Bold and Capitalized Command

Indicates a Menu command

Click the Open command.

Capitalized command>Capitalized command

Indicates Sequential Menu commands

Admin > Refresh

Special typestyle

Used for filenames, directory names, commands, file listings, source code examples and anything that would appear in a Java program, such as methods, variables, and classes.

URL_definition ::= url_string

Boldface type

Options that you select in dialog boxes or drop-down menus. Buttons or icons that you click.

In the Open dialog box, select the file and click the Open button.

Italics

Used to reference other documents, sections, figures, and tables.

caCORE Software Development Kit 1.0 Programmer's Guide

Italic boldface type

Text that you type

In the New Subset text box, enter Proprietary Proteins.

Highlights a concept of particular interest

Highlights information of which you should be particularly aware.

{}

Curly brackets are used for replaceable items.

Replace {LEXBIG_DIRECTORY} with its proper value such as c:\lexbig

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:

  Code Block
  ActivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

ClearOrphanedResources

Clean up orphaned resources - databases and indexes.
Options:

• -li - listIndexes List all unused indexes.
• -ldb - listDatabases List all unused databases (with matching prefix).
• -ri - removeIndex <name> Remove the (unused) index with the given name.
• -rdb - removeDatabase <name> Remove the (unused) database with the given name.

• -a - all Remove all unreferenced indexes and databases (with matching prefix).
  
  Example:

  Code Block
  ClearOrphanedResources -li

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:

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

ExportLgXML

Exports content from the repository to a file in the LexGrid canonical XML format.
Options:

• -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 <id> The assigned tag/label or absolute version identifier of the coding scheme.
• -nf - noFail If specified, indicates that processing should not stop for recoverable errors

• -f - force If specified, allows the destination file to be overwritten if present.

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

  
  
  Examples:

  Code Block
  ExportLgXML -out "file:///path/to/dir" -nf -f

  Code Block
  ExportLgXML -out "file:///path/to/dir" u "NCI_Thesaurus" -v "PRODUCTION" -nf -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.
• -nf - noFail If specified, indicates that processing should not stop for recoverable errors

• -f - force If specified, allows the destination file to be overwritten if present.

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

  
  
  Examples:

  Code Block
  ExportOBO -out "file:///path/to/dir" -nf -f

  Code Block
  ExportOBO -out "file:///path/to/dir" -u "FBbt" -v "PRODUCTION" -nf -f

ExportOWL

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

• -f - force If specified, allows the destination file to be overwritten if present.

  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
  ExportOWL -out "file:///path/to/dir" -nf -f

  Code Block
  ExportOWL -out "file:///path/to/dir" -u "sample" -v "1.0" -nf -f

ListExtensions

List registered extensions to the LexBIG 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:

  Code Block
  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

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 '-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 <tagID> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
  
  Load Example:

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

  
  
  Validation Example:

  Code Block
  LoadLgXML -in "file:///path/to/file.xml" -v 0

LoadNCIHistory

Imports NCI History data to the LexBIG 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.

LoadNCIMeta

Loads the NCI MetaThesaurus, provided as a collection of RRF files.
Options:

• -in - input <uri> The directory containing the RRF files; in URI format.
• -v - validate <level> 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 first 1000 lines per 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 <tagID> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
  
  Load Example:

  Code Block
  LoadNCIMeta -in "file:///path/to/directory" -nf -a

  
  
  Validation Example:

  Code Block
  LoadNCIMeta -in "file:///path/to/directory" -v 0

LoadNCIThesOWL

Loads an OWL file containing a version of the NCI Thesaurus
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 '-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 <tagID> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
  
  Load Example:

  Code Block
  LoadNCIThesOWL -in "file:///path/to/thesaurus.owl" -nf -a

  
  
  Validation Example:

  Code Block
  LoadNCIThesOWL -in "file:///path/to/thesaurus.owl" -v 0

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.
  
