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title
title

Panel
titleContents of this Page
Table of Contents
minLevel2

Introduction

This document is a section of the Administration Guide.

Vocabulary Administration Overview

A set of administrative utilities are provided to manage the LexEVS Service. These utilities are provided for Windows (.bat) and Linux (.sh) operating systems. Each of the commands is located in the {LEXBIG_DIRECTORY}/admin and {LEXBIG_DIRECTORY}/test directory. A full description of the options with example is provided for each of the administration utilities.

Administrative Program

Description

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.
...


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


  •  Examples: 
...
  •  Code Block
...
  • LoadOWL -in "file:///path/to/somefile.owl" -nf -a
...
  •  Code Block
    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 
 http://www.nlm.nih.gov/research/umls/metaa1.html 
.
...

 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. 
...


  •  Examples: 
...
  •  Code Block
...
  • LoadUMLSDatabase -in "jdbc:postgresql://localhost:5432/lexgrid"
-d "org.postgresql.Driver" -u "myDatabaseUser" -p "myPassword"
-s "ICD9CM_2005,ICD9CM_2006" -nf -a
...
  •  Code Block
    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 
 http://www.nlm.nih.gov/research/umls/metaa1.html 
.
...

 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. 
...


  •  Examples: 
...
  •  Code Block
...
  • LoadUMLSFiles -in "file:///path/to/directory/" -s "ICD9CM_2005,ICD9CM_2006" -nf -a
...
  •  Code Block
    LoadUMLSFiles -in "file:///path/to/directory/" -v 0
...
  •  Info
    titleNote
    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 LexEVS 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:
  • 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. 
...


  •  Examples: 
...
  •  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. 
...


  •  Example: 
...
  •  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. 
 Info
titleNote
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.
...
  • -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 
...
 LexEVS 
...
 installation.
...
 Info
...
title
...
Note
...
The 
...
 LexEVS 
...
 runtime 
...
 and 
...
 database 
...
 environments 
...
 must 
...
 still 
...
 be 
...
 configured 
...
 prior 
...
 to 
...
 invoking 
...
 the 
...
 test 
...
 suite. 
...
Options:
...
  • -b,-brief 
...
  •  Runs 
...
  •  the 
...
  •  LexEVS 
...
  •  test 
...
  •  suite 
...
  •  and 
...
  •  produce 
...
  •  a 
...
  •  text 
...
  •  report 
...
  •  with 
...
  •  overall 
...
  •  statistics 
...
  •  and 
...
  •  details 
...
  •  for 
...
  •  failed 
...
  •  tests 
...
  •  only.
...
  • -f,-full 
...
  •  Runs 
...
  •  the 
...
  •  LexEVS 
...
  •  test 
...
  •  suite 
...
  •  and 
...
  •  produce 
...
  •  an 
...
  •  itemized 
...
  •  list 
...
  •  of 
...
  •  all 
...
  •  tests 
...
  •  with 
...
  •  indication 
...
  •  of 
...
  •  success/failure.
...
  • -h,-html 
...
  •  Runs 
...
  •  the 
...
  •  LexEVS 
...
  •  test 
...
  •  suite 
...
  •  and 
...
  •  produce 
...
  •  a 
...
  •  report 
...
  •  suitable 
...
  •  for 
...
  •  view 
...
  •  in 
...
  •  a 
...
  •  standard 
...
  •  web 
...
  •  browser.
...
  • -x,-xml 
...
  •  Runs 
...
  •  the 
...
  •  LexEVS 
...
  •  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" 
...
Installing Sample Vocabularies
This LexEVS installation provides the UMLS Semantic Net and a sampling of the NCI Thesaurus content (sample.owl) 
...
 that 
...
 can 
...
 be 
...
 loaded 
...
 into 
...
 the 
...
 database.
...
  1. In 
...
  1.  a 
...
  1. Command 
...
  1.  Prompt
...
  1.  window, 
...
  1.  enter 
...
  1.  the 
...
  1.  following 
...
  1.  to 
...
  1.  go 
...
  1.  to 
...
  1.  the 
...
  1.  example 
...
  1.  programs: 
...
  1.  Code Block
...
  1. cd {LEXBIG_DIRECTORY}/examples
...
  2. To load the example vocabularies, run the appropriate LoadSampleData script (LoadSampleData.bat 
...
  1.  for 
...
  1.  Windows; 
...
  1.  LoadSampleData.sh 
...
  1.  for 
...
  1.  Linux).
...
 Info
titleNote
Vocabularies should not be loaded until configuration of the LexEVS runtime and database server are complete.
The following figure displays the successful load of the sample vocabulary file.
screenshot of command window showing the successful load of the vocabulary fileImage Added
Running the Sample Query Programs
A set of sample programs are provided in the {LEXBIG_DIRECTORY}/examples directory. To run the sample query programs successfully a vocabulary must have been loaded.
  1. Enter: 
     Code Block
    cd {LEXBIG_DIRECTORY}/examples
...
  2. Execute one of sample programs. .bat for windows or .sh for Linux. 
    • FindConceptNameForCode.bat
    • FindPropsandAssocForCode.bat
    • FindRelatedCodes
    • FindTreeforCodeAndAssoc
The following figure shows sample program output for finding properties and associations for a given code.
 screenshot showing sample program outputImage Added
Installing NCI Vocabularies
NCI Thesaurus Vocabulary
This section describes the steps to download and install a full version of the NCI Thesaurus for the LexEVS Service.
  1. Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
...

