@Book{BioNLP:2012,
  editor    = {Kevin B. Cohen  and  Dina Demner-Fushman  and  Sophia Ananiadou  and  Bonnie Webber  and  Jun'ichi Tsujii  and  John Pestian},
  title     = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  url       = {http://www.aclweb.org/anthology/W12-24}
}

@InProceedings{prudhommeaux-roark:2012:BioNLP,
  author    = {Prud'hommeaux, Emily  and  Roark, Brian},
  title     = {Graph-based alignment of narratives for automated neurological assessment},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {1--10},
  url       = {http://www.aclweb.org/anthology/W12-2401}
}

@InProceedings{movshovitzattias-wcohen:2012:BioNLP1,
  author    = {Movshovitz-Attias, Dana  and  W. Cohen, William},
  title     = {Bootstrapping Biomedical Ontologies for Scientific Text using NELL},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {11--19},
  url       = {http://www.aclweb.org/anthology/W12-2402}
}

@InProceedings{dupuch-EtAl:2012:BioNLP,
  author    = {Dupuch, Marie  and  Dupuch, La\"{e}titia  and  Hamon, Thierry  and  Grabar, Natalia},
  title     = {Semantic distance and terminology structuring methods for the detection of semantically close terms},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {20--28},
  url       = {http://www.aclweb.org/anthology/W12-2403}
}

@InProceedings{raghavan-foslerlussier-lai:2012:BioNLP,
  author    = {Raghavan, Preethi  and  Fosler-Lussier, Eric  and  Lai, Albert},
  title     = {Temporal Classification of Medical Events},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {29--37},
  url       = {http://www.aclweb.org/anthology/W12-2404}
}

@InProceedings{cogley-EtAl:2012:BioNLP,
  author    = {Cogley, James  and  Stokes, Nicola  and  Carthy, Joe  and  Dunnion, John},
  title     = {Analyzing Patient Records to Establish If and When a Patient Suffered from a Medical Condition},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {38--46},
  url       = {http://www.aclweb.org/anthology/W12-2405}
}

@InProceedings{movshovitzattias-wcohen:2012:BioNLP2,
  author    = {Movshovitz-Attias, Dana  and  W. Cohen, William},
  title     = {Alignment-HMM-based Extraction of Abbreviations from Biomedical Text},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {47--55},
  url       = {http://www.aclweb.org/anthology/W12-2406}
}

@InProceedings{mowery-velupillai-chapman:2012:BioNLP,
  author    = {Mowery, Danielle L.  and  Velupillai, Sumithra  and  Chapman, Wendy W.},
  title     = {Medical diagnosis lost in translation -- Analysis of uncertainty and negation expressions in English and Swedish clinical texts},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {56--64},
  url       = {http://www.aclweb.org/anthology/W12-2407}
}

@InProceedings{ferrandez-EtAl:2012:BioNLP,
  author    = {Ferrandez, Oscar  and  South, Brett  and  Shen, Shuying  and  Meystre, Stephane},
  title     = {A Hybrid Stepwise Approach for De-identifying Person Names in Clinical Documents},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {65--72},
  url       = {http://www.aclweb.org/anthology/W12-2408}
}

@InProceedings{miller-dligach-savova:2012:BioNLP,
  author    = {Miller, Timothy  and  Dligach, Dmitriy  and  Savova, Guergana},
  title     = {Active Learning for Coreference Resolution},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {73--81},
  url       = {http://www.aclweb.org/anthology/W12-2409}
}

@InProceedings{bjorne-EtAl:2012:BioNLP,
  author    = {Bj\"{o}rne, Jari  and  Van Landeghem, Sofie  and  Pyysalo, Sampo  and  Ohta, Tomoko  and  Ginter, Filip  and  Van de Peer, Yves  and  Ananiadou, Sophia  and  Salakoski, Tapio},
  title     = {PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {82--90},
  url       = {http://www.aclweb.org/anthology/W12-2410}
}

@InProceedings{islamajdogan-lu:2012:BioNLP,
  author    = {Islamaj Dogan, Rezarta  and  Lu, Zhiyong},
  title     = {An improved corpus of disease mentions in PubMed citations},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {91--99},
  url       = {http://www.aclweb.org/anthology/W12-2411}
}

@InProceedings{pyysalo-EtAl:2012:BioNLP,
  author    = {Pyysalo, Sampo  and  Stenetorp, Pontus  and  Ohta, Tomoko  and  Kim, Jin-Dong  and  Ananiadou, Sophia},
  title     = {New Resources and Perspectives for Biomedical Event Extraction},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {100--108},
  url       = {http://www.aclweb.org/anthology/W12-2412}
}

@InProceedings{hamon-EtAl:2012:BioNLP,
  author    = {Hamon, Thierry  and  Engstr\"{o}m, Christopher  and  Manser, Mounira  and  Badji, Zina  and  Grabar, Natalia  and  Silvestrov, Sergei},
  title     = {Combining Compositionality and Pagerank for the Identification of Semantic Relations between Biomedical Words},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {109--117},
  url       = {http://www.aclweb.org/anthology/W12-2413}
}

@InProceedings{apostolova-EtAl:2012:BioNLP,
  author    = {Apostolova, Emilia  and  Tomuro, Noriko  and  Mongkolwat, Pattanasak  and  Demner-Fushman, Dina},
  title     = {Domain Adaptation of Coreference Resolution for Radiology Reports},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {118--121},
  url       = {http://www.aclweb.org/anthology/W12-2414}
}

@InProceedings{thamrongrattanarit-EtAl:2012:BioNLP,
  author    = {Thamrongrattanarit, Attapol  and  Shafir, Michael  and  Crivaro, Michael  and  Borukhov, Bensiin  and  Meteer, Marie},
  title     = {What can NLP tell us about BioNLP?},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {122--129},
  url       = {http://www.aclweb.org/anthology/W12-2415}
}

