MedEx 1.0 
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Introduction
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Extract structure medication information from clinical notes

Perquisite of running
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Operating System: Windows and Linux
      
      
How to get started?
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1> Download MedEx.tar.gz/MedEx.zip into a directory of your choice '[YourDir]'

2> Uncompress it

3> Enter into the directory [YourDir], then run MedEx with the following command:

	 MedParser_V1 -i [inputdir] -o [outputdir] (For windows)
	 ./MedParser_V1 -i [inputdir] -o [outputdir] (For linux)
	
	 The following is a description of the program options:
	 -h or --help            : print this help
	 -i or --input=<input>   : input file
	 -o or --output=<output> : output file

	 For example, executing command "MedParser_V1 -i .\input -o .\output" at Windows environment or
	 "./MedParser_V1 -i ./input -o ./output" at Linux environment will parse all of the files in the
	 input folder at current directory and store the result into the output folder at current directory.

4> The input of this program is a folder which contains multiple files (it will not process nested folders).
   Each file in input directory should be less than 100M, otherwise MedEx will ignore it. The output is a 
   folder which contains parse result for each input file. For each line in the file, the output includes the 
   following items that are concatenated with tab space:
	 
         NOTEID (if it does not exist, it is assigned '-1')
	 Sentence index 
	 Sentence
	 CUI code
	 RXNORM code (generally, the most specific code MedEx can assign)
	 Generic drug name (e.x. 'simvastatin')
         Brand name (e.x. 'Zocor')
         Drug form (e.x. 'tablet')
         Strength (e.x. '10mg')
         Dose amount (e.x. '2 tablet')
         Route (e.x. 'by mouth')
         Frequency (e.x. 'b.i.d.')
         Duration (e.x. 'for 10 days')
         Neccessity (e.x. 'prn')
	 
   Here is an example of input and output:

   Assume that one sample sentence in the output file could be:
   -1:15		2.  Soma 350 mg, take 1 every 8 hours as needed for pain.	C0702216	204362	soma

   In this output, "15" means the index of sentence in current notes, followed by the content of sentence, then		
   two code "C0702216" and "204362" will be displayed as CUI code and RXnorm code respectively, "soma" is the
   drug detected.
 


