ADE Repository

 

People Involved

Principle Investigator: Hong Yu

Subcontract Principle Investigator: Alexander Turchin, Andrew Evens 

Co-Investigators: Steve Belknap, Dennis West,  Jerry Gurwitz,  Robert Goldberg,  Arlene Ash, Catarina Kiefe, Joel Gore, Alan Rosmarin

Collaborator: Dr. Darrell Abernethy, Edward Benz (Dana Farber), Steven Rosen (Northwestern), Isaac Kohane (Harvard)

Principle Researchers: Feifan Liu

Developers:&nbspWeisong Liu, Abhyuday&nbspJagannatha, Jiaping Zheng, Balaji Polepalli Ramesh

Annotator: Elaine Freund, Nadya Frid, Andrew Hsu, German Chirboga, Heather Keating, Jorge Yarzebski, Victoria Wang

Consultant: Paul Yarnold, Chris Chute, Wendy Chapman

 

PUBLICATIONS

  1. Belknap SM, Georgopoulos CH, West DP, Yarnold PR, Kelly WN. Quality of Methods of Reporting Serious Adverse Drug Event in Cancer Drug Clinical Trials. Clin Pharmacol Ther. 2010 [link] [pdf]
  2. Li ZF, Liu FF, Antieau L, Yu H. 2010. Lancet: a high precision medication event extraction system for clinical text. Journal of American Medical Informatics Association (JAMIA). [link]
  3. Prasad R, McRoy S, Frid N, and Joshi A. Yu H. 2010. BioDRB: The Biomedical Discourse Relation Bank. BMC Bioinformatics. In Press.
  4. Yu H., Cao YG, Cimino JJ, and Ely J. 2010. Automatically extracting information needs from complex clinical questions. Journal of Biomedical Informatics (JBI). [link]
  5. Agarwal S and Yu H. 2010. Biomedical negation scope detection with conditional random fields. Journal of American Medical Informatics Association (JAMIA). [link]
  6. Agarwal S and Yu H. 2010. Detecting hedge cues and their scope in biomedical text with conditional random fields. Journal of Biomedical Informatics (JBI). [link]
  7. Ramesh BP, Prasad R, Yu H. 2010. Identifying explicit discourse connective in biomedical text. American Medical Informatics Association (AMIA) Fall Symposium.[link]
  8. Cao YG, Liu FF, Antieau L, Simpson P, Cimino JJ, Ely J, Yu H. 2010. AskHERMES: An online question answering system for complex clinical questions. Journal of Biomedical Informatics (JBI). In Press.
  9. Cao YG, Li ZF, Liu FF, Agarwal S, Zhang Q, and Yu H. 2010. An IR-aided machine learning framework for the BioCreative II.5 Challenge. IEEE/ACM Transaction on Computational Biology and Bioinformatics. [link]
  10. Haspel, RL, Arnaout, R, Briere, L, Kantarci,S, Marchand,K, Tonellato, PJ, Connolly, C, Boguski, MS,.Saffitz,JE, A Call to Action: Training Pathology Residents in Genomics and Personalized Medicine, American Journal of Clinical Pathology | AJCP-2010-02-0104.R1 (2010) [link]
  11. Zweigenbaum, P, Demner-Fushman DD, Yu H, and Cohen KB. New frontiers for biomedical text mining: current progress. Briefing in Bioinformatics. Sep;8(5):358-75.[link]
  12. Cao YG, Ely J, Antieau L, and Yu H. 2009. Evaluation of the clinical question answering presentation. The North American Chapter of the Association for Computational Linguistics-Human Language Technologies (NAACL-HLT) Conference BioNLP, Boulder, Colorado.[link]
  13. Cao YG, Ely J, and Yu H. 2009. Using weighted keywords to improve clinical question answering. IEEE International Conference on Bioinformatics & Biomedicine Workshop ?NLP Approaches for Unmet Information Needs in Health Care, Washington, DC. Chen et al. Editor, 308-313.[link]
  14. Yu H and Cao YG. 2009. Using the weighted keyword models to improve information retrieval for answering biomedical questions. To appear in AMIA Summit on Translational Bioinformatics. [link]
  15. Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, TaniyaT, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, BarreroRA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB,Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, SanbonmatsuR, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, MashimaJ, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M,Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, IkeoK, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, HortonP, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, DebilyMA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo M, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M,Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato PJ, Isogai T,Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K,Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares M, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T,Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y,Imanishi T, and Gojobori T. Genome Information Integration Project and H-Invitational 2* (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research 36 2008: D793-D799 [link]
