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This project fits within the research context of the Natural Language Systems Program within the Cognitive Science Branch at the Lister Hill Center for Biomedical Commmunications.

The Semantic Knowledge Representation (SKR) project is concerned with reliable and effective management of the information encoded in natural language texts. The project develops programs that provide usable semantic representation of biomedical text by building on resources currently available at the Library, especially the UMLS knowledge sources and the natural language processing tools provided by the SPECIALIST system.

Two programs in particular, MetaMap and SemRep, are being evaluated and enhanced and applied to a variety of problems in the management of biomedical information. These include automatic indexing of MEDLINE citations (Indexing Initiative), concept-based query expansion, analysis of complex Metathesaurus strings, accurate identification of the terminology and relationships in anatomical documents, and the extraction of chemical binding relations from biomedical text.

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SKR Background Papers & Presentations
	(48 kb)	Overview of SKR, 1998
	(42 kb)	Semantic processing in information retrieval. (1993) Proceedings of the 17th Annual Symposium on Computer Applications in Medical Care, 611-15.
	(54 kb)	Natural language processing. (1996) Annual Review of Applied Linguistics 16, 71-85.
MetaMap
	Fundamentals
	(201 kb)	Please Read This Paper First An overview of MetaMap: historical perspective and recent advances, JAMIA 2010
	(12 kb)	The Evolution of MetaMap, a Concept Search Program for Biomedical Text, AMIA 2009
	(723 kb) (1.1 mb)	Presentation: The Evolution of MetaMap, a Concept Search Program for Biomedical Text, Presented November 16, 2009 at AMIA 2009
	(716 kb) (1.1 mb)	Presentation: The Current State of MetaMap and MMTx Webcast, August 20, 2009
	(280 kb)	MetaMap: Mapping Text to the UMLS Metathesaurus, July 2006 <<< UPDATED FOR 2006
	(50 kb)	MetaMap Options and Examples, September 2006 <<< UPDATED FOR 2006
	(58 kb)	Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program, 2001
	2010 AMIA MetaMap Tutorial
	(38 kb)	MetaMap 2010 AMIA Tutorial Description (PDF)
	(3 kb)	MetaMap 2010 AMIA Tutorial Description (Text)
	(3.2 mb)	MetaMap 2010 AMIA Tutorial Slides (PowerPoint)
	(1.6 mb)	MetaMap 2010 AMIA Tutorial Slides (PDF)
	Technical Documents
	(99 kb)	MetaMap Technical Notes, 1996
		Ambiguity in the UMLS Metathesaurus -- 2012 Higher Degree Metathesaurus Ambiguity Report Excel (14 kb) -- 2012 Version Summary Report (28 kb) -- 2011 Higher Degree Metathesaurus Ambiguity Report Excel (13 kb) -- 2011 Version Summary Report (28 kb) -- 2010 Higher Degree Metathesaurus Ambiguity Report Excel (12 kb) -- 2010 Version Summary Report (182 kb) -- 2009 Version Summary Report (384 kb) -- 2008 Version Summary Report (144 kb) -- 2007 Version Summary Report (100 kb) -- 2006 Version Summary Report (201 kb) -- 2005 Version Summary Report (124 kb) -- 2004 Version Summary Report (72 kb) -- 2003 Version Summary Report (92 kb) -- 2002 Version Summary Report (289 kb) -- 2001 Version Summary Report (182 kb) -- 2000 Version Summary Report (112 kb) -- 1999 Version Summary Report (59 kb)
		Filtering the UMLS Metathesaurus for MetaMap -- 2012 Version (22 kb) -- 2011 Version (22 kb) -- 2010 Version (153 kb) -- 2009 Version (22 kb) -- 2008 Version (210 kb) -- 2007 Version (72 kb) -- 2006 Version (68 kb) -- 2005 Version (59 kb) -- 2004 Version (145 kb) -- 2003 Version (51 kb) -- 2002 Version (48 kb) -- 2001 Version (48 kb) -- 2000 Version (48 kb) -- 1999 Version (18 kb)
	(27 kb)	MetaMap Variant Generation, 2001
	(25 kb)	MetaMap Candidate Retrieval, 2001
	(63 kb)	MetaMap Evaluation, 2001
	(19 kb)	MetaMap Mapping Algorithm, 2001
	(36 kb)	MetaMap Update Procedures, 2000
	(41 kb)	Comparison of LVG and MetaMap Functionality, 1994
	Papers
	(46 kb)	*The effect of textual variation on concept based information retrieval*, 1996
	(70 kb)	*Exploiting a large thesaurus for information retrieval.* (1994) Proceedings of RIAO, 197-216.
