UMLS Metathesaurus Programs

This page describes programs run on on UMLS releases (AA and AB):

1.ProcessUmlsFiles

• This is used to get all English terms, concepts (CUI), preferred terms of a concept, synonyms, etc. It is needed for STMT and TC projects. It needs to be run twice annually, {YEAR}AA and ${YEAR}AB.
• Data supported by: Dr. Kin Wah Fung, Joe Chow
• Location: ash2:/u03/umls/Releases/${YEAR}${VERSION}/Full/RRF/META/
• Source files: ${META}/data/${UMLS_RELEASE}/org
  • MRCONSO.RRF
  • MRFILES.RRF
  • MRXNS_ENG.RRF
  • MRXNW_ENG.RRF
• Run Programs:

  	${META}/bin/1.ProcessUmlsFiles
  	${UMLS_RELEASE}
  	${LVG_YEAR}
  	

  • 2: Get English terms
  • 3: Regenerate and test MRXNS_ENG.RRF
  • 4~5: Test Norm on English Strings (MRXNS_ENG.RRF) only if 3 does not work
  • 6: Regenerate and test MRXNW_ENG.RRF
  • 7~8: Test Norm Words from English Strings (MRXNW_ENG.RRF) only if 6 does not work

2.GetAtoms

• This is to get all English terms, atoms files, form MRCONSO.RRF. It retrieves all strings (STR - 15th fields) from MRCONSO.RRF if language (LAT - 2nd field) is either ENG or SPA. LSG starts to generated this files ourselves after 2015+ release. It needs to be run once annually, {YEAR}AA for Lexical Tools - Canonical tables.
• Source files: ${META}/data/${UMLS_RELEASE}/org
  • MRCONSO.RRF
• Run Programs:

  	${META}/bin/2.GetAtoms
  	${UMLS_RELEASE}
  	

  • 1: Get Atoms by Java program
  • 2: Get Atoms by OCCS script
  • 3: Compare abov two files (after sort, they are the same)