Presentation on theme: "Clarity Medication Mapping to NDF-RT"— Presentation transcript:
1Clarity Medication Mapping to NDF-RT Design and Current Status
2Outline Brief Tour of RxNorm Tables Used Design Current Status (Results)Next StepsCode WalkthroughDiscussion
3RxNorm 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.)
4RxNorm 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
5RxNav: Relationships http://rxnav.nlm.nih.gov A couple of references/examples.
6VA Class Ontology http://bioportal. bioontology. org/ontologies/47101/
7Map 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
8The 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
9Map 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”
11The 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”)
12The 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?
14Putting 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
16Results 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)
17Next 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?
18References 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