	Related Papers
	(14 kb)	*MetaMap in the CALBC Workshop II.* J. G. Mork, L. Peters, A. Jimeno Yepes, A. R. Aronson, O. Bodenreider, CALBC Workshop II, 2011.
	(229 kb)	*Semantic processing for enhanced access to biomedical knowledge*, Rindflesch, Thomas C., and Alan R. Aronson. 2002. Vipul Kashyap and Leon Shklar (eds.) Real World Semantic Web Applications, 157-72. IOS Press.
	(50 kb)	*Analysis of biomedical text for chemical names: A comparison of three methods*, 1999
	(92 kb)	*Hierarchical concept indexing of full-text documents in the UMLS information sources map.* Journal of the American Society for Information Science (1998). 50(6):514-23.
	(41 kb)	*Query expansion using the UMLS Metathesaurus.* Proceedings of the 1997 AMIA Annual Fall Symposium, 485-89.
	(51 kb)	*Finding the findings: Identification of findings in medical literature using restricted natural language processing.* Proceedings of the 1996 AMIA Annual Fall Symposium, 239-43.
Clinical
	(148 kb)	*UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (Full Paper)*, JBI 2010
	(25 kb)	*UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (400 Word Abstract)*, AMIA 2009
	(508 kb)	*Extracting Rx Information from Clinical Narrative (Full Paper)*, 2010
	(53 kb)	*Extracting Rx Information from Clinical Narrative (Short Paper)*, JAMIA 2010
	(50 kb)	*Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing*, AMIA 2008
	(158 kb)	*From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches*, BioNLP 2007
TREC Medical Records Track Participation
	(146 kb)	*A knowledge-based approach to medical records retrieval.* D. Demner-Fushman, S. Abhyankar, A. Jimeno-Yepes, R. Loane, B. Rance, F. Lang, N. Ide, E. Apostolova, and A.R. Aronson, In Text Retrieval Conference (TREC 2011) Proceedings, pages 163-172.
Indexing Initiative and The Medical Text Indexer (MTI)
	(1.9 mb)	*2012 Report to the Board of Scientific Counselors*
	(7.9 mb)	*2012 PowerPoint Presentation to the Board of Scientific Counselors*
	(12.8 mb)	*2012 Powerpoint Presentation to the Board of Scientific Counselors* (PDF version, no slide animations)
	(1 mb)	*Presentation for NIH-sponsored Workshop on Natural Language Processing*, April 2012
	(2.1 mb)	*Presentation for NIH-sponsored Workshop on Natural Language Processing*, April 2012 (PDF version, no slide animations)
	(228 kb)	*MeSH indexing: machine learning and lessons learned.* A. Jimeno Yepes, B. Wilkowski, J.G. Mork, D. Demner Fushman, and A.R. Aronson, ACM SIGHIT International Health Informatics Symposium, Miami, FL, USA, 2012.
	(988 kb)	*A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning.* Antonio Jimeno-Yepes, James G. Mork, Dina Demner-Fushman, Alan R. Aronson, JCSE, vol. 6, no. 2, pp.151-160, 2012.
	(78 kb)	*Automatic algorithm selection for MeSH Heading indexing based on meta-learning.* A. Jimeno Yepes, J.G. Mork, D. Demner Fushman, and A.R. Aronson, International Symposium on Languages in Biology and Medicine, Singapore, December, 2011.
	(262 kb)	*A bottom-up approach to MEDLINE indexing recommendations.* A. Jimeno Yepes, B. Wilkowski, J.G. Mork, E. van Lenten, D. Demner Fushman, A. R. Aronson, AMIA, Washington DC, 2011.
