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ActivateScheme

Activates 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 activation (no confirmation).

    Example:

     

    ActivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"
CleanUpMetadata

Clean up metadata entries that are orphaned.

Options:

   -h, --help, Prints usage information

   -f,--force, Force removal without prompting of metadata that doesn't have a corresponding coding scheme entry(orphaned).

Example:

 

CleanUpMetadata -f

DeactivateScheme

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

  • -u,-urn <urn> URN uniquely identifying the code system.
  • -v,-version <versionId> Version identifier.
  • -d,-date <yyyy-MM-dd,HH:mm:ss> Date and time for deactivation to take effect; immediate if not specified.

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

    Example:

     

    DeactivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" -d "01/31/2099,12:00:00

ListExtensions

List registered extensions to the LexEVS runtime environment.
Options:

  • -a,-all List all extensions (default, override by specifying other options).
  • -i,-index List index extensions.
  • -m,-match List match algorithm extensions.
  • -s,-sort List sort algorithm extensions.

  • -g,-generic List generic extensions.

    Example:

     

    ListExtensions -a

ListSchemes

List all currently registered vocabularies.
Options:

  • -b,-brief List only coding scheme name, version, urn, and tags (default).
  • -f,-full List full detail for each scheme.

    Example: ListSchemes
RemoveTagScheme

Removes a tag ID (e.g. 'PRODUCTION' or 'TEST') from a coding scheme URN and version.

Options:

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

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

 

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

Example:

 

RemoveTagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"
RemoveVSResolvedFromCodingScheme

Removes a resolved ValueSet based on coding scheme and version that was used for its resolution.

 

Options:

   -l, List of coding scheme versions to match when removing the ResolvedValueSet.

   -f,--force Force de-activation and removal without confirmation.

Example:

 

RemoveVSResolvedFromCodingSchemes  -l -l \"source.coding.scheme.uri::version1, second.source.uri::version2\" -f
RemoveResolvedValueSet

Removes a resolved ValueSet

Options:

   -l, The list of resolved value sets to remove, separated by comma. format "resolvedValueSetUri1::version1, resolvedValueSetUri2::version2,...".

   -f,--force Force de-activation and removal without confirmation.

 

Load Example:

 

RemoveResolvedValueSet  -l \"resolvedValueSetUri1::version1, resolvedValueSetUri2::version2\" -f
RemoveValueSetDefinition

Removes a coding scheme based on unique URN and version.

Options:

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

 

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

Example:

 

RemoveValueSetDefinition

 

RemoveValueSetDefinition -u http://evs.nci.nih.gov/Valueset/C100110

TagScheme

Associates a tag ID (e.g. 'PRODUCTION' or 'TEST') with a coding scheme URN and version.
Options:

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

  • -t,-tag The tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

    Example:

     

    TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v 05.09e" -t "TEST"

...

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

Load

A generic loader script that allows for the selection of a Loader Extension.

Options:

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

   -l, --loader <name> LexGrid Load Extension name

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

 

Example:

 

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

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
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 <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.
  •    -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 -in "file:///path/to/file.asc" -v 0

 

Load CUI Example:

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 XML file.
  • -v,-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 -in "file:///path/to/file.xml" -o

     

     

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

LoadMIFVocabulary

Loads from an the HL7 Vocabulary mif file.

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


Load Example:

 

LoadMIFVocabulary -in "file:///path/to/file.xml" -a
LoadMrMap

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

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

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