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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
PDF - Overview of SKR paper (48 kb) Overview of SKR, 1998
PDF - Semantic processing in information retrieval paper (42 kb) Semantic processing in information retrieval. (1993) Proceedings of the 17th Annual Symposium on Computer Applications in Medical Care, 611-15.
PDF - Natural language processing paper (54 kb) Natural language processing. (1996) Annual Review of Applied Linguistics 16, 71-85.
MetaMap
Fundamentals
PDF - Effective Mapping of Biomedical Text to the UMLS  Metathesaurus: The MetaMap Program, 2001 paper (58 kb) Animated gif with # 1 metaphorical as #1 reference    Please Read This Paper First
Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program, 2001
PDF - MetaMap: Mapping Text to the UMLS Metathesaurus paper (280 kb) MetaMap: Mapping Text to the UMLS Metathesaurus, July 2006 <<< UPDATED FOR 2006
PDF - MetaMap Examples & Options (50 kb) MetaMap Options and Examples, September 2006 <<< UPDATED FOR 2006
Technical Documents
PDF - MetaMap Technical Notes paper (99 kb) MetaMap Technical Notes, 1996
  Ambiguity in the UMLS Metathesaurus
           --  2008 Version  PDF - Ambiguity in the UMLS Metathesaurus 2008 paper (144 kb)
           --  2007 Version  PDF - Ambiguity in the UMLS Metathesaurus 2007 paper (100 kb)
           --  2006 Version  PDF - Ambiguity in the UMLS Metathesaurus 2006 paper (201 kb)
           --  2005 Version  PDF - Ambiguity in the UMLS Metathesaurus 2005 paper (124 kb)
           --  2004 Version  PDF - Ambiguity in the UMLS Metathesaurus 2004 paper (72 kb)
           --  2003 Version  PDF - Ambiguity in the UMLS Metathesaurus 2003 paper (92 kb)
           --  2002 Version  PDF - Ambiguity in the UMLS Metathesaurus 2002 paper (289 kb)
           --  2001 Version  PDF - Ambiguity in the UMLS Metathesaurus 2001 paper (182 kb)
           --  2000 Version  PDF - Ambiguity in the UMLS Metathesaurus 2000 paper (112 kb)
           --  1999 Version  PDF - Ambiguity in the UMLS Metathesaurus 1999 paper (59 kb)
  Filtering the UMLS Metathesaurus for MetaMap
           --  2008 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2008 paper (83 kb)
           --  2007 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2007 paper (72 kb)
           --  2006 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2006 paper (68 kb)
           --  2005 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2005 paper (59 kb)
           --  2004 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2004 paper (145 kb)
           --  2003 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2003 paper (51 kb)
           --  2002 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2002 paper (48 kb)
           --  2001 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2001 paper (48 kb)
           --  2000 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 2000 paper (48 kb)
           --  1999 Version  PDF - Filtering the UMLS Metathesaurus for MetaMap 1999 paper (18 kb)
PDF - MetaMap Variant Generation paper (27 kb) MetaMap Variant Generation, 2001
PDF - MetaMap Candidate Retrieval paper (25 kb) MetaMap Candidate Retrieval, 2001
PDF - MetaMap Evaluation paper (63 kb) MetaMap Evaluation, 2001
PDF - MetaMap Mapping Algorithm paper (19 kb) MetaMap Mapping Algorithm, 2001
PDF - MetaMap Update Procedures paper (36 kb) MetaMap Update Procedures, 2000
PDF - Comparison of LVG and MetaMap Functionality paper (41 kb) Comparison of LVG and MetaMap Functionality, 1994
Papers
PDF - The effect of textual variation on concept based information retrieval paper (46 kb) The effect of textual variation on concept based information retrieval, 1996
PDF - Exploiting a large thesaurus for information retrieval paper (70 kb) Exploiting a large thesaurus for information retrieval. (1994) Proceedings of RIAO, 197-216.
Related Papers
PDF - Semantic processing for enhanced access to
(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.
PDF - Analysis of biomedical text for chemical names: A comparison of three methods (50 kb) Analysis of biomedical text for chemical names: A comparison of three methods, 1999
PDF - Hierarchical concept indexing of full-text documents in the UMLS information sources map paper (1998) (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.
PDF - Query expansion using the UMLS Metathesaurus paper (41 kb) Query expansion using the UMLS Metathesaurus. Proceedings of the 1997 AMIA Annual Fall Symposium, 485-89.
PDF - Finding the findings: Identification of findings in medical literature using restricted natural language processing paper (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.
PDF - Ambiguity resolution while mapping free text to the UMLS Metathesaurus paper (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.
