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LoadMedDRA

•    -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:

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

Validation Example:

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

LoadMIFVocabulary

•    -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

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

LoadOWL

Loads an OWL file.

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:

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

Example:

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

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\" ""

LoadMetaData