  16. Belknap SM, Moore H, Lanzotti SA, Yarnold PR, Getz M, Deitrick DL, Peterson A, Akeson J, Maurer T, Soltysik RC, Storm GA, Brooks I. Application of software design and debugging to an analgesia prescription reduces severe injury from medical use of opioids. Clin Pharmacol Ther. 2008 Sep;84(3):385-92. [link]
  17. Yu H, Frid N, McRoy S, Prasad R, Lee A, and Joshi A. 2008. A Pilot Annotation to Investigate Discourse Connectivity in Biomedical Text. In The 46th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies BioNLP. 2008. [link]
  18. Yu, H, Cao YG. 2008. Automatically extracting information needs from ad-hoc clinical questions. In Proceedings of American Medical Informatics Association (AMIA) Fall Symposium. [link]
  19. Yu, H, Frid N, McRoy S, Simpson P, Prasad R, Lee A, Joshi A. 2008. Exploring Discourse Connectivity in Biomedical Text for Text Mining. In Proceedings of the 16th Annual International Conference on Intelligent Systems for Molecular Biology BioLINK SIG meeting, Toronto, Canada
  20. Cohen KB, Yu H, Bourne PE, Hirschman L. 2008. Translating biology: text mining tools that work. Pacific Symposium on Biocomputing 13:551-555. [link]
  21. Yu, H, Lee M, Kaufman D, Ely J, Osheroff JA, Hripcsak G, Cimino J. 2007. Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians. Journal of Biomedical Informatics (JBI). Jun;40(3):236-51. [link]
  22. Yu, H, Kim W, Hatzivassiloglou V, and Wilbur J. 2007. Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. Journal of Biomedical Informatics (JBI) 40(2):150-9. [link]
  23. Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB. 2007. New frontiers in biomedical text mining. Pacific Symposium on Biocomputing (PSB) 12:205-208. [link]
  24. Yu, H, Kim W, Hatzivassiloglou V, and Wilbur J. 2006. Disambiguating biomedical abbreviations. ACM Transactions on Information Systems (TOIS) Vol (24), Issue No. 3. page 380-404. [link]
  25. Kwitek AE, Jacob H, Baker J, Dwinell M, Forster H, Greene A, Kunert M, Lombard J, Mattson D, Pritchard K, Roman R, Tonellato PJ, and Cowley AW. BN phenome: detailed characterization of the cardiovascular, renal, and pulmonary systems of the sequenced rat. Physiol Genomics. 2006 Apr 13;25 (2):303-13. [link]
  26. Lee M, Cimino J, Osheroff J, Ely J, and Yu H. 2006. Beyond information retrieval-Medical question answering. In Proceedings of American Medical Informatics Association (AMIA) Fall Symposium: 469-73. [link]
  27. Yu, H and Wei Y. 2006. The semantics of a definiendum constrains both the lexical semantics and the lexicosyntactic patterns in the definiens. Paper in HLT-NAACL 2006 Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis (BioNLPâ??06). [link]
  28. de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Fan C, Harris G, Jin W, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Wang W, Wu W, Zhao L, Kwitek A, Tonellato PJ, Jacob H, The Rat Genome Database (RGD): Developments towards a Phenome Database, Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D485-91. [link]
  29. Yu, H, Sable C and Zhu HR. 2005. Classifying medical questions based on an Evidence Taxonomy. In American Association for Artificial Intelligence (AAAI 05) Workshop on Question Answering in Restricted Domains. [link]
  30. Yu, H and Sable C. 2005. Being Erlang Shen: Identifying Answerable Questions. Paper in International Joint Conference of Artificial Intelligence (IJCAIâ??05) Workshop on Knowledge and Reasoning for Answering Questions. [link]
  31. Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboue PA,  Weng WB, Hatzivassiloglou V and Friedman C. GeneWays: A System for Extracting, Analyzing, Visualizing and Integrating Molecular Pathway Data.  Journal of Biomedical Informatics 2004 Feb;37(1):43-53. [link]
  32. Zhou G, Wen X, Liu H, Schlicht MJ, Hessner MJ, Tonellato PJ, Datta MW. B.E.A.R. GeneInfo: a tool for identifying gene-related biomedical publications through user modifiable queries. BMC Bioinformatics. 2004 Apr 29;5(1):46 [link]>
  33. Halligan, B. D.; Dratz, E. A.; Feng, X.; Twigger, S. N.; Tonellato, P. J.; Greene, A. S. Peptide Identification Using Peptide Amino Acid Attribute Vectors. J. Proteome Res.; (Article); 2004. [link]
