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ExportDDLScripts

Exports the database create/drop scripts.
Options:

  • -db, -databaseType, required=true, usage="Target database type.")
  • -p, -prefix Prefix to append to all tables
  • -o,-out Output directory, a required option

  • -f, -force Force output directory creation.

    Example:

     

    ExportDDLScripts -p lb -0 "file:///path/to/dir" -f

PasswordEncryptor

Encrypts the given password.
Argument:

  • -p,-password password for encryption.

Example:

 

PasswordEncryptor -p lexgrid

LexEVS Export Scripts

RebuildTransitivityTable

Rebuilds transitivity table associated with the specified coding scheme.

Options:

   -u,--urn <urn> URN uniquely identifying the code system.

   -v,--version <id> Version identifier.

   -f,--force Force clear (no confirmation).

Note: If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.

Example:

 

RebuildTransitivityTable -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

LexEVS Export Scripts

Exports content from the repository to a file in the LexGrid canonical XML format.
Usage:
ExportLgXML [-xc] [-an null] [-xall] -v null -u name -out uri [-xa] [-f]

  • -an,--associationsName Export associations with this name. Only valid with export type 'xa'

  • -f,-force If specified, allows the destination file to be overwritten if present.
  • -out,-output <uri> URI or path of the directory to contain the resulting XML file. The file name will be automatically derived from the coding scheme name.
  • -u,-urn <name> URN or local name of the coding scheme to export.
  • -v,-version The assigned tag/label or absolute version identifier of the coding scheme.
  • -xa,-exportAssociations Type of export: export only associations.
  • -xall,-exportAll Type of export: export all content. Default behavior.
    • -xc,-exportConcepts Type of export: export only concepts.
    Example:

     

    ExportLgXML

    ExportLgXML

    ExportLgXML -out "file:///path/to/dir" -u "NCI Thesaurus" -v "05.06e" -f

    ExportOBO

    Exports content from the repository to a file in the Open Biomedical Ontologies (OBO) LexGrid canonical XML format.
    Options: Usage:
    ExportLgXML [-xc] [-an null] [-xall] -v null -u name -out uri [-xa] [-f]

    • -an,--associationsName Export associations with this name. Only valid with export type 'xa'

    • -f,-force If specified, allows the destination file to be overwritten if present.
    • --out,-output <uri> URI or path of the directory to contain the resulting OBO XML file. The file name will be automatically derived from the coding scheme name.
    • -u,-urn <name> URN or local name of the coding scheme to export.
    • -v,-version <id> The assigned tag/label or absolute version identifier of the coding scheme.
    • -f,-force If specified, allows the destination file to be overwritten if present.xa,-exportAssociations Type of export: export only associations.
    • -xall,-exportAll Type of export: export all content. Default behavior.

    • -xc,-exportConcepts Type of export: export only concepts.

      Example:

       

      ExportLgXML

      Note

       

      If the coding scheme and version values are unspecified, a list of available coding schemes will be presented for user selection.

      Note:

       

      Available for Linux based OS only.

      Examples:

       

      ExportOBO -out "file:///path/to/dir" -u "NCI Thesaurus" -v "05.06e" -f

       

       

      ExportOBO -out "file:///path/to/dir" -u "FBbt" -v "PRODUCTION" -f

    ExportOBO

    Exports

    ExportOwlRdf

    Exports content from the repository to a file in OWL the Open Biomedical Ontologies (OBO) format.
    Options:

    • -out,-output <uri> URI or path of the directory to contain the resulting OWL OBO file. The file name will be automatically derived from the coding scheme name.
    • -u,-urn <name> URN or local name of the coding scheme to export.
    • -v,-version <id> The assigned tag/label or absolute version identifier of the coding scheme.

    • -f,-force If specified, allows the destination file to be overwritten if present.

      Note

       

      If the URN coding scheme and version values are unspecified, a list of available coding schemes will be presented for user selection.

      Note:

       

      Available for Linux based OS only.



      Examples:

       

      ExportOwlRdf ExportOBO -out "file:///path/to/dir" -f

       

       

      ExportOwlRdf ExportOBO -out "file:///path/to/dir" -u "sampleFBbt" -v "1.0PRODUCTION" -f

    LexEVS Loader Scripts

    ExportOwlRdf

    Exports content from the repository to a file in OWL

    LoadLgXML

    Loads a vocabulary file, provided in LexGrid canonical xml

    format.
    Options:

    • -
    in
    • out,-
    input

    -t, -tag <tagID> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
    Load Example:

     

    LoadLgXML -in
    • output <uri> URI
    specifying location of the source file.
  • -v, -validate <level> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:
    • 0 = Verify document is well-formed
    • 1 = Verify document is valid
  • -a,-activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
    • or path of the directory to contain the resulting OWL file. The file name will be automatically derived from the coding scheme name.
    • -u,-urn <name> URN or local name of the coding scheme to export.
    • -v,-version <id> The assigned tag/label or absolute version identifier of the coding scheme.

