1 / 19

Clarity Medication Mapping to NDF-RT

Clarity Medication Mapping to NDF-RT. Design and Current Status. Outline. Brief Tour of RxNorm Tables Used Design Current Status (Results) Next Steps Code Walkthrough Discussion. RxNorm Concept Names and Sources ( rxnconso ).

wing-carson
Download Presentation

Clarity Medication Mapping to NDF-RT

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

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) http://www.nlm.nih.gov/research/umls/rxnorm/docs/2012/rxnorm_doco_full_2012-3.html (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: Relationshipshttp://rxnav.nlm.nih.gov

  6. VA Class Ontology http://bioportal.bioontology.org/ontologies/47101/?p=terms&conceptid=N0000029067

  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 MedExNLPhttp://knowledgemap.mc.vanderbilt.edu/research/content/medex-tool-finding-medication-information • 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 210319, 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 Togetheri2b2 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: http://informatics.kumc.edu/work/attachment/ticket/1246/unmapped_meds_20120823.csv • Review in more detail code from Dustin Key from Group Health (ghc.org) • Basic approach is the same as per overview • How to test/validate?

  18. References RxNormdocumentation http://www.nlm.nih.gov/research/umls/rxnorm/docs/2012/rxnorm_doco_full_2012-3.html KUMC Work Ticket http://informatics.kumc.edu/work/ticket/1246 UMLS Reference Manual http://www.ncbi.nlm.nih.gov/books/NBK9676/ RxNav http://rxnav.nlm.nih.gov/ BioOntology.org http://bioportal.bioontology.org Paper: “Enabling Hierarchical View of RxNorm with NDF-RT Drug Classes” http://www.ncbi.nlm.nih.gov/pubmed/21347044 MedEx http://knowledgemap.mc.vanderbilt.edu/research/content/medex-tool-finding-medication-information

  19. Code Walkthrough! epic_med_mapping.sql

More Related