	(395 kb)	*Automatic inference of indexing rules for MEDLINE*, BMC Bioinformatics, 2008
	(1.5 mb)	*2008 Report to the Board of Scientific Counselors*
	(1.1 mb)	*User-centered Evaluation of the MTI System*, 2007
	(39 kb)	*Fine-Grained Indexing of the Biomedical Literature: MeSH Subheading Attachment for a MEDLINE Indexing Tool*, AMIA 2007
	(103 kb)	*Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature*, Proc Pacific Symposium on Biocomputing 2007
	(44 kb)	*Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations*, BioNLP 2007
	(100 kb)	*Semi-Automatic Indexing of Full Text Biomedical Articles*, AMIA 2005
	(50 kb)	*Evaluation of French and English MeSH Indexing Systems with a Parallel Corpus*, AMIA 2005
	(54 kb)	*The NLM Indexing Initiative's Medical Text Indexer*, MedInfo 2004
	(319 kb)	*Application of a Medical Text Indexer to an Online Dermatology Atlas*, MedInfo 2004
	(510 kb)	*A MEDLINE Indexing Experiment Using Terms Suggested by MTI*, June 2002
	(2.1 mb)	*Automated and Semi-automated Indexing, Report to the Board of Regents 2002*
	(130 kb)	*Automatic MeSH Term Assignment and Quality Assessment*, AMIA 2001
	(139 kb)	*The NLM Indexing Initiative, 2000*
	(203 kb)	*1999 Report to the Board of Scientific Counselors*
	(203 kb)	*1999 AMIA Poster Presentation: Automated Assignment of Medical Subject Headings* (HTML)
	(503 kb)	*Medical Text Indexer (MTI) Processing Flow*
Word Sense Disambiguation (WSD)
	(150 kb)	*Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation.* A. Jimeno Yepes, A.R. Aronson, ACM SIGHIT International Health Informatics Symposium, 2012.
	BMC Bioinformatics	*Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts*, Laura Plaza, Antonio J Jimeno-Yepes, Alberto Díaz, Alan R Aronson, BMC Bioinformatics, August 2011
	BMC Bioinformatics	*Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation*, Antonio J Jimeno-Yepes, Bridget T McInnes, Alan R Aronson, BMC Bioinformatics, June 2011
	BMC Bioinformatics	*Collocation analysis for UMLS knowledge-based word sense disambiguation*, Antonio J Jimeno-Yepes, Bridget T McInnes, Alan R Aronson, BMC Bioinformatics, June 2011
	(202 kb)	*Preliminary results for Biomedical Word Sense Disambiguation based on Semantic Clustering.* Martín-Wanton, R. Berlanga-Llavori, A. Jimeno Yepes, Proceedings of DEXA, Toulouse, France, 2011.
	(18 kb)	*Self-training and co-training in biomedical word sense disambiguation.* A. Jimeno Yepes, A. R. Aronson, Proceedings of ACL BioNLP, Portland, USA, 2011.
	BMC Bioinformatics	*Knowledge-based biomedical word sense disambiguation: comparison of approaches*, Antonio Jimeno-Yepes, Alan R. Aronson, BMC Bioinformatics, November 2010
	(51 kb)	*Query expansion for UMLS Metathesaurus disambiguation based on automatic corpus extraction.* A. Jimeno Yepes, A. R. Aronson, Proceedings of ICMLA, Bethesda, USA, 2010.
	(87 kb)	*Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation*, Antonio Jimeno-Yepes, Alan R. Aronson, BioSEPLN, 2010.
	(386 kb)	*Word sense disambiguation by selecting the best semantic type based on Journal Discriptor Indexing: preliminary experiment.* Humphrey, SM; Rogers, WJ; Kilicoglu H; Demner-Fushman, D; Rindflesch, TC. J Am Soc Inf Sci Technol 2006 Jan;57(1):96-113. *Erratum* in: J AM Soc Inf Sci, Mar. 2006, 57(4):726. (20.6kb)
	(93 kb)	*Developing a Test Collection for Biomedical Word Sense Disambiguation*, Marc Weeber, James G. Mork, Alan R. Aronson, AMIA 2001
	(76 kb)	*Automatic indexing by discipline and high-level categories: methodology and potential applications.* Humphrey, SM; Rindflesh, TC; Aronson, AR. In: Soergel D, Srinivasan P, Kwasnik B, editors. Proceedings of the 11th ASIST SIG/CR Classification Research Workshop; 2000 Nov 12; Chicago. Silver Spring (MD): American Society for Information Science and Technology; 2000. p. 103-16.
	(551 kb)	*Automatic indexing of documents from journal descriptors: a preliminary investigation.* Humphrey, SM. J Am Soc Inf Sci. 1999 Jun;50(8):661-74.
	(38 kb)	*Ambiguity resolution while mapping free text to the UMLS Metathesaurus.* (1994) Proceedings of the 18th Annual Symposium on Computer Applications in Medical Care, 240-4.
Semantic Interpretation
	(224 kb)	*Strategies for Mapping Concepts in Gastrointestinal Endoscopy Reports to the UMLS Metathesaurus.* Tringali M, Rindflesch TC, Kilicoglu H, Fiszman M, Bodenreider O. Medinfo. 2004 Sept.;2004: 1885.
	(275 kb)	*Summarization of an Online Medical Encyclopedia.* Fiszman M, Rindflesch TC, Kilicoglu H. MedInfo. 2004 Sept.;2004: 506-510.