    • -f,-force If specified, allows the destination file to be overwritten if present.

      Note

       

      If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.



      Examples:

       

      ExportOwlRdf -out
    file.xml
    nf -a
    • f

       

    Validation Example:

    •  

    LoadLgXML
    • ExportOwlRdf -
    in
    file.xml
    • dir" -u "sample" -v "1.0" -f

    LexEVS Loader Scripts

    LoadMedDRA specified in the Medical Dictionary for Regulatory Activities (MedDRA)    - or path    -mf,-manifest <uri> URI or path specifying location of the manifest file   -- <int> candidate  options    -   - <id>
  •    -cui  Uri to MRCONSO.RRF from the NCI Metathesaurus allows loading of CUI's  for a given term. (Slows load time considerably)
    • LoadMedDRA asc

     

    LoadMedDRA asc

     

    Load CUI Example:

     

    LoadLgXML

    Loads a vocabulary file

    , provided in LexGrid canonical xml format.
    Options:

    • -in,
    • -input <uri> URI
    • specifying location of the source file.
    • -
    • v, -
    • validate
    • <level> Perform validation of the
    • candidate resource without loading data.  If specified, the '-a' and '-t'
    •  options are ignored.  Supported levels of validation include:
      • 0 = Verify document is well-formed
      • 1 = Verify document is valid
    • -a,-
    • activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

    • -t, -

    • tag

    • <tagID> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

    • Load Example:

       


    • Validation Example:

       

    LoadMedDRA  -in "file:///path/to/MedDRAFolder" -cui "file:///path/to/MRCONSO.RRF
    LoadMetaData
    LoadMedDRALoads a file specified in the Medical Dictionary for Regulatory Activities (MedDRA) format.

    Options:
    •    -in,--input <uri> URI or path specifying location of the source file
    •    -mf,--manifest

    Loads optional XML-based metadata to be associated with an existing coding scheme.

  • -u,-urn <name> URN uniquely identifying the code system.
  • -v,-version <id> Version identifier.
    • -in,-input
    • <uri> URI or path specifying location of the
    XML
    • manifest file
    .
    •    -v, --validate <int> Perform validation of the
    input file
    • candidate  resource without loading data.  If specified, the '-
    f
    • a'
    ,
    • and '-
    o
    • t' options are ignored.  Supported levels of validation include:
     
    • 0 = Verify document is valid
    •    -
    o
    • a,
    -overwrite If specified, existing metadata for the code system will be erased. Otherwise, new metadata will be appended to existing metadata (if present).
    • --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
    •    -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
    •    -cui  Uri to MRCONSO.RRF from the NCI Metathesaurus allows loading of CUI's  for a given term. (Slows load time considerably)


    Load Example:

     

    LoadMedDRA -in "file:///path/to/file.asc" -a

     

    Validation Example:

     

    LoadMedDRA
    -f,-force Force overwrite (no confirmation).

    Note

     

    If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.

    Examples:

     

    LoadMetadata xml
    asc"-
    o
    v 0

     

    Load CUI Example:

     

    LoadMetadata
    LoadMedDRA  -in "file:///path/to/MedDRAFolder" -cui "file
    .xml"

    LoadMIFVocabulary

    LoadMetaData

    Loads optional XML-based metadata to be associated with an existing coding scheme.

    • -u,-urn <name> URN uniquely identifying the code system.
    • -v,-version <id> Version identifier.
    • -in,-
    Loads from an the HL7 Vocabulary mif file.
     Options:   -in,--
    • input <uri> URI or path specifying location of the
    source
    • XML file.
      
    • -
    a
    • v,-
    -activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
    • validate <int> Perform validation of the input file without loading data.  If specified, the '-f', and '-o' options are ignored.  Supported levels of validation include:  0 = Verify document is valid
    • -o, -overwrite If specified, existing metadata for the code system will be erased. Otherwise, new metadata will be appended to existing metadata (if present).
    • -f,-force Force overwrite (no confirmation).

      Note

       

      If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.


      Examples:

       

      LoadMetadata
  •    -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
    • Load Example:

     

    LoadMIFVocabulary
    a

    LoadMIFVocabulary

    Loads from an the HL7 Vocabulary mif file.

