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LoadLgXMLLoads

•    -in,--input <uri> URI or path specifying location of the source file.file
•    -mf,--manifest <uri> URI or path specifying location of the manifest file
•    -v, --validate <level> <int> Perform validation of the candidate 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-formed1 = Verify document is valid
• -nf,-noFail If specified, indicates that processing should not stop for recoverable errors.
• -a,   -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
•    -t, --tag <tagID> <id> 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.
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 '-nf' and '-r' options are ignored. Supported levels of validation include:
  • 0 = Verify top 10 lines are correct format
  • 1 = Verify correct format for the entire file
• -nf,-noFail If specified, indicates that processing should not stop for recoverable errors

• -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:

  Code Block
  LoadNCIHistory -nf -in "file:///path/to/history.file" -vf "[file:///path/to/version.file]"

  
  Validation Example:

  Code Block
  LoadNCIHistory -in "file:///path/to/history.file" -v 0

  Versions File Format Information:

  Code Block
  releaseDate | isLatest | releaseAgency | releaseId | releaseOrder | entityDescription

  Sample record:

  Code Block
  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:

  Code Block
  LoadOBO -in "file:///path/to/file.obo" -nf -a

  Code Block
  LoadOBO -in "file:///path/to/file.obo" -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

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
  title Note
  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"