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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
LoadManifest

Load manifest data onto the codingscheme based on unique

RemoveTagScheme

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

Options:

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

   -v,--version <id> "versionId"; Version identifier.

   -mf,--manifest "manifest"; location of manifest xml file.

 

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

Example:

 

RemoveTagScheme
LoadManifest -u \"urn:oid:2.16.840.1.113883.3.26.1.1\" -v \"05.09e\" -mf \"
file://path//to//manifest.xml\""
LoadManifest -mf \"file://path//to//manifest.xml\"
RemoveTagScheme

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

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

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

Example:

 

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

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.

 

RemoveResolvedValueSet

Removes a resolved ValueSet

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 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 versionURN 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"

Lucene Index Administration

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

-u, <versionId> t-tag The tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
ExampleTagScheme " -t "TEST
BuildAssertedValueSetIndex

Builds indexes associated with the source asserted value sets of 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.

Load Example:

 

RemoveValueSetDefinition

 

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

TagScheme

"urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"
BuildResolvedAndAssertedValueSetIndexes

Builds indexes associated with the source asserted value sets of the specified coding scheme. Adds the value set entities of any resolved value sets external to the asserted source

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:

 

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

...

CleanUpLuceneIndex

Clean up orphaned indexes.
Options:

  • -h, -help, Prints usage information

  • -r, -reindex, Reindex any missing indices.

    Note

     

    Lucene Clean Up can only be executed in the default Single Index Mode.



    Example:

     

    CleanUPLuceneIndex -r

RebuildIndex

Rebuilds indexes associated with the specified coding scheme.
Options:

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

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

    Example:

     

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

RemoveIndex

Clears an optional named index associated with the specified coding scheme.

Note

 

Built-in indices required by the LexEVS runtime cannot be removed.

Options:

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

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

    Example:

     

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

...

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

...