     Options:
    •    -in,-
    LoadMrMap

    Loads mappings file(s), provided in UMLS RRF format. Specifically MRMAP.RRF and MRSAT.RRF.
    Options:

    -inMap,
    • -input <uri> URI or path specifying location of the
    MRMAP
    • source file.
    •    -
    inSat
    • a,
    -input <uri> URI or path specifying location of the MRSAT source file.
    Example:

     

    LoadMrMap -inMap "
    • --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
    •    -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.


    Load Example:

    file:///path/to/MRMAP.RRF -inSat

     

    LoadMIFVocabulary -in
    MRSATRRF
    xml" -a

    LoadNCIHistory

    LoadMrMap

    Loads mappings file(s), provided in UMLS RRF format. Specifically MRMAP.RRF and MRSAT.RRF

    Imports NCI History data to the LexEVS repository

    .
    Options:

    • -
    in
    • inMap,-input <uri> URI or path specifying location of the
    history
    • MRMAP source file.

    • -

    vf

    • inSat,-

    versionFile

    LoadNCIHistory

    Imports NCI History data to the LexEVS repository.
    Options:

    • -in,-input <uri> URI specifying location of the history file
    • -vf,-versionFile <uri> URI specifying location of the file containing version identifiers for the history to be loaded.
    • -v, -validate <level>Perform validation of the candidate resource without loading data.  If specified, the '-r' option is ignored.  Supported levels of validation include:
      • 0 = Verify top 10 lines are correct format
      • 1 = Verify correct format for the entire file

    • -r, -replace If not specified, the provided history file will be added into the current history database; otherwise the current database will be replaced by the new content.
      Load Example:


      Validation Example:

       

      LoadNCIHistory -in "file:///path/to/history.file" -v 0

       

      Versions File Format Information:

       

      releaseDate | isLatest | releaseAgency | releaseId | releaseOrder | entityDescription

       

      Sample record:

       

      28-NOV-05 | false | [http://nci.nih.gov] | 05.10e | 26 | Editing of NCI Thesaurus 05.10e was completed on October 31, 2005.  Version 05.10e was October's fifth build in our development cycle.

    LoadOBO

    Loads a file specified in the Open Biomedical Ontologies (OBO) format.
    Options:

    • -in,-input <uri> URI or path specifying location of the source file
    • -v,-validate <int> Perform validation of the candidate resource without loading data. If specified, the '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
      • 0 = Verify document is valid
    • -nf,-noFail If specified, indicates that processing should not stop for recoverable errors
    • -a, -activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated

    • -t, -tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
      Examples:

       

      LoadOBO -in "file:///path/to/file.obo" -nf -a

       

       

      LoadOBO -in "file:///path/to/file.obo" -v 0

    LoadOWL

    Loads an OWL file.

    Note

     

    Load of the NCI Thesaurus should be performed via the LoadNCIThesOWL counterpart, since it will allow more precise handling of NCI semantics.

    Options:

    • -in,-input <uri> URI or path specifying location of the source file
    • -mf,--manifest <uri> URI or path specifying location of the manifest file
    • -v, -validate <int> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:
      • 0 = Verify document is well-formed
      • 1 = Verify document is valid
    • -a, -activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated

    • -t, -tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
      Example:

       

      LoadOWL -in "file:///path/to/somefile.owl" -a

       

       

      LoadOWL -in "file:///path/to/somefile.owl" -v 0
    LoadOWL2

     Loads an OWL file. You can provide a manifest file to configure coding scheme# meta data.

     Options:

    •    -in,--input <uri> URI or path specifying location of the source file
    •    -mf,--manifest <uri> URI or path specifying location of the manifest file
    •    -lp,--loaderPrefs<uri> URI or path specifying location of the loader preference file
    •    -v, --validate <int> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:
    •          0 = Verify document is well-formed
    •          1 = Verify document is valid
    •    -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
    •    -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.


     Load Example:

     

    LoadOWL2 -in "file:///path/to/somefile.owl" -a

     

     

    LoadOWL2 -in "file:///path/to/somefile.owl" -v 0
    LoadResolvedValueSetDefinition

    Loads Value Set Definition content, provided in LexGrid canonical xml format.


     Options:
       -u, The valueset definition URI to use
       -l, The list of coding schemes to revolve against. The format is codingschemeName::version
       -csVersionTag, The tag to use for resolving coding scheme
           
    Load Example:

     

    LoadResolvedValueSetDefinition -u \"Automobiles:valuesetDefinitionURI\" -l \"Automobiles::version1, GM::version2\" -csVersionTag \"production\" ""

     


    LoadText

    Loads a file in LexGrid Text format.

    Options:

       -in,--input <uri> URI or path specifying location of the source file

       -d, --delimiter <character> defaults to tab the character used to delimit pair or triple components and the nesting.