  1.  screenshot of navigating to the ftp client in WindowsImage Added 
  2. Select the version of NCI Thesaurus OWL you wish to download. Save the file to a directory on your machine.
  3. Extract the OWL file from the zip download and save in a directory on your machine. This directory will be referred to as NCI_THESAURUS_DIRECTORY
  4. Using the LexEVS utilities load the NCI Thesaurus 
     Code Block
    cd {LexBIG_DIRECTORY}/admin
...
  1.  For 
...
  1.  Windows 
...
  1.  installation 
...
  1.  use 
...
  1.  the 
...
  1.  following 
...
  1.  command: 
...
  1.  Code Block
...
  1. LoadNCIThesOWL.bat -nf -in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_05.12f.owl"
...
  1.  For 
...
  1.  Linux 
...
  1.  installation 
...
  1.  use 
...
  1.  the 
...
  1.  following 
...
  1.  command: 
...
  1.  Code Block
...
  1. LoadNCIThesOWL.sh -nf -in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_05.12f.owl"
     Info
    titleNote
    This step will require about three hours on a Pentium 3.0 Ghz machine. The total time to load NCI Thesaurus will vary depending on machine, memory, and disk speed.
The following example shows output from load of NCI Thesaurus 05.12f:
 Code Block
{code}
{info:title=Note}This step will require about three hours on a Pentium 3.0 Ghz machine.  The total time to load NCI Thesaurus will vary depending on machine, memory, and disk speed.{info}

The following example shows output from load of NCI Thesaurus 05.12f:

{code}
 ...
 [LexBIG] Processing TOP Node... Retired_Kind
 [LexBIG] Clearing target of NCI_Thesaurus...
 [LexBIG] Writing NCI_Thesaurus to target...
 [LexBIG] Finished loading DB - loading transitive expansion table
 [LexBIG] ComputeTransitive - Processing Anatomic_Structure_Has_Location
 [LexBIG] ComputeTransitive - Processing Anatomic_Structure_is_Physical_Part_of
 [LexBIG] ComputeTransitive - Processing Biological_Process_Has_Initiator_Process
 [LexBIG] ComputeTransitive - Processing Biological_Process_Has_Result_Biological_Process
 [LexBIG] ComputeTransitive - Processing Biological_Process_Is_Part_of_Process
 [LexBIG] ComputeTransitive - Processing Conceptual_Part_Of
 [LexBIG] ComputeTransitive - Processing Disease_Excludes_Finding
 [LexBIG] ComputeTransitive - Processing Disease_Has_Associated_Disease
 [LexBIG] ComputeTransitive - Processing Disease_Has_Finding
 [LexBIG] ComputeTransitive - Processing Disease_May_Have_Associated_Disease
 [LexBIG] ComputeTransitive - Processing Disease_May_Have_Finding
 [LexBIG] ComputeTransitive - Processing Gene_Product_Has_Biochemical_Function
 [LexBIG] ComputeTransitive - Processing Gene_Product_Has_Chemical_Classification
 [LexBIG] ComputeTransitive - Processing Gene_Product_is_Physical_Part_of
 [LexBIG] ComputeTransitive - Processing hasSubtype
 [LexBIG] Finished building transitive expansion - building index
 [LexBIG] Getting a results from sql (a page if using mysql)
 [LexBIG] Indexed 0 concepts.
 [LexBIG] Indexed 5000 concepts.
 [LexBIG] Indexed 10000 concepts.
 [LexBIG] Indexed 15000 concepts.
 [LexBIG] Indexed 20000 concepts.
 [LexBIG] Indexed 25000 concepts.
 [LexBIG] Indexed 30000 concepts.
 [LexBIG] Indexed 35000 concepts.
 [LexBIG] Indexed 40000 concepts.
 [LexBIG] Indexed 45000 concepts.
 [LexBIG] Indexed 46000 concepts.
 [LexBIG] Getting a results from sql (a page if using mysql)
 [LexBIG] Closing Indexes Mon, 27 Feb 2006 01:44:22
 [LexBIG] Finished indexing
{code}

