Pharmacogenomics Data Standardization using Clinical Element Models

Pharmacogenomics Ontology (PHONT) Network Resource Pharmacogenomics Research Network (PGRN) Diverse network of PGx research sites Goal: Understand how genetic variations affect an individual's response to medications Normalize data representations Disease phenotypes Drugs and drug classes

PGRN Data Dictionary Standardization 4483 PGRN Variables SHARPn CEMs: Patient, Noted Drug, Disease/Disorder, Lab Observation UMLS Semantic Types

Categories of Mapped Variables

Person Model Examples of Variables Person PatientExternalId (0-M) Medical Record Number data (II) SSN Study ID PersonName (1-M) First Name GivenName (0-1) Last Name data (ST) … Date of Birth Birthdate (0-1) Year of Birth data (TS) AdministrativeGender (0-1) Patient Gender data (CD) AdministrativeRace (0-1) Patient Race AdministrativeEthnicGroup (0-1) Self-Reported Ethnicity …

Drug Administration Model Examples of Variables NotedDrug Code Is the patient taking a diuretic? data (CD) Has the subject started any new medications? StartTimeUnconstrained data (TS/CD/ST) EstimatedInd Date of last antihypertensives data (CO) Medication start date TakenDoseLowerLimit Dose Have you taken digoxin in the past? data (PQ) RouteMethodDevice data (CD) Time on tamoxifen StatusChange Subject If potassium supplementation added, specify daily dose …

Example: Patient Took 300 mg Acetaminophen "300"

Categories of Unmapped Variables

Unmapped Variables Some variables are not currently represented by PHONT (SHARP) CEMs Computed research data (e.g., PK/PD) Genomic data Psychometric data Work with SDOs to address these gaps CIMI community on extant or new CEMs HL7 and CDISC for clinical genomics data W3C, NLM, & SNOMED PGx ontologies

Conclusions Demonstrated CEMs can be used to normalize PGRN data dictionaries Future Work Incorporate recently developed SHARP CEMs Collaborate with SHARP to fill gaps for PGx Establish best practices Complex data elements (e.g., semantic links) Project-specific/workflow data vs EMR

PHONT Personnel Scientific Nosologist IT Project Management Christopher G. Chute Robert R. Freimuth Jyotishman Pathak Qian Zhu Guoqian Jiang Nosologist Donna Ihrke IT Zonghui Lian Scott Bauer Deepak Sharma Project Management Mandy Ager Matthew Durski