UMLS-Core: SMT Requirements

1. Objective:
   • Develop a set of software that map a term (multiple words) to CUI
2. Software Specification:
   • A command-line software to provides functions described in the next section
3. Functions:
   • Inputs:
     • list of terms:
       • clinterms0610.xlsx (only use 1st field)
       • VATerm.csv (use 1st & 2nd field)
       • KP_SynMap_out.txt

       • remove header (1 row)
     • Synonyms Standardization
     • Term to CUI mapping:
       • MRXNS_ENG.RRF & MRCONSO.RRF
       • only use 2nd and 3rd fields
       • remove duplications
       • exclude suppressible atoms
     • Preferred term:
       • MRCONSO.RRF
   • Outputs:
     • Format:

       Term ID

       Original Term

       Matching term (normalized with synonyms)

       CUI

       Flag

       Preferred Terms

       where:
       • Flag:

         Value	Description
         0	CUI found, with no replaced synonym
         1	CUI found, with one replaced synonym
         2	CUI found, with two replaced synonyms
         3	no CUI found (C0000000)

4. Processes:
   • Pre-Processes:
     • Non-Suppressible atoms:
       • MRCONSO.RRF
         • SUPPRESS=N (non-suppressible)

         • SUPPRESS=O (suppressible)
         • SUPPRESS=E (suppressible)
         • SUPPRESS=Y (suppressible)
       • Outputs: CUI|LUI|SUI
     • Preferred Terms:
       • MRCONSO.RRF
         • LAT=ENG
         • TS=P
         • STT=PF
         • ISPREF=Y
       • Only one preferred term per CUI
       • Outputs: CUI|preferred term
   • Processes:
     • normalize input term (use norm) and map to CUI (from MRXNS_ENG.RRF)
     • if no CUI found from above, replace input term with one synonym and map to CUI
     • if no CUI found from above, replace input term with two synonyms and map to CUI
     • if no CUI found from above, use "orginal term|original term|C000000|3

     • print out results
   • Post-Processes:
     • Add preferred term to the result file (by CUI|preferred term mapping)
5. Examples:
   • KP103521|HIV positive|hiv positive|C0019699|0|HIV Seropositivity
   • KP103221|EXAM, FOOT, DIABETIC|diabetic examination foot|C1303165|1|Diabetic foot examination
   • KP168981|HX OF VARICELLA|chickenpox history|C0455469|2|H/O: chickenpox

   • VA1000|Alcohol Withdrawal|alcohol withdrawal|C0236663|0|Alcohol withdrawal syndrome
   • VA10137|Leg Condition|infection leg|C0745687|1|leg; infection
   • VA14760|Pneumonia due to other virus|other pneumonia viral|C0348677|2|Other viral pneumonia