h3. NCI Metathesaurus Vocabulary

This section describes the steps to download and install a full version of the NCI Metathesaurus for the LexEVS Service.  

# Using a web or ftp client go to URL: 
NCI Metathesaurus Vocabulary
This section describes the steps to download and install a full version of the NCI Metathesaurus for the LexEVS Service. 
  1. Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
...

  1.  screenshot of navigating to the ftp client in WindowsImage Added 
  2. Select the version of NCI Metathesaurus RRF you wish to download. Save the file to a directory on your machine.
  3. Extract the RRF files from the zip download and save in a directory on your machine. This directory will be referred to as NCI_METATHESAURUS_DIRECTORY. 
...
  1.  Info
...
  1. title
...
  1. Note
...
  1. RELEASE_INFO.RRF 
...
  1.  is 
...
  1.  required 
...
  1.  to 
...
  1.  be 
...
  1.  present 
...
  1.  for 
...
  1.  the 
...
  1.  load 
...
  1.  utility 
...
  1.  to 
...
  1.  work. 
...
  2. Using the LexEVS utilities load the NCI Thesaurus 
     Code Block
    cd {LexBIG_DIRECTORY}/admin
...
  1.  For 
...
  1.  Windows 
...
  1.  installation 
...
  1.  use 
...
  1.  the 
...
  1.  following 
...
  1.  command: 
...
  1.  Code Block
...
  1. LoadNCIMeta.bat -nf -in "file:///{NCI_METATHESAURUS_DIRECTORY}/" 
...
  1.  For 
...
  1.  Linux 
...
  1.  installation 
...
  1.  use 
...
  1.  the 
...
  1.  following 
...
  1.  command: 
...
  1.  Code Block
...
  1. LoadNCIMeta.sh -nf -in "file:///{NCI_THESAURUS_DIRECTORY}/"
...
 Info
titleNote
NCI Metathesaurus contains many individual vocabularies and requires several hours to load and index. This step requires about 15 hours on a Pentium 3.0 Ghz machine with 7200rpm disk. The total time to load NCI MetaThesaurus will vary depending on machine, memory, and disk speed.
NCI History
This section describes the steps to download and install a history file for NCI Thesaurus.
  1. Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
...
  2. Select 
...
  1.  the 
...
  1.  version 
...
  1.  of 
...
  1.  NCI 
...
  1.  History 
...
  1.  you 
...
  1.  wish 
...
  1.  to 
...
  1.  download. 
...
  1.  Save 
...
  1.  the 
...
  1.  file 
...
  1.  to 
...
  1.  a 
...
  1.  directory 
...
  1.  on 
...
  1.  your 
...
  1.  machine. 
...
  1.  Select 
...
  1.  the 
...
  1.  VersionFile 
...
  1.  download 
...
  1.  to 
...
  1.  the 
...
  1.  same 
...
  1.  directory 
...
  1.  as 
...
  1.  the 
...
  1.  history 
...
  1.  file.
...
  2. Extract 
...
  1.  the 
...
  1.  History 
...
  1.  files 
...
  1.  from 
...
  1.  the 
...
  1.  zip 
...
  1.  download 
...
  1.  and 
...
  1.  save 
...
  1.  in 
...
  1.  a 
...
  1.  directory 
...
  1.  on 
...
  1.  your 
...
  1.  machine. 
...
  1.  This 
...
  1.  directory 
...
  1.  will 
...
  1.  be 
...
  1.  referred 
...
  1.  to 
...
  1.  as 
...
  1.  NCI_HISTORY_
...
  1. DIRECTORY
  2. Using the LexEVS utilities load the NCI Thesaurus: 
     Code Block
    cd {LexBIG_DIRECTORY}/admin_*</tt>
...
  1.  For 
...
  1.  Windows 
...
  1.  installation 
...
  1.  use 
...
  1.  the 
...
  1.  following 
...
  1.  command: 
...
  1.  Code Block
...
  1. LoadNCIHistory.bat -nf -in "file:///{NCI_HISTORY_DIRECTORY}" -vf "file:///NCI_HISTORY_DIRECTORY}/VersionFile"
...
  1.  For 
...
  1.  Linux 
...
  1.  installation 
...
  1.  use 
...
  1.  the 
...
  1.  following 
...
  1.  command: 
...
  1.  Code Block
...
  1. LoadNCIHistory.sh -nf -in "file:///{NCI_HISTORY_DIRECTORY}" -vf "file:///NCI_HISTORY_DIRECTORY}/VersionFile" 
 Info
titleNote
If a 
{code}

