A Natural Language Processing Resource

The long-term objective of this project is to perform technological research and development of methods to facilitate refinement, extension and adaptation of the MedLEE NLP system by creating plug-in components in order to encourage experimentation and widespread use of NLP technology by other users, and to enable the processing of a wide range of clinical reports and textual articles that encompass many different biomedical sub-fields. This includes development of tools that facilitate utilization of the structured and encoded output generated by the NLP system to encourage widespread utilization of the NLP output. This also includes developing complete clinical applications, as well as tools that visualize and organize the information, and that facilitate retrieval and mining of the information.

Funding

This project has been funded in part by Grant R01LM008635 from the National Library of Medicine, and by the NYC/DOHMH Center of Excellence in Public Health Informatics.

Carol Friedman PhD Professor &Vice-Chair Department of Biomedical Informatics Email: friedman@dbmi.columbia.edu Tel: (212) 305-5399

Lyudmila Shagina Sr. Programmer Analyst Email: shagina@dbmi.columbia.edu Tel: (212) 305-1481

Jianhua Li MA Sr. Programmer Analyst Email: jianhua.li@dbmi.columbia.edu Tel: (212) 305-0514

Rave Harpaz Email: rave.harpaz@dbmi.columbia.edu Tel: (212) 342-1644

Jungwei Fan Email: jungwei.fan@dbmi.columbia.edu Tel: (212) 342-1637

MedLEE Demo: Medical Language Extraction and Encoding System Processing System

Resources

• PG Model: An information model representing genotypic and phenotypic entities, modifiers, and relations
• PhenoGO: Database providing phenotypic context to Gene Ontology (GO) terms as specified in GOA for multiple organisms
• Semantic reclassification of UMLS concepts based on automated methods
• Disease-Symptom Knowledge Base
• Pre-processor to handle poorly defined section and sentence boundaries
• Parenthetical Expression Tagger

Publications

• Tao Y, Friedman C, Lussier YA. Visualizing information across multidimensional post-genomic structured and textual databases. Bioinformatics. 2005 Apr 15;21(8):1659-67. Epub 2004 Dec 14.
• Mendonca EA, Haas J, Shagina L, Larson E, Friedman C. Extracting information on pneumonia in infants using natural language processing of radiology reports. J Biomed Inform. 2005 Aug;38(4):314-21. Epub 2005 Mar 30.
• Hass JP, Mendonca EA, Ross B, Friedman C, Larson E. Use of computerized surveillance to detect nosocomial pneumonia in neonatal intensive care unit patients. Am J Infect Control. 2005 Oct;33(8):439-43.
  
• Zhou L, Tao Y, Cimino JJ, Chen ES, Liu H, Lussier YA, Hripcsak G, Friedman C. Terminology model discovery using natural language processing and visualization techniques. J Biomed Inf.
  
• Bakken S, Hyun S, Friedman C, Johnson SB. ISO reference terminology models for nursing: applicability for natural language processing of nursing narratives. Int J Med Inf. 2005;74:615-622.
  
• Zhou L, Friedman C, Parsons S, Hripcsak G. System architecture for temporal information extraction, representation, and reasoning in clinical narrative reports.2005 AMIA Symp. 2005:869-874. PMCID: PMC1560711.
  
• Bales ME, Kukafka R, Burkhardt A, Friedman C. Qualitative assessment of International Classification of Functioning, Disability, and Health with respect to the desiderata for controlled medical vocabularies. Int J Med Inform. 2005 Aug 22; Epub Aug 22.
  
