UMLS-Core: Process

I. SMT Package files
Use smt to get the result of CUI mapping. Need to make sure the files are updated, see STMT preProcess for details:

• Metathesaurus
  • nonSuppressCui.data (for nonSuprees|CUI mapping)
  • normTermCui.data (for normTerm|CUI mappig)
  • preferredTerms.data (for preferred term mapping)
• UMLS-Core Synonym files
  • normTermSynonyms.data (corpus)

II. Input file

• Convert the original input file to
  • Location: ${UMLS_CORE_DIR}/data/${DATA_YEAR}/${DATA_NAME}/inputs/inTerms.data
  • Format:

    Field 1	Field 2
    Term ID	Term

  • Methods:
    • Convert the file as pipe ("|") separated field if the original file is *.cvs
      shell> cd ${UMLS_CORE_DIR}/bin
shell> ConvertCsvToPipe
...
    • Retrieve the term ID and term
      flds inTerm.allFields > inTerm.data.1.4
    • Manually remove the banner (first line) of the file
      inTerm.data

III. Process: Run UMLS-Core CUI mapping
shell> cd ${UMLS_CORE_DIR}/bin
shell> UmlsCore
...

IV. Output files

• Location: ${UMLS_CORE_DIR}/data/${DATA_YEAR}/${DATA_NAME}/outputs/
  • log.${DATA_NAME}
    Detail log and statistic for all synonym substitution mapping
  • out.${DATA_NAME}
    Final results in following format

    Term ID

    Term

    Norm Term

    CUI

    Preferred Term

    Synonym substitution flag