@InProceedings{south-EtAl:2012:BioNLP,
  author    = {South, Brett  and  Shen, Shuying  and  Leng, Jianwei  and  Forbush, Tyler  and  DuVall, Scott  and  Chapman, Wendy},
  title     = {A Prototype Tool Set to Support Machine-Assisted Annotation},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {130--139},
  url       = {http://www.aclweb.org/anthology/W12-2416}
}

@InProceedings{meteer-EtAl:2012:BioNLP,
  author    = {Meteer, Marie  and  Bensiin, Borukhov  and  Crivaro, Mike  and  Shafir, Michael  and  Thamrongrattanarit, Attapol},
  title     = {MedLingMap: A growing resource mapping the Bio-Medical NLP field},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {140--145},
  url       = {http://www.aclweb.org/anthology/W12-2417}
}

@InProceedings{sharma-EtAl:2012:BioNLP,
  author    = {Sharma, Shefali  and  Lange, Leslie  and  Ambite, Jose Luis  and  Arens, Yigal  and  Hsu, Chun-Nan},
  title     = {Exploring Label Dependency in Active Learning for Phenotype Mapping},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {146--154},
  url       = {http://www.aclweb.org/anthology/W12-2418}
}

@InProceedings{balasubramanyan-EtAl:2012:BioNLP,
  author    = {Balasubramanyan, Ramnath  and  Rivard, Kathryn  and  Cohen, William W.  and  Jakovljevic, Jelena  and  Woolford, John L.},
  title     = {Evaluating Joint Modeling of Yeast Biology Literature and Protein-Protein Interaction Networks},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {155--162},
  url       = {http://www.aclweb.org/anthology/W12-2419}
}

@InProceedings{tudor-vijayshanker:2012:BioNLP,
  author    = {Tudor, Catalina Oana  and  Vijay-Shanker, K},
  title     = {RankPref: Ranking Sentences Describing Relations between Biomedical Entities with an Application},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {163--171},
  url       = {http://www.aclweb.org/anthology/W12-2420}
}

@InProceedings{yan-EtAl:2012:BioNLP,
  author    = {Yan, Ying  and  Kim, Jee-Hyub  and  Croset, Samuel  and  Rebholz-Schuhmann, Dietrich},
  title     = {Finding small molecule and protein pairs in scientific literature using a bootstrapping method},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {172--175},
  url       = {http://www.aclweb.org/anthology/W12-2421}
}

@InProceedings{gyawali-solorio-benajiba:2012:BioNLP,
  author    = {Gyawali, Binod  and  Solorio, Thamar  and  Benajiba, Yassine},
  title     = {Grading the Quality of Medical Evidence},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {176--184},
  url       = {http://www.aclweb.org/anthology/W12-2422}
}

@InProceedings{kim-EtAl:2012:BioNLP,
  author    = {Kim, Sun  and  Kim, Won  and  Comeau, Don  and  Wilbur, W. John},
  title     = {Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {185--192},
  url       = {http://www.aclweb.org/anthology/W12-2423}
}

@InProceedings{matykiewicz-pestian:2012:BioNLP,
  author    = {Matykiewicz, Pawel  and  Pestian, John},
  title     = {Effect of small sample size on text categorization with support vector machines},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {193--201},
  url       = {http://www.aclweb.org/anthology/W12-2424}
}

@InProceedings{kim-wang:2012:BioNLP,
  author    = {Kim, Jin-Dong  and  Wang, Yue},
  title     = {PubAnnotation - a persistent and sharable corpus and annotation repository},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {202--205},
  url       = {http://www.aclweb.org/anthology/W12-2425}
}

@InProceedings{boyce-gardner-harkema:2012:BioNLP,
  author    = {Boyce, Richard  and  Gardner, Gregory  and  Harkema, Henk},
  title     = {Using Natural Language Processing to Extract Drug-Drug Interaction Information from Package Inserts},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {206--213},
  url       = {http://www.aclweb.org/anthology/W12-2426}
}

@InProceedings{sutton-EtAl:2012:BioNLP,
  author    = {Sutton, Nate  and  Wojtulewicz, Laura  and  Mehta, Neel  and  Gonzalez, Graciela},
  title     = {Automatic Approaches for Gene-Drug Interaction Extraction from Biomedical Text: Corpus and Comparative Evaluation},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {214--222},
  url       = {http://www.aclweb.org/anthology/W12-2427}
}

@InProceedings{wang-EtAl:2012:BioNLP,
  author    = {Wang, Yaqiang  and  Liu, Yiguang  and  Yu, Zhonghua  and  Chen, Li  and  Jiang, Yongguang},
  title     = {A Preliminary Work on Symptom Name Recognition from Free-Text Clinical Records of Traditional Chinese Medicine using Conditional Random Fields and Reasonable Features},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {223--230},
  url       = {http://www.aclweb.org/anthology/W12-2428}
}

@InProceedings{cheng-preiss-stevenson:2012:BioNLP,
  author    = {Cheng, Weiwei  and  Preiss, Judita  and  Stevenson, Mark},
  title     = {Scaling up WSD with Automatically Generated Examples},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {231--239},
  url       = {http://www.aclweb.org/anthology/W12-2429}
}

@InProceedings{wang-kim:2012:BioNLP,
  author    = {Wang, Yue  and  Kim, Jin-Dong},
  title     = {Boosting the protein name recognition performance by bootstrapping on selected text},
  booktitle = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  month     = {June},
  year      = {2012},
  address   = {Montr{\'e}al, Canada},
  publisher = {Association for Computational Linguistics},
  pages     = {240--243},
  url       = {http://www.aclweb.org/anthology/W12-2430}
}