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LoadOBO


 Load Example:

Shell Script

Use and Function

LoadMedDRA

 Loads 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.


Load Example:

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


Validation Example:

Code Block
 LoadMedDRA -in "file:///path/to/file.asc" -v 0

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:

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

LoadOBOLoadOWL2

 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.
 Example:
          LoadOWL2 -in "file:///path/to/somefile.owl" -v 0
Code Block
Code Block
LoadOWL2 -in "file:///path/to/
file
somefile.
obo
owl"
-nf
 -a
Code Block
LoadOBO
LoadOWL2 -in "file:///path/to/
file
somefile.
obo
owl" -v 0

LoadOWL

Loads an OWL file.

Info
titleNote

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
  • -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 well-formed
    • 1 = 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.
    Example:

    Code Block
    LoadOWL -in "file:///path/to/somefile.owl" -nf -a
    Code Block
    LoadOWL -in "file:///path/to/somefile.owl" -v 0 

LoadRadLexProtegeFrames

URI or path specifying location of the pprj file. Imports from a RadLex xml file to a LexBIG repository. Requires that the pprj file be configured with reference to a RadLex xml file as follows:

Code Block
([radlex_ProjectKB_Instance_66] of String (name "source_file_name") (string_value "radlex.xml"))" );

Example:

Code Block
java org.LexGrid.LexBIG.admin.LoadRadLexProtegeFrames
  • -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 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:

    Code Block
    java -Xmx800m -cp lgRuntime.jar -Djava.ext.dirs=../runtime/sqlDrivers org.LexGrid.LexBIG.admin.LoadRadLexProtegeFrames -in "file:///path/to/RadLex.pprj" -a -or- org.LexGrid.LexBIG.admin.LoadRadLexProtegeFrames -in "file:///path/to/RadLex.pprj" -v 0 

LoadUMLSSemnet

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 '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
    • 0 = Verify the existence of each required file
  • -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.
  • -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.
    Example:

    Code Block
    LoadUMLSSemnet -in "file:///path/to/directory/" -nf --a --il 1
    Code Block
    LoadUMLSSemnet -in "file:///path/to/directory/" -v 0 

LoadFMA

Imports from an FMA database to a LexEVS repository. Requires that the pprj file be configured with a database URN, username, password for an FMA MySQL based database. The FMA.pprj file and MySQL dump file are available at http://sig.biostr.washington.edu/projects/fm/ upon registration.
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 well-formed
    • 1 = 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:

    Code Block
    LoadFMA -in "file:///path/to/FMA.pprj" -nf -a
    Code Block
    LoadFMA -in "file:///path/to/FMA.pprj" -v 0 

LoadHL7RIM

Converts an HL7 RIM MS Access database to a LexGrid database

  • -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,-load preferences <uri> URI or path specifying location of the load preferences 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.
    Example:

    Code Block
    LoadHL7RIM -in "file:///path/to/file.mdb" -nf -a
    Code Block
    LoadHL7RIM -in "file:///path/to/file.mdb" -v 0 

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 '-nf', '-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).
  • -nf,-noFail If specified, indicates that processing should not stop for recoverable errors

    Info
    titleNote

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


    Examples:

    Code Block
    LoadMetadata -in "file:///path/to/file.xml" -nf -o
    Code Block
    LoadMetadata -in "file:///path/to/file.xml" 

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

    Code Block
    LoadMrMap -inMap "file:///path/to/MRMAP.RRF -inSat "file:///path/to/MRSAT.RRF" 

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