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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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link to MetaMap Papers link to UMLS Knowledge Source Metathesaurus link to Medical Text Indexer (MTI) papers link to SemRep Information link to UMLS Knowledge Source Specialist Lexicon link to UMLS Knowledge Source Semantic Network
Please Note: We are transitioning!
October 31, 2013:
The skr.nlm.nih.gov URL/website is transitioning. We are in the process of moving the Scheduler under the Indexing Initiative umbrella and creating a new dedicated Semantic Knowledge Representation Project web site.

The Indexing Initiative is focused on mapping biomedical free text to UMLS Metathesaurus concepts using MetaMap and indexing MEDLINE articles using the NLM Medical Text Indexer (MTI), while the Semantic Knowledge Representation Project focuses on extracting semantic relations from biomedical text using SemRep and exploiting these relations for applications such as automatic summarization and literature-based discovery.

During this transition all existing links, APIs, and programs will continue to work with the skr.nlm.nih.gov URL. All of the original functionality of the site is still available via the two new web sites. We are hoping to slowly migrate all users over to the new URLs during the next six months or so.

We are sorry for any inconvenience during this time of transition and ask that you update your bookmarks and links to reflect the new URLs. If you have any questions or concerns during this time period, please contact us at metamap@nlm.nih.gov.

The Semantic Knowledge Representation Project:
This link will take you to the web site for the Semantic Knowledge Representation Project. The new Semantic Knowledge Representation Project web site will provide you with the information on all of the research, publications, tools, and personnel associated with the Semantic Knowledge Representation Project in a much richer and more up-to-date environment solely dedicated to the project.

The Scheduler:
The Scheduler is moving under the Indexing Initiative umbrella. All of the existing functionality will still be available including the Interactive and Batch facilities and API. All of the access to our tools (MetaMap, MTI, and SemRep) will also still be available.

