STMT - HSqlDb Files

I. Database Tables

The preprocessed files are loaded to HSqlDb tables for DB query to reduce the Java VM size and increase performance. These DB tables include:

HSqlDb TableSource FilePurpose
NormTerm_CUInormTermCui.dataFind CUI
NormInflVar_EUInormInflvarEui.datafind EUI
CUI_PTcuiPreferredTerm.dataFind Preferred Term

II. Run Program

  • Make sure Lvg is installed under ${PROJECTS}
  • Deploy tables from Table Files
    shell> cd ${STMT_DIR}/PreProcess/bin
    shell> 3.DeployTables
    STMT release (2015)
    STMT data year (the release year, 2018, ...)
    table type
    • 1 (AA), 2 (Ascii), 3(AB)

  • Link tables to the specified one (tables.${YEAR}AA|tables.${YEAR}Ascii|tables.${YEAR}AB)
    shell> ln -sf tables.2015AA tables
    shell> ln -sf tables.2015Ascii tables
    shell> ln -sf tables.2015AB tables

  • Load Db tables
    shell> cd ${STMT_DIR}/PreProcess/bin
    shell> 4.LoadDb
    Db Year (2015AA|2015AB|2015Ascii)
    STMT release (the release year, 2018, ...)
    1, 2, 3: for all three tables
    1: analysis
    2: load
    • Update db.config.${TABLE_TYPE} in ${STMT_PRE_PROCESS}/data/HsqlDb/config/

    3: check
    • Add readonly=true in ${HSQLDB}/HSqlDb.${DbYear}/stmt${DbYear}.properties
    • check above 3 tables:
      • CUI table: disease => C0012634
      • EUI table: disease => E0023270
      • CUI_PT table: C0012634 => Disease

  • zip the HSqlDb files

  • Update documents

III. Version

Directory: ${STMT_DIR}/PreProcess/data/HSqlDb/

VersionSources DirHSqlDb VersionNotes
HSqlDb.2021AA../Tables/2021AA2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2020AB../Tables/2020AB2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2020AA../Tables/2020AA2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2019AB../Tables/2019AB2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2019AA../Tables/2019AA2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2018AB../Tables/2018AB2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2018AA../Tables/2018AA2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2017AB../Tables/2017AB2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2017AA../Tables/2017AA2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2016AB../Tables/2016AB2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2016AA../Tables/2016AA2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2015AB../Tables/2015AB2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2015AA../Tables/2015AA2.3.2All 3 tables for SMT, MT, LSF
HSqlDb.2014AB../Tables/2014AB2.3.0All 3 tables for SMT, MT, LSF
HSqlDb.2014AA../Tables/2014AA2.3.0All 3 tables for SMT, MT, LSF
HSqlDb.2013AB../Tables/2013AB2.2.5All 3 tables for SMT, MT, LSF
HSqlDb.2013AA../Tables/2013AA2.2.5All 3 tables for SMT, MT, LSF
HSqlDb.2012AB../Tables/2012AB2.2.5All 3 tables for SMT, MT, LSF
HSqlDb.2012AA../Tables/2012AA2.2.5All 3 tables for SMT, MT, LSF
HSqlDb.2011AB../Tables/2011AB2.2.5All 3 tables for SMT, MT, LSF
HSqlDb.2011AA../Tables/2011AA2.2.5All 3 tables for SMT, MT, LSF
ASCII Tables
HSqlDb.2021Ascii../Tables/2021Ascii2.3.2only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2020Ascii../Tables/2020Ascii2.3.2only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2019Ascii../Tables/2019Ascii2.3.2only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2018Ascii../Tables/2018Ascii2.3.2only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2017Ascii../Tables/2017Ascii2.3.2only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2016Ascii../Tables/2016Ascii2.3.2only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2015Ascii../Tables/2015Ascii2.3.2only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2014Ascii../Tables/2014Ascii2.3.0only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2013Ascii../Tables/2013Ascii2.2.5only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2012Ascii../Tables/2012Ascii2.2.5only 1 table (NormInflVar_EUI) for LSF used in MetaMap
HSqlDb.2011Ascii../Tables/2011Ascii2.2.5only 1 table (NormInflVar_EUI) for LSF used in MetaMap