       -mf,--manifest <uri> URI or path specifying location of the manifest file.

       -v, --validate <int> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:

          0 = Verify document is valid

       -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

       -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

     

    Load Example:

     

    LoadText -in "file:///path/to/file.txt" -a
    LoadText -in "file:///path/to/file.txt" -v 0
    LoadUMLSHistory

    Loads UMLS History


     Options:

       -in,--input <uri> URI or path specifying location of the source file

       -v, --validate <int> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:

          0 = Verify document is valid

       -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

       -r, --replace Replace exisiting file.

       -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.


    Load Example:

     

    LoadUMLSHistory -in "file:///path/to/META.folder" -r
     LoadUMLSHistory -in "file:///path/to/META.folder" -v 0
    LoadUMLSSemnet.sh

    Loads the UMLS Semantic Network, provided as a collection of files in a single directory.  The following files are expected to be provided from the National Library of Medicine (NLM) distribution:
       - LICENSE.txt (text from distribution terms and conditions)
       - SRFIL.txt (File Description)
       - SRFIL.txt (Field Description)
       - SRDEF.txt (Basic information about the Semantic Types and Relations)
       - SRSTR.txt (Structure of the Network)
       - SRSTRE1.txt (Fully inherited set of Relations (UIs))
       - SRSTRE2.txt (Fully inherited set of Relations (Names))
       - SU.txt (Unit Record)
    These files can be downloaded from the NLM web site at http://semanticnetwork.nlm.nih.gov/Download/index.html.

    Options:

       -in,--input <uri> URI or path of the directory containing the NLM files

       -v, --validate <int> Perform validation of the candidate resource without loading data.  If specified, the '--a' and '-t' options are ignored.  Supported levels of validation include:

            0 = Verify the existence of each required file

       -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

       -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

       -il,--InheritanceLevel <int> If specified, indicates the extent of inherited relationships to import.  

            0 = none; 1 = all; 2 = all except is_a (default).

            All direct relationships are imported, regardless of option.

    Load Example:

     

    LoadUMLSSemnet -in "file:///path/to/directory/" -a
    LoadUMLSSemnet -in "file:///path/to/directory/" -v 0

    Special Batch Loading Functions

    ...

    RemoveScheme

    Removes a coding scheme based on unique URN and version.
    Options:

    • -u,-urn <urn> URN uniquely identifying the code system.
    • -v,-version <versionId> Version identifier.

    • -f,-force Force deactivation and removal without confirmation.
      Example:

       

      RemoveScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

    RemoveMetadata

    Clears optionally loaded metadata associated with the specified coding scheme.
    Options

    • -u,-urn <urn> URN uniquely identifying the code system.
    • -v,-version <id> Version identifier.

    • -f,-force Force clear (no confirmation).

      Note

       

      If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.


      Examples:

       

      RemoveMetadata

       

       

      RemoveMetadata -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

    Pick List and Value Set Load Administration

    •  

      RemoveMetadata -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

    Pick List and Value Set Load Administration

    Loads Pick List -input -validate
    LoadPickListDefinition .xml"

    Loads All Value Set Definitions for a given uri as resolved coding scheme.
    Options:

    -u, Uri uniquely identifying the coding scheme to resolve from defaults to http://ncicb.nci.nihgov//owl/EVS/Thesaurus.owl#

     

    LoadValueSetDefinition  -uri "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#

    LoadPickListDefinition

    Loads Pick List Definition content, provided in LexGrid canonical xml format.
    Options:

    • -in,-input <uri> URI or path specifying location of the source file.
    • -v, -validate <int> Perform validation of the candidate resource without loading data.
      Supported levels of validation include:
      • 0 = Verify document is well-formed

      • 1 = Verify document is valid
        Example:

         

        LoadPickListDefinition -in "file:///path/to/file.xml"

    LoadAllDefinitionsToResolvedValueSet

    Loads All Value Set Definitions for a given uri as resolved coding scheme.
    Options:

     

    LoadAllDefinitionsToResolvedValueSet  -uri "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"
    LoadValueSetDefinition.sh

    Loads Value Set

    LoadPickListDefinition

    Definition content, provided in LexGrid canonical xml format.

    Options:

    • -in,
    • Input <uri> URI or path specifying location of the source file.
    • -v,
    • Validate <int> Perform validation of the candidate

      resource without loading data.

    •   Supported levels of validation include:

         0 = Verify document is well-formed

         1 = Verify document is valid


      Load Example:

       

    LoadAllDefinitionsToResolvedValueSet

    • "

    Expert Admin Scripts (Focused on Mass Loads of Value Sets)

    ...