U. S. National Library of Medicine The Current State of MetaMap and MMTx UMLS Webcast Alan (Lan) R. Aronson Lister Hill Center/NLM/NIH

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Presentation transcript:

U. S. National Library of Medicine The Current State of MetaMap and MMTx UMLS Webcast Alan (Lan) R. Aronson Lister Hill Center/NLM/NIH August 20, 2009 (updated December 10, 2009)

U. S. National Library of Medicine Outline Historical background Distribution modes MetaMap and MMTx* similarities MetaMap and MMTx differences Recent MetaMap development * MMTx – MetaMap Transfer

U. S. National Library of Medicine Historical Background Programs that map biomedical text to a thesaurus CLARIT (Evans et al., 1991) SAPHIRE (Hersh et al., 1990) MetaMap (Aronson et al., 1994) Metaphrase (Tuttle et al., 1998) MMTx (2001) KnowledgeMap (Denny et al., 2003) Mgrep (2009) Characteristics of MetaMap/MMTx Linguistic rigor Flexible partial matching Emphasis on thoroughness rather than speed

U. S. National Library of Medicine MetaMap/MMTx Example PMID – TI –Bile duct stricture due to caused by portal biliopathy: Treatment with one-stage portal-systemic shunt and biliary bypass. Stricture of bile ductCausingHepatic Administration procedureOnePhase Portasystemic shuntBiliaryBypass

U. S. National Library of Medicine MetaMap/MMTx Distribution Modes

U. S. National Library of Medicine MetaMap/MMTx Distribution Modes

U. S. National Library of Medicine MetaMap and MMTx Similarities Same purpose: mapping biomedical text to concepts in the UMLS Metathesaurus Same basic algorithm Tokenization and parsing into phrases Variant generation Candidate retrieval Candidate evaluation Final mapping construction

U. S. National Library of Medicine MetaMap and MMTx Differences (1/2) Algorithmic details Overall organization of the algorithm Tokenization Results Occasional differences, MetaMap’s generally preferred Programming language Prolog/C (MetaMap) Java (MMTx)

U. S. National Library of Medicine MetaMap and MMTx Differences (2/2) Platform availability MMTx: Solaris, Linux, Windows, OS X MetaMap: Solaris, Linux, Windows (soon), OS X (soon) Performance MetaMap is 2-5 times faster than MMTx (as of 2008)

U. S. National Library of Medicine Recent/Current MetaMap Development Technical algorithm enhancements resulting in at least 3x speedup in MetaMap execution MetaMap is now 3-10 times faster than MMTx (2009) Further technical development Migration from Sun/Solaris to Linux environment Update to current Berkeley DB to prepare for Migration from Quintus to SICStus Prolog MetaMap now detects negation (via NegEx) MetaMap 3D (colorized MetaMap output)

U. S. National Library of Medicine MetaMap 3D

U. S. National Library of Medicine Pointers: Website and Contributors Alan (Lan) R. Aronson James G. Mork Willie J. Rogers François M. Lang