  34. Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ. Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. Genome Res. 2004 Apr;14 (4):651-60. [link]
  35. The Rat Genome Project Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428 (6982):493-521. [link]
  36. Harris MA, Tonellato P.J, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1; 32(1): D258-61. [link]
  37. Yu, H, Kim W and Wilbur WJ.  2004.  Using MEDLINE as a knowledge source for disambiguating abbreviations in biomedical full-text articles. In 17th IEEE Symposium on Computer-Based Medical Systems.[link]
  38. Bethard S, Yu H, Thornton A, Hatzivassiloglou V, and Jurafsky D. 2004. Semantic analysis of propositional opinions. National Conference on Artificial Intelligence (AAAI) Spring Symposium on Exploring Attitude and Affect in Text: Theories and Applications, Palo Alto, California.
  39. Moreno C, Dumas P, Kaldunski ML, Tonellato PJ, Greene AS, Roman RJ, Cheng Q, Wang Z, Jacob HJ, Cowley AW Jr. Genomic map of cardiovascular phenotypes of hypertension in female Dahl S rats. Physiol Genomics. 2003 Nov 11; 15(3): 243-57. [link]
  40. Yu, H, Hatzivassiloglou V, Rzhetsky A and Wilbur WJ. 2003.  Automatically Identifying Gene/Protein Terms in MEDLINE abstracts.  Journal of Biomedical Informatics (JBI), Vol 35 (5-6): 322-330. [link]
  41. Yu, H and Agichtein E. 2003. Extracting Synonymous Gene and Protein Terms from Biological Literature.  Bioinformatics  Vol 19 (Suppl 1): i340-i349. [link]
  42. Tatay JW, Feng X, Sobczak N, Jiang H, Chen C, Kirova R, Struble C, Wang N, Tonellato PJ. Mining MALDI-TOF Data: Multiple Approaches to Data-Mining of Proteomic Data based on Statistical and Pattern Classification Methods, Proteomics, 3(9) 1659-132, Sept., 2003 [link]
  43. Yu, H and Hatzivassiloglou V.  2003. Towards Answering Opinion Questions: Separating Facts from Opinions and Identifying the Polarity of Opinion Sentences.  In Proceedings of 2003 Conference on Empirical Methods in Natural Language Processing (EMNLP).  [link]
  44. Yu, H, Hripcsak G and Friedman C. 2002. Mapping Abbreviations to Full Forms in Biomedical Articles. Journal of American Medical Informatics Association (JAMIA) 9(3): 262-272. [link]
  45. Kendziorski CM, Cowley AW Jr, Greene AS, Salgado HC, Jacob HJ, Tonellato PJ. Mapping baroreceptor unction to genome: a mathematical modeling approach. Genetics 160:1687-1695, 2002. [link]
  46. Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen CF, Nigam R, Kwitek-Black A, Eppig J, Maltais L, Maglott D, Schuler G, Jacob H, Tonellato PJ. Rat Genome Database (RGD) ? mapping disease onto the genome. Nucleic Acids Research 30(1):125-128, 2002. [link]
  47. Hafner JW Jr. Belknap SM. Squillante MD. Bucheit KA. Adverse drug events in emergency department patients. Ann Emer Med. 39(3):258-67, 2002 March. [link]
  48. Friedman C, Kra P, Yu H, Krauthammer M, and Rzhetsky A. 2001. GENIES: A Natural-Language Processing System for the Extraction of Molecular Pathways from Journal Articles. Bioinformatics 2001 Suppl 1:S74-82. [link]
  49. Stoll M, Cowley AW Jr, Tonellato PJ, Greene AS, Kaldunski ML, Roman RJ, Dumas P, Schork NJ, Wang Z, Jacob HJ. A genomic-systems biology map for cardiovascular function. Science 294:1723-1726, 2001. [link]
  50. Cohen M. Belknap S. Phillips J. 'High-alert' medications and patient safety. International Journal for Quality in Health Care. 2001 13(4):339-340 [link]
  51. Graumlich JF. Belknap SM. Bullard SA. Storm GA. Brunsman KS. Howerton JA. Pharmaceutical care of postoperative nausea and vomiting: balanced scorecard for outcomes. Pharmacotherapy. 20(11):1365-74, 2000 Nov. [link]
  52. Yu, H and Hripcsak G. 2000. A Large Scale, Cross-Disease Family Health History. In Proceedings of American Medical Informatics Association (AMIA) Symposium 2001: 1162.[link]
  53. Yu, H and Hripcsak G. 2000. Hereditary Disease Discovery from a Clinical Data Warehouse. In Proceedings of American Medical Informatics Association (AMIA) Symposium 2001:1161.[link]
  54. Lu J, Kwitek-Black A, Jacob HJ, Tonellato PJ. A web-based rat radiation hybrid map server. Rat Genome 5(2):77, 1999.
  55. Lentino J. Belknap S. Byrne R. Once Daily Aminoglycosides Achieve Peaks Twice Those of Multiple Daily Dosing without Toxicity. ICAAC Abstracts 1992
  56. Belknap SM. Chicago Kinetic Simulator: A Mathematica Program For Simulation of Mathematical Models. The Mathematica J 1991 Vol 1, No 4, pp. 68-86. [link]

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