Presentation on theme: "Clarity Medication Mapping to NDF-RT"— 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 StepsCode WalkthroughDiscussion
3 RxNorm Concept Names and Sources (rxnconso) (starting section 12.4)“Primary” table – consists of all RxNorm ConceptsExample: 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 IdentifierThe 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 typesRelated 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 http://rxnav.nlm.nih.gov A couple of references/examples.
6 VA Class Ontology http://bioportal. bioontology. org/ontologies/47101/
7 Map Clarity Medications to RxCUI: GCN/NDC Clarity Medication Listclarity.clarity_medicationGCN (Generic Code Sequence Number - First Databank Inc.)clarity.rx_med_gcnseqnorxnorm.rxnconso (code column when sab = NDDF, and tty != ‘IN’)NDC (National Drug Code)clarity.clarity_ndc_codesrxnorm.rxnsat (atv column where atn = NDC)atv = attribute valueatn = attribute namesab = source abbreviation
8 The Leftovers: Match with MedEx NLPFor 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”IssuesClosed 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”
11 The Leftovers: No SCDF, SBDF, or VA Class! Some medications didn’t map directly to SCDF, SBDF, or VA ClassSometimes, 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” relationshipsUse “isa” relationships to get SCDF/SBDFHelp! Results in 21.7 Million results from 20,354 Medications!A huge number of components, packs, and associated SCDFs/SBDFsReduce this by mapping to the SCDF/SBDFs we already have mapped from direct linksIs there a better way?
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 relationshipsUse these relationships to build i2b2 compatible ontology
16 Results Based on June 2012 data (Cimarron) “Round 1”:GCN + NDC Mapping89.4% of medication observations covered (100,395,527 total facts, 10,636,780 missing facts)“Round 2”:Added MedEx NLPlinking 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 conceptsProblem children thus far:Review in more detail code from Dustin Key from Group Health (ghc.org)Basic approach is the same as per overviewHow to test/validate?
18 References RxNorm documentation KUMC Work Ticket UMLS Reference Manual KUMC Work TicketUMLS Reference ManualRxNavBioOntology.orgPaper: “Enabling Hierarchical View of RxNorm with NDF-RT Drug Classes”MedEx