@proceedings{ws-2011-bionlp,
    title = "Proceedings of {B}io{NLP} 2011 Workshop",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0200/"
}
@inproceedings{thomas-etal-2011-links,
    title = "Not all links are equal: Exploiting Dependency Types for the Extraction of Protein-Protein Interactions from Text",
    author = "Thomas, Philippe  and
      Pietschmann, Stefan  and
      Solt, Ill{\'e}s  and
      Tikk, Domonkos  and
      Leser, Ulf",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0201/",
    pages = "1--9"
}
@inproceedings{rei-briscoe-2011-unsupervised,
    title = "Unsupervised Entailment Detection between Dependency Graph Fragments",
    author = "Rei, Marek  and
      Briscoe, Ted",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0202/",
    pages = "10--18"
}
@inproceedings{hsu-etal-2011-learning,
    title = "Learning Phenotype Mapping for Integrating Large Genetic Data",
    author = "Hsu, Chun-Nan  and
      Kuo, Cheng-Ju  and
      Cai, Congxing  and
      Pendergrass, Sarah  and
      Ritchie, Marylyn  and
      Ambite, Jose Luis",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0203/",
    pages = "19--27"
}
@inproceedings{van-landeghem-etal-2011-evex,
    title = "{EVEX}: A {P}ub{M}ed-Scale Resource for Homology-Based Generalization of Text Mining Predictions",
    author = "Van Landeghem, Sofie  and
      Ginter, Filip  and
      Van de Peer, Yves  and
      Salakoski, Tapio",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0204/",
    pages = "28--37"
}
@inproceedings{cohen-etal-2011-fast,
    title = "Fast and simple semantic class assignment for biomedical text",
    author = "Cohen, K. Bretonnel  and
      Christiansen, Thomas  and
      Baumgartner Jr., William  and
      Verspoor, Karin  and
      Hunter, Lawrence",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0205/",
    pages = "38--45"
}
@inproceedings{pokkunuri-etal-2011-role,
    title = "The Role of Information Extraction in the Design of a Document Triage Application for Biocuration",
    author = "Pokkunuri, Sandeep  and
      Ramakrishnan, Cartic  and
      Riloff, Ellen  and
      Hovy, Eduard  and
      Burns, Gully",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0206/",
    pages = "46--55"
}
@inproceedings{ben-abacha-zweigenbaum-2011-medical,
    title = "Medical Entity Recognition: A Comparaison of Semantic and Statistical Methods",
    author = "Ben Abacha, Asma  and
      Zweigenbaum, Pierre",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0207/",
    pages = "56--64"
}
@inproceedings{usami-etal-2011-automatic,
    title = "Automatic Acquisition of Huge Training Data for Bio-Medical Named Entity Recognition",
    author = "Usami, Yu  and
      Cho, Han-Cheol  and
      Okazaki, Naoaki  and
      Tsujii, Jun{'}ichi",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0208/",
    pages = "65--73"
}
@inproceedings{tan-etal-2011-building,
    title = "Building frame-based corpus on the basis of ontological domain knowledge",
    author = "Tan, He  and
      Kaliyaperumal, Rajaram  and
      Benis, Nirupama",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0209/",
    pages = "74--82"
}
@inproceedings{batista-navarro-ananiadou-2011-building,
    title = "Building a Coreference-Annotated Corpus from the Domain of Biochemistry",
    author = "Batista-Navarro, Riza Theresa  and
      Ananiadou, Sophia",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0210/",
    pages = "83--91"
}
@inproceedings{marciniak-mykowiecka-2011-towards,
    title = "Towards Morphologically Annotated Corpus of Hospital Discharge Reports in {P}olish",
    author = "Marciniak, Malgorzata  and
      Mykowiecka, Agnieszka",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0211/",
    pages = "92--100"
}
@inproceedings{blake-zheng-2011-search,
    title = "In Search of Protein Locations",
    author = "Blake, Catherine  and
      Zheng, Wu",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0212/",
    pages = "101--102"
}
@inproceedings{neveol-etal-2011-automatic,
    title = "Automatic extraction of data deposition statements: where do the research results go?",
    author = "N{\'e}v{\'e}ol, Aur{\'e}lie  and
