Clarity Medication Mapping

Clarity Medication Mapping to
Design and Current Status
Brief Tour of RxNorm Tables Used
Current Status (Results)
Next Steps
Code Walkthrough
RxNorm Concept Names and Sources
(starting section 12.4)
• “Primary” table – consists of all RxNorm Concepts
– Example: A medication and synonyms - there may be several rows for a single
– Disulfiram (generic) and Antabuse (brand name) are both the same concept and
have the same RxCUI.
• RxCUI: Concept Unique Identifier (unique per concept, may be
many rows with the same CUI)
• RxAUI: Atom Unique Identifier (unique per entry in the table)
• SCUI: Source-asserted Concept Identifier
– The identifier as provided by the source (NDDF, NDFRT, RXNORM, etc.)
• TTY: Term Type (preferred term, synonym, ingredient, etc.)
RxNorm Tables: Others
• Simple Concept and Atom Attributes (RXNSAT)
– Example: Used to match NDC and find VA Class types
• Related Concepts (RXNREL)
– Example: Parent/Child relationships of VA classes,
“ingredient_of”, etc.
• Source Information (RXNSAB)
– Source abbreviation/full name (NDFRT/National Drug File),
version, etc.
• Documentation for Abbreviated Values (RXNDOC)
– Full name for abbreviations used in other tables
RxNav: Relationships
VA Class Ontology
Map Clarity Medications to RxCUI:
• Clarity Medication List
– clarity.clarity_medication
• GCN (Generic Code Sequence Number - First
Databank Inc.)
– clarity.rx_med_gcnseqno
– rxnorm.rxnconso (code column when sab = NDDF, and tty
!= ‘IN’)
• NDC (National Drug Code)
– clarity.clarity_ndc_codes
– rxnorm.rxnsat (atv column where atn = NDC)
The Leftovers: Match with MedEx NLP
• For the medications that don’t match using
GCN/NDC, use MedEx (NLP)
– map directly to RxCUI via the drug name in clarity
– “NAME” (arbitrarily preferred)
• Issues
– Closed source (though, open source soon as per authors)
– Windows Only right now (Linux binaries won’t run with our
current configuration on our servers)
– Not integrated into our ETL (“manual technical-debt”)
– Linking results with input is problematic
Map to Drug Form and VA Class
• Map Medications to Semantic Clinical Drug
and Form (SCDF) or Semantic Branded Drug
and Form (SBDF)
– Example Clarity Medication: “ANTABUSE 250 MG
– Example SBDF: “Disulfiram Oral Tablet”
• Map Medications to Veterans Administration
class (VA Class)
Resulting I2B2 Hierarchy
The Leftovers:
No SCDF, SBDF, or VA Class!
• Some medications didn’t map directly to SCDF,
SBDF, or VA Class
– Sometimes, it was because the drug mapped to an
– Example: “CEFAZOLIN INJ 1GM IVP” (medication id
210319, MedEx mapped to RxCui 2180 “CEFAZOLIN” an
The Leftovers:
Map via “ingredient” relationships
• Use “ingredient_of” and “constitutes”
• Use “isa” relationships to get SCDF/SBDF
• Help! Results in 21.7 Million results from 20,354
– A huge number of components, packs, and associated
• Reduce this by mapping to the SCDF/SBDFs we
already have mapped from direct links
– Is there a better way?
RxNav (Cefazolin)
Putting Relationships Together
i2b2 Ontology
• Use prior mappings (Medications to
SCDF/SBDF and Medications to VA Class) to
then map the SCDF/SBDF to VA class.
• Create table with parent/child relationships
– Use these relationships to build i2b2 compatible
Resulting I2B2 Hierarchy
Based on June 2012 data (Cimarron)
• “Round 1”:
– GCN + NDC Mapping
– 89.4% of medication observations covered
(100,395,527 total facts, 10,636,780 missing facts)
• “Round 2”:
– Added MedEx NLP
– linking missing medications to SCDF/SBDF via
"ingredient_of" relationship.
– 94.39% of medication observations (100,395,527 total
facts, 5,630,904 missing facts)
Next Steps
• Peer review of the code!
• Manual mapping of some top concepts
– Problem children thus far:
• Review in more detail code from Dustin Key
from Group Health (
– Basic approach is the same as per overview
• How to test/validate?
RxNorm documentation
KUMC Work Ticket
UMLS Reference Manual
Paper: “Enabling Hierarchical View of RxNorm with NDF-RT Drug Classes”
Code Walkthrough!

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