UMLS Integration

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• Data about MST:
  • GI database and its Semantic Types - Retrived GI terms (from UMLS) and their Refined Sematic Types.
    
  • The matched/unmatched terms from GI to UMLS in different situations: (Total GI terms: 1944)
    

    Situation	Matched/Unmatched	Percentage %
    Original terms	215/1729	11.06/88.94
    Use terms with all lowercases	237/1707	12.19/87.81
    Replace '-' (dash) with space*	216/1728	11.11/88.89
    Replace '_' (underscore) with space**	215/1729	11.06/88.94
    Replace '-' (dash) and use lowercases	238/1706	12.24/87.76

    *Has same result if we replace all ",-_():[]|" with spaces
    **There is no string with underscore in GI domain.
    
  • MST ISA and Source Code
  • MST ISA in text file
  • MST Multiple parents
  • Synonyms
  • List of all Relationships
  • Matched Terms Have IS-A in MST, UMLS' and their Intersection
  • WordNet Piecewise Results
  • *MST tables with concepts
  • *MST concepts with Semantic Types
• Integration Tools:
  • SourceForge Integration search worksheet and results
    
  • Note for OntoFusion paper/project.
    
  • Note for Lexical Tools
    
• Notes:
  • CYC note
  • Note for JAVA, PERL and PL/SQL
    
  • Paper Read:
    • Note for paper - An Evaluation of Hybrid Methods for Matching Biomedical Terminologies: Mapping the Gene Ontology to the UMLS
      
    • Note for paper - Mapping the Gene Ontology into the UMLS
      
    • Note for paper - Utilizing the UMLS for Semantic Mapping between Terminologies
    • MST version 2.0 from OMED
    • Note for paper - Automated Terminology Networks for the Integration of Heterogeneous Databases
      
    • Note for paper - Linking Biomedical Language Information and Knowledge Resources in the 21st Century: GO and UMLS
      
    • Integration of a Standard Gastrointestinal Endoscopy Terminology in the UMLS Metathesaurus
  
  
• Paper To Read:
  • Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics
    
  
  
• Lexical Tools/Algorithms
  Tables from UMLS:
  • Word Index: MRXW_ENG
  • Normalized Word Index: MRXNW_ENG
  • Normalized String Index: MRXNS_ENG
  • MRMAP, MRSMAP, MRCOC
  
  
• Questions:
  • Check 1. why there are IS-A to itself? 2. why there is no MST row in mrhier table?
  • How to get all synonyms?
  
  
• Flowchart
  
• Modified Simple Flowchart
  
  
• Concepts of MST and UMLS^- (Intersections): UMST
  
  
• New Tables/Views in UMLS database (umls6ac): Commands
  Tables
  • kh_mrconso_mst_en : includes all fields from MRCONSO except sab and lat fields. (English version of MST)
  • kh_mrrel_mst_en : includes all fields from MRREL except sab field. (sab='MTHMST')
  • kh_mrsty_mst_en : includes all fields from MRSTY (SN with CUI of MST)
  
  
  Views
  • kh_mrconso_umls_en : includes all fields from MRCONSO. (English version of UMLS' (without terms from MST))
  • kh_mrrel_umls_en : includes all fields from MRREL. (Relatiooships of UMLS' (excludes MST))
  • kh_mrsty_umls_en : includes all fields from MRSTY. (SN with CUI of UMLS' (excludes MST))
• Some code

• A diagram of the UMLS Semantic Network

*Newly updated (1/10/2007)