• Lussier YA, Borlawski T, Rappaport D, Liu Y, Friedman C. PhenoGO: assigning phenotypic context to Gene Ontology annotations with natural language processing. Pac Symp Bio. 2006:64-75.
• Tulipano P.K., Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier YA, Friedman C. Natural language processing and visualization in the molecular imaging domain. J.Biomed.Inform. 2006 Sep 26. (DOI:http://dx.doi.org/10.1016/j.jbi.2006.08.002). PMCID: PMC1560602.
• *Friedman C, Borlawsky T, Shagina L, Xing HR, Lussier YA. Bio-Ontology and text: bridging the modeling gap. Bioinformatics. 2006 Oct 1;22(19):2421-9.
• Liu H, Hu ZZ, Torii M, Wu C, Friedman C. Quantitative assessment of dictionary-based protein named entity tagging. J.Am.Med.Inform.Assoc. 2006 Sep;13(5):497-507. PMCID: PMC1561801.
• Kukafka R, Bales ME, Burkhardt A, Friedman C. Human and automated coding of rehabilitation discharge summaries according to the International Classification of Functioning, Disability, and Health. J.Am.Med.Inform.Assoc. 2006 Sep;13(5):508-15. PMCID: PMC1561799.
• Zhou L, Tao Y, Cimino JJ, Chen ES, Liu H, Lussier YA, Hripcsak G, Friedman C. Terminology model discovery using natural language processing and visualization techniques. J.Biomed.Inform. 2006 Dec;39(6):626-36.
• Chen ES, Hripcsak G, Friedman C. Disseminating natural language processed clinical narratives. In Proc 2006 AMIA Symp; 2006. p. 126-30. PMCID: PMC1839529. PMCID: PMC1839529.
• Borlawsky T, Friedman C, Lussier Y. Generating executable knowledge for evidence-based medicine using natural language and semantic processing. In Proc. AMIA 2006 Symp; 2006. p. 56-60. PMCID: PMC1839756.
• Hristovski D, Friedman C, Rindflesch T, Peterson BJ. Exploiting semantic relations for literature-based discovery. In Proc AMIA 2006 Symp; 2006. p. 349-53. PMCID: PMC1839258.
• Xu H, Markatou M, Dimova R, Liu H, Friedman C. Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinformatics. 2006;7:334. PMCID: PMC1550263.
• Sam L, Liu Y, Li Jianrong, Friedman C, Lussier YA. Discovery of protein interaction networks shared by diseases. Pac Symp Bio. 2007:76-87.
• Xu H, Fan JW, Hripcsak G, Mendonca EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics. 2007 Feb 21 [Epub ahead of print].
• Tao Y, Sam L, Li J, Friedman C, Lussier YA. Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics. 2007 Jul 1;23(13):i529-38.
• Hristovski D, Friedman C, Rindflesch T. Implementing a literature-based discovery system using semantic relations. Medinfo 2007.
• Xu H, Fan JW, Hripcsak G, Mendonca EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics. 2007 Apr 15;23(8):1015-22. Epub 2007 Feb 21.
• Fan JW, Xu H, Friedman C. Using distributional analysis to semantically classify UMLS concepts. In Proceedings of Medinfo 2007, Brisbane, Australia: 519-23.
• Xu H, Fan JW, Friedman C. Combining multiple evidence for gene symbol disambiguation. In Proc BioNLP Workshop 2007:pp. 41–48.
• Fan JW, Friedman C. Classification of biomedical concepts using distributional similarity. J.Am.Med.Inform.Assoc. 2007 Jul-Aug;14(4):467-77. Epub 2007 Apr 25. PMCID: PMC2244895.
• Fan JW, Xu H, Friedman, C. Using contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007 Jul 24;8(1):264 [Epub ahead of print]. PMCID: PMC2014782.
• Fan JW, Friedman C. Combining contextual and lexical features to classify UMLS concepts. In Proc 2007 AMIA Symp; 2007. p. 231-4. PMCID: PMC2655898.
• Chen CE, Stetson PD, Lussier YA, Markatou M, Hripcsak G, Friedman C. Detection of practice pattern trends through natural language processing of clinical narratives and biomedical literature. In Proc 2007 AMIA Symp:2007, p 120-124. PMCID: PMC2655911.
• Sam LT, Borlawsky T, Tao Y, Li J, Friedman C, Smith B, Lussier YA. Information-theoretic classification of SNOMED improves the organization of context-sensitive excerpts from Cochrane reviews. In Proc 2007 AMIA Symp; 2007. p. 645-9. PMCID: PMC2655812.
• Xu H, Stetson P, Friedman C. A study of abbreviations in clinical notes. In Proc 2007 AMIA Symp; 2007. p. 821-4. PMCID: PMC2655910.
• Chen ES, Hripcsak G, Xu H, Markatou M, Friedman C. Automatic acquisition of disease drug knowledge from biomedical and clinical documents: an initial study. J Am Med Inf Assoc 2008. PMCID: PMC2274872.
• Fan JW, Friedman C. Semantic reclassification of the UMLS concepts. Bioinformatics. 2008 Sep 1;24(17):1971-3. PMCID: PMC2519163.
• Li L, Chase HS, Patel CO, Friedman C, Weng C. Comparing ICD9-encoded diagnoses and NLP-processed discharge summaries for clinical trials pre-screening: a case study. AMIA Annu Symp Proc. 2008. p. 404-8. PMCID: PMC2656007.
• Wang X, Chused A, Elhadad N, Friedman C, Markatou M. Automated knowledge acquisition from clinical reports. AMIA Annu Symp Proc. 2008. p. 783-7. PMCID: PMC2656103.
• Fan JW, Friedman C. Word sense disambiguation via semantic type classification. AMIA Annu Symp Proc. 2008. p. 177-81. PMCID: PMC2655949.
• Xu H, Stetson P, Friedman C. Methods for building sense inventories of abbreviations in clinical notes. J Am Med Inf Assoc 2009 Jan-Feb;15(1):87-98. PMCID: PMC2605589.
• Sam LT, Mendonca EA, Li J, Blake J, Friedman C, Lussier YA. PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinformatics 2009;10 Suppl 2:S8. PMCID: PMC2646241.
• Wang X, Hripcsak G, Markatou M, Friedman C. Active Computerized Pharmacovigilance using Natural Language Processing, Statistics, and Electronic Health Records: a Feasibility Study. J Am Med Inform Assoc 2009 March 4. PMCID: PMC2732239.
• Xu H, Stetson PD, Friedman C. Methods for building sense inventories of abbreviations in clinical notes. J Am Med Inform Assoc 2009 January;16(1):103-8. PMCID: PMC2605589.
• Hripcsak G, Soulakis ND, Li L et al. Syndromic Surveillance Using Ambulatory Electronic Health Records. J Am Med Inform Assoc 2009 March 4;16(3):354-361. PMCID: PMC2732227.