Indexing Initiative
PDF: User-centered Evaluation of the MTI System, 2007 (1.1 mb) User-centered Evaluation of the MTI System, 2007
PDF: Fine-Grained Indexing of the Biomedical Literature: MeSH Subheading Attachment for a MEDLINE Indexing Tool, AMIA 2007 (39 kb) Fine-Grained Indexing of the Biomedical Literature: MeSH Subheading Attachment for a MEDLINE Indexing Tool, AMIA 2007
PDF: Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature, 2007 (103 kb) Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature, Proc Pacific Symposium on Biocomputing 2007
PDF: Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations, BioNLP 2007 (44 kb) Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations, BioNLP 2007
PDF: From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches, BioNLP 2007 (158 kb) From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches, BioNLP 2007
PDF: Semi-Automatic Indexing of Full Text Biomedical Articles, AMIA 2005 (100 kb) Semi-Automatic Indexing of Full Text Biomedical Articles, AMIA 2005
PDF: Evaluation of French and English MeSH Indexing Systems ..., AMIA 2005 (50 kb) Evaluation of French and English MeSH Indexing Systems with a Parallel Corpus, AMIA 2005
PDF - The NLM Indexing Initiative's Medical Text Indexer, MedInfo 2004 (54 kb) The NLM Indexing Initiative's Medical Text Indexer, MedInfo 2004
PDF: Application of a Medical Text Indexer to an Online Dermatology Atlas, MedInfo 2004 (319 kb) Application of a Medical Text Indexer to an Online Dermatology Atlas, MedInfo 2004
PDF: A MEDLINE Indexing Experiment Using Terms Suggested by MTI, June 2002 (510 kb) A MEDLINE Indexing Experiment Using Terms Suggested by MTI, June 2002
PDF: Automated and Semi-automated Indexing, Report to the Board of Regents 2002 (2.1 mb) Automated and Semi-automated Indexing, Report to the Board of Regents 2002
PDF: Automatic MeSH Term Assignment and Quality Assessment, AMIA 2001 (130 kb) Automatic MeSH Term Assignment and Quality Assessment, AMIA 2001
PDF - The NLM Indexing Initiative paper (139 kb) The NLM Indexing Initiative, 2000
PDF: 1999 Report to the Board of Scientific Counselors (203 kb) 1999 Report to the Board of Scientific Counselors
PDF: 1999 AMIA Poster Presentation: Automated Assignment of Medical Subject Headings (203 kb) 1999 AMIA Poster Presentation: Automated Assignment of Medical Subject Headings (HTML)
PDF: Medical Text Indexer (MTI) Processing Flow (503 kb) Medical Text Indexer (MTI) Processing Flow
Semantic Interpretation
PDF - Strategies for Mapping Concepts in Gastrointestinal Endoscopy Reports to the UMLS Metathesaurus (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.
PDF - Summarization of an Online Medical Encyclopedia (275 kb) Summarization of an Online Medical Encyclopedia Fiszman M, Rindflesch TC, Kilicoglu H. MedInfo. 2004 Sept.;2004: 506-510.
PDF - Identifying Anatomical Concepts in Biomedical Text for Automatic Selection of Images (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.
PDF - Integrating a hypernymic
(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.
PDF - The Interaction of Domain Knowledge and Linguistic Structure in Natural Language Processing: Interpreting Hypernymic Propositions in Biomedical Text (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.
PDF - Exploring text mining from MEDLINE (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.
PDF - Argument identification for arterial branching predications asserted in cardiac catheterization reports paper (49 kb) Argument identification for arterial branching predications asserted in cardiac catheterization reports. Submitted to AMIA 2000.
Presentation - Semantic interpretation (30 kb) Semantic interpretation, 1999
PDF - Identification of anatomical terminology in medical text paper (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.
PDF - Integrating natural language processing and biomedical domain knowledge for increased information retrieval effectiveness paper (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
PDF - Semantic relations asserting the etiology of genetic
(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.
PDF - Discovering protein similarity using
(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.
PDF - NLP-based information extraction for managing
(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.
PDF - Extracting molecular binding relationships from biomedical text paper (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.
PDF - EDGAR: Extraction of drugs, genes and relations from the biomedical literature paper (64 kb) EDGAR: Extraction of drugs, genes and relations from the biomedical literature. (2000) Pacific Symposium on Biocomputing 5:514-25.
PDF - Mining molecular binding terms from biomedical text paper (47 kb) Mining molecular binding terms from biomedical text. Proceedings of the 1999 AMIA Fall Symposium, 127-31.
MMI
PDF - MMI project description paper (5 kb) MMI project description, 1997
PDF - MMI ranking function paper (32 kb) MMI ranking function, 1997
PDF - A MEDLINE indexing experiment paper (39 kb) A MEDLINE indexing experiment, 1997
PhraseX
PDF - Finding
(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
PDF - Combining Resources to Find Answers to Biomedical Questions (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.
PDF - Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort (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.
PDF - Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents (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.
PDF - Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations (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.
PDF - Methods for Accurate Retrieval of MEDLINE Citations in Functional Genomics (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.

Last Modified: August 01, 2008 ii-public
Links to Our Sites
MetaMap Public Release
NEW: Distributable version of the actual MetaMap program.
Indexing Initiative (II)
Investigating computer-assisted and fully automatic methodologies for indexing biomedical text. Includes the NLM Medical Text Indexer (MTI).
Semantic Knowledge Representation (SKR)
Develop programs to provide usable semantic representation of biomedical text. Includes the MetaMap and SemRep programs.
MetaMap Transfer (MMTx)
Java-Based distributable version of the MetaMap program.
Word Sense Disambiguation (WSD)
Test collection of manually curated MetaMap ambiguity resolution in support of word sense disambiguation research.
Medline Baseline Repository (MBR)
Static MEDLINE Baselines for use in research involving biomedical citations. Allows for query searches and test collection creation.
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