Publications:
The publications from the skr.nlm.nih.gov site have been separated into their respective projects. We have provided links below for each of the existing areas.
SKR Background Papers & Presentations
Overview of SKR paper - PDF (48 kb) Overview of SKR, 1998
Semantic processing in information retrieval paper - PDF (42 kb) Semantic processing in information retrieval. (1993) Proceedings of the 17th Annual Symposium on Computer Applications in Medical Care, 611-15.
Natural language processing paper - PDF (54 kb) Natural language processing. (1996) Annual Review of Applied Linguistics 16, 71-85.
MetaMap
Fundamentals
An overview of MetaMap: historical perspective and
recent advances - PDF (201 kb) Animated gif with # 1 metaphorical as #1 reference    Please Read This Paper First
An overview of MetaMap: historical perspective and recent advances, JAMIA 2010
The Evolution of MetaMap, a Concept Search Program for Biomedical Text, AMIA 2009 - PDF (12 kb) The Evolution of MetaMap, a Concept Search Program for Biomedical Text, AMIA 2009
The Evolution of MetaMap, a Concept Search Program for Biomedical Text, Presented November 16, 2009 at AMIA 2009 - PDF (723 kb)
The Evolution of MetaMap, a Concept Search Program for Biomedical Text, Presented November 16, 2009 at AMIA 2009 - PPT (1.1 mb)
Presentation: The Evolution of MetaMap, a Concept Search Program for Biomedical Text, Presented November 16, 2009 at AMIA 2009
The Current State of MetaMap and MMTx Webcast, August 20, 2009 - PDF (716 kb)
The Current State of MetaMap and MMTx Webcast, August 20, 2009 - PPT (1.1 mb)
Presentation: The Current State of MetaMap and MMTx Webcast, August 20, 2009
MetaMap: Mapping Text to the UMLS Metathesaurus paper - PDF (280 kb) MetaMap: Mapping Text to the UMLS Metathesaurus, July 2006 <<< UPDATED FOR 2006
MetaMap Examples & Options - PDF (50 kb) MetaMap Options and Examples, September 2006 <<< UPDATED FOR 2006
Effective Mapping of Biomedical Text to the UMLS  Metathesaurus: The MetaMap Program, 2001 paper - PDF (58 kb) Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program, 2001
2010 AMIA MetaMap Tutorial
MetaMap 2010 AMIA Tutorial Description - PDF (38 kb) MetaMap 2010 AMIA Tutorial Description (PDF)
MetaMap 2010 AMIA Tutorial Description - Text (3 kb) MetaMap 2010 AMIA Tutorial Description (Text)
MetaMap 2010 AMIA Tutorial Slides - PowerPoint (3.2 mb) MetaMap 2010 AMIA Tutorial Slides (PowerPoint)
MetaMap 2010 AMIA Tutorial Slides - PDF (1.6 mb) MetaMap 2010 AMIA Tutorial Slides (PDF)
Technical Documents
MetaMap Technical Notes paper - PDF (99 kb) MetaMap Technical Notes, 1996
  Ambiguity in the UMLS Metathesaurus
           --  2013 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2013 paper - PDF (201 kb)
           --  2012 Higher Degree Metathesaurus Ambiguity Report Excel (14 kb)
           --  2012 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2012 paper - PDF (29 kb)
           --  2011 Higher Degree Metathesaurus Ambiguity Report Excel (13 kb)
           --  2011 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2011 paper - PDF (28 kb)
           --  2010 Higher Degree Metathesaurus Ambiguity Report Excel (12 kb)
           --  2010 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2010 paper - PDF (182 kb)
           --  2009 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2009 paper - PDF (384 kb)
           --  2008 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2008 paper - PDF (144 kb)
           --  2007 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2007 paper - PDF (100 kb)
           --  2006 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2006 paper - PDF (201 kb)
           --  2005 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2005 paper - PDF (124 kb)
           --  2004 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2004 paper - PDF (72 kb)
           --  2003 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2003 paper - PDF (92 kb)
           --  2002 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2002 paper - PDF (289 kb)
           --  2001 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2001 paper - PDF (182 kb)
           --  2000 Version Summary Report  Ambiguity in the UMLS Metathesaurus 2000 paper - PDF (112 kb)
           --  1999 Version Summary Report  Ambiguity in the UMLS Metathesaurus 1999 paper - PDF (59 kb)
  Filtering the UMLS Metathesaurus for MetaMap
           --  2012 Version  Filtering the UMLS Metathesaurus for MetaMap 2012 paper - PDF (22 kb)
           --  2011 Version  Filtering the UMLS Metathesaurus for MetaMap 2011 paper - PDF (22 kb)
           --  2010 Version  Filtering the UMLS Metathesaurus for MetaMap 2010 paper - PDF (153 kb)
           --  2009 Version  Filtering the UMLS Metathesaurus for MetaMap 2009 paper - PDF (22 kb)
           --  2008 Version  Filtering the UMLS Metathesaurus for MetaMap 2008 paper - PDF (210 kb)
           --  2007 Version  Filtering the UMLS Metathesaurus for MetaMap 2007 paper - PDF (72 kb)
           --  2006 Version  Filtering the UMLS Metathesaurus for MetaMap 2006 paper - PDF (68 kb)
           --  2005 Version  Filtering the UMLS Metathesaurus for MetaMap 2005 paper - PDF (59 kb)
           --  2004 Version  Filtering the UMLS Metathesaurus for MetaMap 2004 paper - PDF (145 kb)
           --  2003 Version  Filtering the UMLS Metathesaurus for MetaMap 2003 paper - PDF (51 kb)
           --  2002 Version  Filtering the UMLS Metathesaurus for MetaMap 2002 paper - PDF (48 kb)
           --  2001 Version  Filtering the UMLS Metathesaurus for MetaMap 2001 paper - PDF (48 kb)
           --  2000 Version  Filtering the UMLS Metathesaurus for MetaMap 2000 paper - PDF (48 kb)
           --  1999 Version  Filtering the UMLS Metathesaurus for MetaMap 1999 paper - PDF (18 kb)
MetaMap Variant Generation paper - PDF (27 kb) MetaMap Variant Generation, 2001
MetaMap Candidate Retrieval paper - PDF (25 kb) MetaMap Candidate Retrieval, 2001
MetaMap Evaluation paper - PDF (63 kb) MetaMap Evaluation, 2001
MetaMap Mapping Algorithm paper - PDF (19 kb) MetaMap Mapping Algorithm, 2001
