MEDLINE Tokenizer

• Description:

  Read in Medline file and retrieve specified fields. The output is used as the input for JDI (both phrases and MeSHs).

• Usage:

  > mlt -h
  
  Synopsis:
    Mlt [options]
  
  Description:
    Mlt is a program to tokenize MEDLINE citations by specifying field tags
  
  Options:
    -ci       Show configuration information
    -h        Print program help information (this is it)
    -i:STR    Specify input file (must specify)
    -pmid     Preserve PMID in the first field
    -s        Sort output by PMID
    -o:STR    Specify output file (must specify)
    -t:STR    Specify MEDLINE field tag:TI|AB|TIAB|MHs|TIABMHs|ALL|S_ALL (must specify)
              or any MEDLINE field tag
    -v        Print the current version of Mlt
    -x:STR    Specify an alternate configuration file
   
  

• Sample Inputs:
  • 9801.2004.baseline.sorted
  • 9801.2005.baseline.sorted

• Algorithm:
  • Read in file and save MEDLINE records into Java objects, CitationObjs.
  • Sort Citations by PMID if -s sorting flag is chose
  • Print out field data by specified field tags:
    • MHs: starred MeSHs (MH and SH are separated by '|');
    • TIABMHs: combination of TI, AB, and MHs
    • ALL: the original format
    • TIAB: combination of TI and AB
    • Field tag: legal field tag in MEDLINE, such as TI, AB, etc.. Please refer MEDLINE field tags for details.
  • Re-format MHs:
    • read in MEDLINE file and generate MH (Mesh)
    • Take care of multiple lines MH
    • Filter out MH without star (*)
    • Tokenize MeSH Main heading
    • Tokenize MeSH sub heading and only keep those with *
      => Indexing rules do not allow * on both MH and SH. However, our code is able to handle this situation
    • MeSH Main heading is always unique
    • Unify MeSH sub headings (sub heading may be duplicated)
    • Sub heading is changed to its abbreviation form
    • Print out main heading and sub heading use separator "|"

• Sample commands:

  > mlt -t:TIAB -i:9801.2004.baseline.sorted -o:9801.2004.TIAB
  

  => Read in file 9801.2004.baseline.sorted, retrieve field TI and AB and send the results to file 9801.2004.TIAB

• Sample outputs:
  • 9801.2004.TI
  • 9801.2004.AB
  • 9801.2004.TIAB
  • 9801.2004.MH
  • 9801.2004.TIABMH