{info:title=Note}If a 
 'releaseId' 
 
 occurs 
 
 twice 
 
 in 
 
 the 
 
 file, 
 
 the 
 
 last 
 
 occurrence 
 
 will 
 
 be 
 
 stored. 
 
 If 
 
 LexEVS 
 
 already 
 
 knows 
 
 about 
 
 a 
 
 releaseId 
 
 (from 
 
 a 
 
 previous 
 
 history 
 
 load), 
 
 the 
 
 information 
 
 is 
 
 updated 
 
 to 
 
 match 
 
 what 
 
 is 
 
 provided 
 
 in 
 
 the 
 
 file.



This 
 
 file 
 
 has 
 
 to 
 
 be 
 
 provided 
 
 to 
 
 the 
 
 load 
 
 API 
 
 on 
 
 every 
 
 load 
 
 because 
 
 you 
 
 will 
 
 need 
 
 to 
 
 maintain 
 
 it 
 
 in 
 
 the 
 
 future 
 
 as 
 
 each 
 
 new 
 
 release 
 
 is 
 
 made. 
  
 We 
 
 have 
 
 created 
 
 this 
 
 file 
 
 that 
 
 should 
 
 be 
 
 valid 
 
 as 
 
 of 
 
 today 
 
 from 
 
 the 
 
 information 
 
 that 
 
 we 
 
 found 
 
 in 
 
 the 
 
 archive 
 
 folder 
 
 on 
 
 your 
 
 ftp 
 
 server. 
   
 You 
 
 can 
 
 find 
 
 this 
 
 file 
 
 in 
 
 the 
 
 'resources' 
 
 directory 
 
 of 
 
 the 
 
 LexEVS 
 
 install.
{info}

h2. Deactivating and Removing a Vocabulary

This section describes the steps to deactivate a coding scheme and remove coding scheme from LexEVS Service.

# Change directory to LexEVS administration directory. Enter:
{code}
Deactivating and Removing a Vocabulary
This section describes the steps to deactivate a coding scheme and remove coding scheme from LexEVS Service.
  1. Change directory to LexEVS administration directory. Enter: 
     Code Block
    cd {LEXBIG_DIRECTORY}/admin_*
...
  2. Use the DeactiveScheme utility to prevent access to coding scheme. Once a coding scheme is deactivated, client programs will not be able to access the content for the specific coding scheme and version. Example: 
     Code Block
    DeactivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.12f" 
...
  2. Use RemoveScheme utility to remove coding scheme from LexEVS service and database. Example: 
     Code Block
    RemoveScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.12f"
...
  1.  
Tagging a Vocabulary
This section describes the steps to tag a coding scheme to be used via LexEVS API. 
  1. Change directory to LexEVS administration directory and enter: 
     Code Block
    cd {LEXBIG_DIRECTORY}/admin_*
...
  2. Use the TagScheme to tag a coding system and version with a local tag name (e.g. 
...
  1.  PRODUCTION). 
...
  1.  This 
...
  1.  tag 
...
  1.  name 
...
  1.  can 
...
  1.  be 
...
  1.  used 
...
  1.  via 
...
  1.  LexEVS 
...
  1.  API 
...
  1.  for 
...
  1.  query 
...
  1.  restriction. 
...
  1.  Example: 
...
  1.  Code Block
...
  1. TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.12f"  -t "PRODUCTION" 
...
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