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Clarity Medication Mapping to NDF-RT Design and Current Status.

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Presentation on theme: "Clarity Medication Mapping to NDF-RT Design and Current Status."— Presentation transcript:

1 Clarity Medication Mapping to NDF-RT Design and Current Status

2 Outline Brief Tour of RxNorm Tables Used Design Current Status (Results) Next Steps Code Walkthrough Discussion

3 RxNorm Concept Names and Sources (rxnconso) (starting section 12.4) “Primary” table – consists of all RxNorm Concepts – Example: A medication and synonyms - there may be several rows for a single concept. – 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.)

4 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

5 RxNav: Relationships

6 VA Class Ontology

7 Map Clarity Medications to RxCUI: GCN/NDC 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)

8 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) – “GENERIC_NAME” 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

9 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 PO TAB” – Example SBDF: “Disulfiram Oral Tablet” Map Medications to Veterans Administration class (VA Class) Example: “[AD100] ALCOHOL DETERRENTS”

10 Resulting I2B2 Hierarchy

11 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 ingredient. – Example: “CEFAZOLIN INJ 1GM IVP” (medication id , MedEx mapped to RxCui 2180 “CEFAZOLIN” an “ingredient”)

12 The Leftovers: Map via “ingredient” relationships Use “ingredient_of” and “constitutes” relationships Use “isa” relationships to get SCDF/SBDF Help! Results in 21.7 Million results from 20,354 Medications! – A huge number of components, packs, and associated SCDFs/SBDFs Reduce this by mapping to the SCDF/SBDFs we already have mapped from direct links – Is there a better way?

13 RxNav (Cefazolin)

14 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 ontology

15 Resulting I2B2 Hierarchy

16 Results 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)

17 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?

18 References RxNorm documentation KUMC Work Ticket UMLS Reference Manual RxNav Paper: “Enabling Hierarchical View of RxNorm with NDF-RT Drug Classes” MedEx

19 Code Walkthrough! epic_med_mapping.sql

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