj, Vlado",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1317/",
    pages = "133--141"
}
@inproceedings{conway-etal-2009-using,
    title = "Using Hedges to Enhance a Disease Outbreak Report Text Mining System",
    author = "Conway, Mike  and
      Doan, Son  and
      Collier, Nigel",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1318/",
    pages = "142--143"
}
@inproceedings{neveol-etal-2009-exploring,
    title = "Exploring Two Biomedical Text Genres for Disease Recognition",
    author = "N{\'e}v{\'e}ol, Aur{\'e}lie  and
      Kim, Won  and
      Wilbur, W. John  and
      Lu, Zhiyong",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1319/",
    pages = "144--152"
}
@inproceedings{leonhard-2009-towards,
    title = "Towards Retrieving Relevant Information for Answering Clinical Comparison Questions",
    author = "Leonhard, Annette",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1320/",
    pages = "153--161"
}
@inproceedings{uematsu-etal-2009-bridging,
    title = "Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics",
    author = "Uematsu, Sumire  and
      Kim, Jin-Dong  and
      Tsujii, Jun{'}ichi",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1321/",
    pages = "162--170"
}
@inproceedings{cao-etal-2009-evaluation,
    title = "Evaluation of the Clinical Question Answering Presentation",
    author = "Cao, Yong-Gang  and
      Ely, John  and
      Antieau, Lamont  and
      Yu, Hong",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1322/",
    pages = "171--178"
}
@inproceedings{matykiewicz-etal-2009-clustering,
    title = "Clustering Semantic Spaces of Suicide Notes and Newsgroups Articles.",
    author = "Matykiewicz, Pawel  and
      Duch, Wlodzislaw  and
      Pestian, John",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1323/",
    pages = "179--184"
}
@inproceedings{aramaki-etal-2009-text2table,
    title = "{TEXT}2{TABLE}: Medical Text Summarization System Based on Named Entity Recognition and Modality Identification",
    author = "Aramaki, Eiji  and
      Miura, Yasuhide  and
      Tonoike, Masatsugu  and
      Ohkuma, Tomoko  and
      Mashuichi, Hiroshi  and
      Ohe, Kazuhiko",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1324/",
    pages = "185--192"
}
@inproceedings{liakata-etal-2009-semantic,
    title = "Semantic Annotation of Papers: Interface {\&} Enrichment Tool ({SAPIENT})",
    author = "Liakata, Maria  and
      Q, Claire  and
      Soldatova, Larisa N.",
    editor = "Cohen, K. Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-ccl/W09-1325/",
    pages = "193--200"
}