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ExportLgXML

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 -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) format.
Options:

  • -out,-output <uri> URI or path of the directory to contain the resulting 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 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" -f

     

     

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

ExportOwlRdf

Exports content from the repository to a file in OWL format.
Options:

  • -out,-output <uri> URI 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:///path/to/dir" -f

     

     

    ExportOwlRdf -out "file:///path/to/dir" -u "sample" -v "1.0" -f

LexEVS Loader Scripts

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:

     

    LoadLgXML -in "file:///path/to/file.xml" -nf -a


    Validation Example:

     

    LoadLgXML -in "file:///path/to/file.xml" -v 0

LoadNCIHistory

Imports NCI History data to the LexEVS repository
LoadMedDRALoads a file specified in the Medical Dictionary for Regulatory Activities (MedDRA) format.

Options:
  •    -in,--input <uri> URI or path specifying location of the
history
  • source file
  •    -
vf
  • mf,--
versionFile
  • manifest <uri> URI or path specifying location of the
file containing version identifiers for the history to be loaded.
  • manifest file
  •    -v, --validate
<level>Perform
  • <int> Perform validation of the
candidate
  • candidate  resource without loading data.  If specified, the '-a' and '-
r
  • t'
option is
  • options are ignored.  Supported levels of validation include:
  • 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:

     

    LoadNCIHistory -in "file:///path/to/history.file" -vf "[
    • 0 = Verify
    top 10 lines are correct format
    • 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.
    •    -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 "
    version
    file]
    asc" -a

     

    Validation Example:

     

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

     

    Versions File Format Information

    LoadOBO

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

    Load CUI Example:

     

    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.
    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,-input <uri> URI or path specifying location of the
    source
    • XML file.
    • -v,-validate <int> Perform validation of the
    candidate resource
    • input file without loading data.  If specified, the '-
    nf
    • f',
    -a'
    • and '-
    t
    • o' options are ignored.  Supported levels of validation include:
    •   0 = Verify document is valid
    • -
    nf
    • o, -
    noFail
    • overwrite If specified,
    indicates that processing should not stop for recoverable errors
    • 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

  • -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
    obo
    nf -a
    • o

       

       

    LoadOBO
    obo
    -v 0
    LoadOWL

    LoadMIFVocabulary

    		Loads from an
    OWL
    the HL7 Vocabulary mif 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:


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

     

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

     

     

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

    LoadMetaData

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

    LoadMrMap

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

    • -inMap
  • -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
    • MRMAP source file.

    • -

    v

    • inSat,-

    validate <int> Perform validation of the input file without loading data.  If specified, the '-f', and '-o' options are

    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 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.

      • 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:

       

      LoadNCIHistory
    Examples:

     

    LoadMetadata
    .xml
    • "-
    o

     

     

    LoadMetadata -in "
    .xml
    • ]"

    LoadMrMap

    •  


      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

    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,-input <uri> URI or path specifying location of the MRSAT source file.
    Example:

     

    LoadMrMap -inMap
    MRMAP.RRF -inSat
    META.folder" -r
     LoadUMLSHistory -in "file:///path/to/
    MRSAT
    RRF
    folder" -v 0
      
    "

    Special Batch Loading Functions

    ...