MetaMap BDB Tables

BDB (Berkeley-DB) tables were generated based on the request from MetaMap group in Jan., 2013. The requirements of above documents have been modified after several Email discussions. Five tables are generated and are detailed as follows:

MetaMap Dir:

The source codes and scripts are at: ${DEV_DIR}/Lexicon/Components/MetaMapTables

Setup:

  • Create input directory under the target release (${METAMAP_TABLES}/data/${YEAR}/inputs})
  • Create symbolic link for the following files:
    • inflVars.data.ascii (from Lexicon.ASCII)
    • LEXICON.ascii (from Lexicon.ASCII)

    • normInflvarEui.data
      • Before 2014
        • from STMT, (must run STMT preProcess first)
        • need data from UMLS MRCONSO.RRF (release.AA or release.AB)

      • After 2015+, added to the MetaMap BDB script - option 6
  • Must install the associate release of lvg and configuration file for generating derivation table.

Run Program:

  • shell>cd ${METAMAP_TABLE}/bin
  • shell>GetMetaMapTables ${YEAR}

  • Pre-process
    1

  • Pre-process
    2
    3
    4
    5.1
    5.5
    6
    2015 (use the latest version of STMT, no need to get the data from UMLS-Meta)

  • Post-process (deploy):
    10
    11