  Example:

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

LoadUMLSDatabase

Loads UMLS content, provided as a collection of RRF files in a single directory. Files may comprise the entire UMLS distribution or pruned via the MetamorphoSys tool. A complete list of source vocabularies is available online at

.
Options:

• -in - input <uri> Location of the source database. Typically this is specified in the form of a URL that indicates the database server, port, name, and optional properties.
• -u - uid User ID for authenticated access, if required and not specified as part of the input URL.
• -p - pwd Password for authenticated access, if required and not specified as part of the input URL.
• -d - driver Name of the JDBC driver to use when accessing the database.
• -s - sources Comma-delimited list of source vocabularies to load. If absent, all available vocabularies are loaded.
• -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.
  
  Example:

  Code Block
  LoadUMLSDatabase -in "jdbc:postgresql://localhost:5432/lexgrid" -d "org.postgresql.Driver" -u "myDatabaseUser" -p "myPassword" -s "ICD9CM_2005,ICD9CM_2006" -nf -a LoadUMLSDatabase -in "jdbc:postgresql://localhost:5432/lexgrid" -d "org.postgresql.Driver" -u "myDatabaseUser" -p "myPassword" -v 0

LoadUMLSFiles

Loads UMLS content, provided as a collection of RRF files in a single directory. Files may comprise the entire UMLS distribution or pruned via the MetamorphoSys tool. A complete list of source vocabularies is available online at

.
Options:

• -in - input <uri> URI or path of the directory containing the NLM files
• -s - sources Comma-delimited list of source vocabularies to load. If absent, all available vocabularies are loaded.
• -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.
  
  Example:

  Code Block
  LoadUMLSFiles -in "file:///path/to/directory/" -s "ICD9CM_2005,ICD9CM_2006" -nf -a LoadUMLSFiles -in "file:///path/to/directory/" -v 0

  Info
  title Note
  UMLS Metathesaurus RRF files are a very large fileset. Many users prefer to subset these files using the Metamorphosys tool included with the UMLS Metathesaurus in order to move a single terminology from a central location of these files. When generating source RRF files from the Metathesaurus, the Metamorphosys tool should be set to output versionless source abbreviations rather than versioned source abbreviations. Failing to do so before loading RRF files to LexBIG will cause an incomplete database to be created leaving the association and concept tables empty.

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. These files can be downloaded from the NLM web site at

.

• 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)
  
  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 LoadUMLSSemnet -in "file:///path/to/directory/" -v 0

LoadFMA

Imports from an FMA database to a LexBIG 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

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.
  
  Examples:

  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.
Options:

• -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"

RebuildIndex

Rebuilds indexes associated with the specified coding scheme.
Options:

• -u - urn <urn> URN uniquely identifying the code system.
• -v - version <versionId> Version identifier.
• -i - index <name> Name of the index extension to rebuild (if absent, rebuilds all built-in indices and named extensions).

• -f - force Force clear (no confirmation).
  
  Example:

  Code Block
  RebuildIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" -i "myindex"

RemoveIndex

Clears an optional named index associated with the specified coding scheme. Note: built-in indices required by the LexBIG runtime cannot be removed.
Options

• -u - urn <urn> URN uniquely identifying the code system.
• -v - version <versionId> Version identifier.
• -i - index <name> Name of the index extension to clear.

• -f - force Force clear (no confirmation).
  
  Example:

  Code Block
  RemoveIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" -i "myindex"

RemoveScheme

Removes 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 deactivation and removal without confirmation.
  
  Example:

  Code Block
  RemoveScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

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:

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

TestRunner

Located in {LEXBIG_DIRECTORY}/test. Executes a suite of tests for the LexBIG installation.

Options:

• -b - brief Runs the LexBIG test suite and produce a text report with overall statistics and details for failed tests only.
• -f - full Runs the LexBIG test suite and produce an itemized list of all tests with indication of success/failure.
• -h - html Runs the LexBIG test suite and produce a report suitable for view in a standard web browser.

• -x - xml Runs the LexBIG test suite and produce a report with extensive information for each test case in xml format.
  
  Example:

  Code Block
  TestRunner -f -h

TransferScheme

Tool to help gather information necessary to transfer data from one SQL server to another.
Options:

• -u - urn The Coding Scheme URN or local name to transfer.

• -v - version The version of the coding scheme to transfer.
  
  Example:

  Code Block
  TransferScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v 05.09e"