Sub-Term Mapping Tools

Frequently Asked Questions

(Please read before asking a question)

• How can I ask a question?
  See Contact Us

• I can't install STMT successfully?
  One of the most common mistakes is that users install STMT from the wrong directory. Make sure to run the STMT installation script from the top directory of ${STMT_DIR}. Please refer to installation instruction for details.

• Can I install STMT to Mac (other than Linux and MS Windows)?
  Yes, it requires manual installation

• Do I need to install STMT if I just to want use Java APIs to get sub-terms?
  No. You don't need to install STMT if you just want to get the sub-term with your own defined corpus file. All you need is the stmt${YEAR}api.jar or stmt${YEAR}dist.jar. If you want to use the preloaded corpus (Lexicon or UMLS-Core synonyms) or run the command line tools, then you will need to install STMT. Please refer to STMT files usage for details.

• How many different tools are included in STMT? What are they?
  Five, please see details at STMT user documents

  Tools	Full Name	Usage
  lsf	LexItem Sub-Term Finder	Find a term, subterms, longest prefix subterm in Lexicon
  mt	Mapping Tool	Map a term to CUIs, EUIs, (recursive) synonyms, and preferred term
  nt	Normalization Tool	Includes LexNorm, SynonymNorm, and LvgNorm
  smt	Synonym Mapping Tool	Find CUIs|preferred terms by substituting synonym for subterms
  stmt	Sub-Term Mapping Tool	Generic sub-term tool to find subterms, prefix subterms, longest prefix subterms, and all permutation of synonym substitutions

• How to setup STMT with different data release?
  Please refer to user documents - data version setup for details.

• Which file should I configure as corpus in configuration file? SYNONYM_FILE or CORPUS_FILE
  It depends on your application:
  • If you only deal with sub-terms or prefixes: use CORPUS_FILE
  • If you need to find the synonym substitutions for sub-terms: use SYNONYM_FILE.
  Please note that all terms in corpus (from both files) should be normalized. Also, CORPUS_FILE is ignored by STMT when SYNONYM_FILE is specified. The first field (key term) in SYNONYM_FILE is used for corpus. Please refer to configuration setup for details.

• How to use different version of LVG in SMT?
  • Download and install the desired version of Lexical Tools
  • Change ROOT_DIR to the installed Lexical Tools in lvg configuration file, ${STMT}/data/Config/lvg.properties

• How to use different version of Lexicon or UMLS-Metathesaurus in SMT to find concepts?
  • Update HSqlDb
    • Download the desired version of HSqlDb data HSqlDb files
    • unpack and put it under ${STMT}/data/
  • Update Lvg
    The version of Lexical Tools should be synchronized, see above to update Lexical Tools
  • Update configuration file
    Update DB_NAME in smt configuration file, smt.properties

  It is a good idea to use -X option with different smt configuration file by saving different versions information in different smt.properties.X

• How to customize my own synonym file?
  • Update SMT standard normalized synonym file by STMT Java classes
    • GenSynonymsFileFromAFile:
      Convert a user's synonym file to the SMT standard normalized synonym file
    • GenSynonymsFileFromFiles
      Add a user's synonym file to the SMT standard normalized synonym file
  • Update configuration file
    Update SYNONYM_FILE in smt configuration file, smt.properties