MetaMap Update Procedures paper - PDF (36 kb) MetaMap Update Procedures, 2000
Comparison of LVG and MetaMap Functionality paper - PDF (41 kb) Comparison of LVG and MetaMap Functionality, 1994
Papers
The effect of textual variation on concept based information retrieval paper - PDF (46 kb) The effect of textual variation on concept based information retrieval, 1996
Exploiting a large thesaurus for information retrieval paper - PDF (70 kb) Exploiting a large thesaurus for information retrieval. (1994) Proceedings of RIAO, 197-216.
Related Papers
MetaMap in the CALBC Workshop II - PDF (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.
Semantic processing for enhanced access to biomedical knowledge - PDF (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.
Analysis of biomedical text for chemical names: A comparison of three methods - PDF (50 kb) Analysis of biomedical text for chemical names: A comparison of three methods, 1999
Hierarchical concept indexing of full-text documents in the UMLS information sources map paper (1998) - PDF (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.
Query expansion using the UMLS Metathesaurus paper - PDF (41 kb) Query expansion using the UMLS Metathesaurus. Proceedings of the 1997 AMIA Annual Fall Symposium, 485-89.
Finding the findings: Identification of findings in medical literature using restricted natural language processing paper - PDF (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
UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (Full Paper), JBI 2010 - PDF (148 kb) UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (Full Paper), JBI 2010
UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (400 Word Abstract), AMIA 2009 - PDF (25 kb) UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (400 Word Abstract), AMIA 2009
Extracting Rx Information from Clinical Narrative (Full Paper), 2010 - PDF (508 kb) Extracting Rx Information from Clinical Narrative (Full Paper), 2010
Extracting Rx Information from Clinical Narrative (Short Paper), JAMIA 2010 - PDF (53 kb) Extracting Rx Information from Clinical Narrative (Short Paper), JAMIA 2010
Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing, AMIA 2008 - PDF (50 kb) Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing, AMIA 2008
From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches, BioNLP 2007 - PDF (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
A knowledge-based approach to medical records retrieval - PDF (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)
Comparison and combination of several MeSH indexing approaches - PDF (283 kb) Comparison and combination of several MeSH indexing approaches. Jimeno-Yepes, Antonio, Mork JG, Demner-Fushman D, Aronson AR. AMIA Annual Symposium Proceedings. Vol. 2013. American Medical Informatics Association, 2013.
2012 Report to the Board of Scientific Counselors - PDF (1.9 mb) 2012 Report to the Board of Scientific Counselors
2012 Presentation to the Board of Scientific Counselors - PowerPoint (7.9 mb) 2012 PowerPoint Presentation to the Board of Scientific Counselors
2012 Presentation to the Board of Scientific Counselors - PDF (12.8 mb) 2012 Powerpoint Presentation to the Board of Scientific Counselors (PDF version, no slide animations)
Presentation for NIH-sponsored Workshop on Natural Language Processing, April 2012 - PowerPoint (1 mb) Presentation for NIH-sponsored Workshop on Natural Language Processing, April 2012
Presentation for NIH-sponsored Workshop on Natural Language Processing, April 2012 - PDF (2.1 mb) Presentation for NIH-sponsored Workshop on Natural Language Processing, April 2012 (PDF version, no slide animations)
MeSH indexing: machine learning and lessons learned - PDF (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.
A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning - PDF (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.
Automatic algorithm selection for MeSH Heading indexing based on meta-learning - PDF (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.
A bottom-up approach to MEDLINE indexing recommendations - PDF (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.
Automatic inference of indexing rules for MEDLINE, 2008 - PDF (395 kb) Automatic inference of indexing rules for MEDLINE, BMC Bioinformatics, 2008
2008 Report to the Board of Scientific Counselors - PDF (1.5 mb) 2008 Report to the Board of Scientific Counselors
Automatic inference of indexing rules for MEDLINE, 2008 - PDF (100 kb) Automatic inference of indexing rules for MEDLINE, BioNLP 2008
User-centered Evaluation of the MTI System, 2007 - PDF (1.1 mb) User-centered Evaluation of the MTI System, 2007
Fine-Grained Indexing of the Biomedical Literature: MeSH Subheading Attachment for a MEDLINE Indexing Tool, AMIA 2007 - PDF (39 kb) Fine-Grained Indexing of the Biomedical Literature: MeSH Subheading Attachment for a MEDLINE Indexing Tool, AMIA 2007
Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature, 2007 - PDF (103 kb) Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature, Proc Pacific Symposium on Biocomputing 2007
Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations, BioNLP 2007 - PDF (44 kb) Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations, BioNLP 2007
Semi-Automatic Indexing of Full Text Biomedical Articles, AMIA 2005 - PDF (100 kb) Semi-Automatic Indexing of Full Text Biomedical Articles, AMIA 2005
Evaluation of French and English MeSH Indexing Systems ..., AMIA 2005 - PDF (50 kb) Evaluation of French and English MeSH Indexing Systems with a Parallel Corpus, AMIA 2005
The NLM Indexing Initiative's Medical Text Indexer, MedInfo 2004 - PDF (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
A MEDLINE Indexing Experiment Using Terms Suggested by MTI, June 2002 - PDF (510 kb) A MEDLINE Indexing Experiment Using Terms Suggested by MTI, June 2002
Automated and Semi-automated Indexing, Report to the Board of Regents 2002 - PDF (2.1 mb) Automated and Semi-automated Indexing, Report to the Board of Regents 2002