      Wilbur, W. John  and
      Lu, Zhiyong",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0213/",
    pages = "103--104"
}
@inproceedings{ohta-etal-2011-pathways,
    title = "From Pathways to Biomolecular Events: Opportunities and Challenges",
    author = "Ohta, Tomoko  and
      Pyysalo, Sampo  and
      Tsujii, Jun{'}ichi",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0214/",
    pages = "105--113"
}
@inproceedings{pyysalo-etal-2011-towards,
    title = "Towards Exhaustive Event Extraction for Protein Modifications",
    author = "Pyysalo, Sampo  and
      Ohta, Tomoko  and
      Miwa, Makoto  and
      Tsujii, Jun{'}ichi",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0215/",
    pages = "114--123"
}
@inproceedings{chowdhury-etal-2011-study,
    title = "A Study on Dependency Tree Kernels for Automatic Extraction of Protein-Protein Interaction",
    author = "Chowdhury, Faisal Md.  and
      Lavelli, Alberto  and
      Moschitti, Alessandro",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0216/",
    pages = "124--133"
}
@inproceedings{white-etal-2011-hypothesis,
    title = "Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles",
    author = "White, Elizabeth  and
      Cohen, K. Bretonnel  and
      Hunter, Larry",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0217/",
    pages = "134--135"
}
@inproceedings{stenetorp-etal-2011-simsem,
    title = "{S}im{S}em: Fast Approximate String Matching in Relation to Semantic Category Disambiguation",
    author = "Stenetorp, Pontus  and
      Pyysalo, Sampo  and
      Tsujii, Jun{'}ichi",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0218/",
    pages = "136--145"
}
@inproceedings{jung-etal-2011-building,
    title = "Building Timelines from Narrative Clinical Records: Initial Results Based-on Deep Natural Language Understanding",
    author = "Jung, Hyuckchul  and
      Allen, James  and
      Blaylock, Nate  and
      de Beaumont, William  and
      Galescu, Lucian  and
      Swift, Mary",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0219/",
    pages = "146--154"
}
@inproceedings{yeganova-etal-2011-text,
    title = "Text Mining Techniques for Leveraging Positively Labeled Data",
    author = "Yeganova, Lana  and
      Comeau, Donald C.  and
      Kim, Won  and
      Wilbur, W. John",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0220/",
    pages = "155--163"
}
@inproceedings{hara-etal-2011-parsing,
    title = "Parsing Natural Language Queries for Life Science Knowledge",
    author = "Hara, Tadayoshi  and
      Tateisi, Yuka  and
      Kim, Jin-Dong  and
      Miyao, Yusuke",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0221/",
    pages = "164--173"
}
@inproceedings{liang-etal-2011-unlocking,
    title = "Unlocking Medical Ontologies for Non-Ontology Experts",
    author = "Liang, Shao Fen  and
      Scott, Donia  and
      Stevens, Robert  and
      Rector, Alan",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0222/",
    pages = "174--181"
}
@inproceedings{jimeno-yepes-aronson-2011-self,
    title = "Self-training and co-training in biomedical word sense disambiguation",
    author = "Jimeno-Yepes, Antonio  and
      Aronson, Alan",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0223/",
    pages = "182--183"
}
@inproceedings{verhagen-pustejovsky-2011-medstract,
    title = "Medstract - The Next Generation",
    author = "Verhagen, Marc  and
      Pustejovsky, James",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0224/",
    pages = "184--185"
}
@inproceedings{haruechaiyasak-etal-2011-thaiherbminer,
    title = "{T}hai{H}erb{M}iner: A {T}hai Herbal Medicine Mining and Visualizing Tool",
    author = "Haruechaiyasak, Choochart  and
      Pailai, Jaruwat  and
      Viratyosin, Wasna  and
      Kongkachandra, Rachada",
    editor = "Cohen, Kevin Bretonnel  and
      Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Pestian, John  and
      Tsujii, Jun{'}ichi  and
      Webber, Bonnie",
    booktitle = "Proceedings of {B}io{NLP} 2011 Workshop",
    month = jun,
    year = "2011",
    address = "Portland, Oregon, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/volume-fixes/W11-0225/",
    pages = "186--187"
}