	(251 kb)	*Identifying Anatomical Concepts in Biomedical Text for Automatic Selection of Images.* Bernhardt PJ, Rindflesch TC, Kilicoglu H, Tringali M. Medinfo. 2004 Sept.;2004: 1521.
	(188 kb)	*Integrating a hypernymic proposition interpreter into a semantic processor for biomedical text.* Fiszman, Marcelo; Thomas C. Rindflesch; and Halil Kilicoglu. 2003. Proceedings of the 2003 AMIA Annual Symposium.
	(232 kb)	*The Interaction of Domain Knowledge and Linguistic Structure in Natural Language Processing: Interpreting Hypernymic Propositions in Biomedical Text.* Rindflesch TC , Fiszman M. Journal of Biomedical Informatics. 2003;36(6):462-77.
	(158 kb)	*Exploring text mining from MEDLINE.* Srinivasan, Padmini, and Thomas C. Rindflesch. 2002. Isaac Kohane (ed.) Proceedings of the 2002 AMIA Annual Symposium, 722-6.
	(49 kb)	*Argument identification for arterial branching predications asserted in cardiac catheterization reports.* Submitted to AMIA 2000.
	(30 kb)	*Semantic interpretation, 1999*
	(41 kb)	*Identification of anatomical terminology in medical text.* Proceedings of the 1998 AMIA Annual Fall Symposium, 428-32.
	[HTML]	*Automatic semantic interpretation of anatomic spatial relationships in clinical text.* Proceedings of the 1998 AMIA Fall Symposium, 897-901.
	(51 kb)	*Integrating natural language processing and biomedical domain knowledge for increased information retrieval effectiveness.* (1995) Proceedings of the 5th Annual Dual-use Technologies and Applications Conference, 260-5.
Biomedical
	(65 kb)	*Semantic relations asserting the etiology of genetic diseases.* Rindflesch, Thomas C.; Bisharah Libbus; Dimitar Hristovski; Alan R. Aronson; and Halil Kilicoglu. 2003. Proceedings of the AMIA Annual Symposium.
	(211 kb)	*Discovering protein similarity using natural language processing.* Sarkar, Indra Neil, and Thomas C. Rindflesch. 2002. Isaac Kohane (ed.) Proceedings of the AMIA Annual Symposium, 677-81.
	(90 kb)	*NLP-based information extraction for managing the molecular biology literature.* Libbus, Bisharah, and Thomas C. Rindflesch. 2002. Isaac Kohane (ed.) Proceedings of the AMIA Annual Symposium, 445-9.
	(69 kb)	*Extracting molecular binding relationships from biomedical text.* (2000) Proceedings of the 6th Applied Natural Language Processing Conference, 188-95. Association for Computational Linguistics.
	(64 kb)	*EDGAR: Extraction of drugs, genes and relations from the biomedical literature.* (2000) Pacific Symposium on Biocomputing 5:514-25.
	(47 kb)	*Mining molecular binding terms from biomedical text.* Proceedings of the 1999 AMIA Fall Symposium, 127-31.
MMI
	(5 kb)	*MMI project description, 1997*
	(32 kb)	*MMI ranking function, 1997*
	(39 kb)	*A MEDLINE indexing experiment, 1997*
PhraseX
	(163 kb)	*Finding UMLS Metathesaurus concepts in MEDLINE*. Srinivasan, Suresh; Thomas C. Rindflesch; William T. Hole; and Alan R. Aronson. 2002. Isaac Kohane (ed.) Proceedings of the AMIA Annual Symposium, 727-31.
	external webpage	*PhraseX and the SPECIALIST Minimal Commitment Parser*
TREC Genomics Track Participation
	(112 kb)	*Combining Resources to Find Answers to Biomedical Questions*, Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, et al. Proc TREC 2007, 2005-14.
	(156 kb)	*Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort*, Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ, Aronson AR. Proc TREC 2006, 569-76.
	(296 kb)	*Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents*, Aronson AR, Demner-Fushman D, Humphrey SM, Lin J, Liu H, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ. Proc TREC 2005, 36-45.
	(275 kb)	*Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations*, Aronson AR, Demner D, Humphrey SM, Ide NC, Kim W, Liu H, Loane RR, Mork JG, Smith LH, Tanabe LK, Wilbur WJ, Xie N. Proc TREC 2004, 503-11.
	(357 kb)	*Methods for Accurate Retrieval of MEDLINE Citations in Functional Genomics*, Kayaalp, Mehmet, Aronson, Alan R, Humphrey, Susanne M, Ide, Nicholas C, Tanabe, Lorraine K. Proc TREC 2003, 175-84.