Automatic MeSH Term Assignment and Quality Assessment, AMIA 2001 - PDF (130 kb) Automatic MeSH Term Assignment and Quality Assessment, AMIA 2001
The NLM Indexing Initiative paper - PDF (139 kb) The NLM Indexing Initiative, 2000
1999 Report to the Board of Scientific Counselors - PDF (203 kb) 1999 Report to the Board of Scientific Counselors
1999 AMIA Poster Presentation: Automated Assignment of Medical Subject Headings - HTML (203 kb) 1999 AMIA Poster Presentation: Automated Assignment of Medical Subject Headings (HTML)
Medical Text Indexer (MTI) Processing Flow - PDF (503 kb) Medical Text Indexer (MTI) Processing Flow
Word Sense Disambiguation (WSD)
Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation - PDF (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
Preliminary results for Biomedical Word Sense Disambiguation based on Semantic Clustering - PDF (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.
Self-training and co-training in biomedical word sense disambiguation - PDF (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
Query expansion for UMLS Metathesaurus disambiguation based on automatic corpus extraction - PDF (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.
Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation - PDF (87 kb) Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation, Antonio Jimeno-Yepes, Alan R. Aronson, BioSEPLN, 2010.
Word sense disambiguation by selecting the best semantic type based on Journal Discriptor Indexing: preliminary experiment. - PDF (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.   PDF: Erratum for Word sense disambiguation by selecting ... paper  (20.6kb)
Developing a Test Collection for Biomedical Word Sense Disambiguation, AMIA 2001 - PDF (93 kb) Developing a Test Collection for Biomedical Word Sense Disambiguation, Marc Weeber, James G. Mork, Alan R. Aronson, AMIA 2001
Automatic indexing by discipline and high-level categories: methodology and potential applications. - PDF (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.
Automatic indexing of documents from journal descriptors: a preliminary investigation. - PDF (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.
Ambiguity resolution while mapping free text to the UMLS Metathesaurus paper - PDF (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
Strategies for Mapping Concepts in Gastrointestinal Endoscopy Reports to the UMLS Metathesaurus - PDF (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.
Summarization of an Online Medical Encyclopedia - PDF (275 kb) Summarization of an Online Medical Encyclopedia. Fiszman M, Rindflesch TC, Kilicoglu H. MedInfo. 2004 Sept.;2004: 506-510.
Identifying Anatomical Concepts in Biomedical Text for Automatic Selection of Images - PDF (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.
Integrating a hypernymic proposition interpreter into a semantic processor for biomedical text - PDF (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.
The Interaction of Domain Knowledge and Linguistic Structure in Natural Language Processing: Interpreting Hypernymic Propositions in Biomedical Text - PDF (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.
Exploring text mining from MEDLINE - PDF (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.
Argument identification for arterial branching predications asserted in cardiac catheterization reports paper - PDF (49 kb) Argument identification for arterial branching predications asserted in cardiac catheterization reports. Submitted to AMIA 2000.
Semantic interpretation - HTML Presentation (30 kb) Semantic interpretation, 1999
Identification of anatomical terminology in medical text paper - PDF (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.
Integrating natural language processing and biomedical domain knowledge for increased information retrieval effectiveness paper - PDF (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
Semantic relations asserting the etiology of genetic diseases - PDF (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.
Discovering protein similarity using natural language processing - PDF (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.
NLP-based information extraction for managing the molecular biology literature - PDF (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.
Extracting molecular binding relationships from biomedical text paper - PDF (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.
EDGAR: Extraction of drugs, genes and relations from the biomedical literature paper - PDF (64 kb) EDGAR: Extraction of drugs, genes and relations from the biomedical literature. (2000) Pacific Symposium on Biocomputing 5:514-25.
Mining molecular binding terms from biomedical text paper - PDF (47 kb) Mining molecular binding terms from biomedical text. Proceedings of the 1999 AMIA Fall Symposium, 127-31.
MMI
MMI project description paper - PDF (5 kb) MMI project description, 1997
MMI ranking function paper - PDF (32 kb) MMI ranking function, 1997
A MEDLINE indexing experiment paper - PDF (39 kb) A MEDLINE indexing experiment, 1997
PhraseX
Finding UMLS Metathesaurus concepts in MEDLINE - PDF (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
Combining Resources to Find Answers to Biomedical Questions - PDF (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.
Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort - PDF (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.
Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents - PDF (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.
Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations - PDF (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.
Methods for Accurate Retrieval of MEDLINE Citations in Functional Genomics - PDF (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: November 14, 2013 ii-public2
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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.
Structured Abstracts (SA)
Information about NLM's research on Structured Abstracts in the MEDLINE® Baselines.
 
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