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November 20-22, Amsterdam | @HL7 @FirelyTeam | #fhirdevdays | www.devdays.com
Mapping FHIR to OMOP CDM
SeyedSohrab Hejazi
Using FHIR as an Intermediate Platform
FHIR Clinical
Datawarehouse
transMART
OMOP
cBioPortal
XNAT
i2b2
OMOP Common Data Model
• The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) allows for the systematic analysis of disparate observational databases.
• Bringing data into a common format (data model) as well as a common terminologies (vocabulary).
• Once a database has been converted to the OMOP CDM, evidence can be generated using standardized analytics tools.
OMOP Major Components and Tables
Semantic Mapping
FHIR Resource OMOP Table
Patient Person
location
Condition condition_occurrence
fact_relationship
Procedure procedure_occurrence
Encounter visit_occurrence
Observation Measurement (laboratory data)
observation (other data)
Syntactic Mapping
• Converter Tool
• Stu3 & R4 to OMOP version 5.2.2
• Java 12
• HAPI FHIR Library version 3.8.0
• ConceptMap Resource to map different value sets
Mapping Patient Ressource to Person Table
FHIR OMOP
birthDate month_of_birth, year_of_birth,
day_of_birth, birth_datetime
address mapped to location table and
corresponding location_id stored in
location_id.
generated ID from FHIR Server person_source_value
gender.display gender_source_value
gender.display
gender_concept_id Male 8507
Female 8532
Other 8521
Unknown 8551
Difference and Limitation for Mapping
• Mandatory fields in OMOP vs. optional items in FHIR.
• Mandatory element in OMOP but there is no relevant value in FHIR.
• Different code for the unit
• "U/L": in FHIR enzyme unit per liter but the appropriate element in OMOP is [U]/L as unit per liter.
• Using an extension to insert data in FHIR
• for example secondary diagnoses in Condition resource.
• Using fact_relationship table in OMOP to show the relationship between primary and secondary diagnoses.
Open Issues
• Constraints due to German source data
• The reason of admission can not be documented in FHIR (only with extension is possible).
• The cause of admission (e.g. emergency) just partially can be documented in FHIR.
• The reason of dismission just partially can be documented in FHIR.
• German level of diagnosis surely (only with extension is possible).
• Data loss
• Name does not exist in OMOP
• Image data like DICOM, PDF etc. cannot be inserted (but meta data)
• Status in observation (there is no measurement_status in OPOP)
Deployment
• MIRACUM consortium in the Medical Informatics Initiative
• The goal is to take advantage of digitalization in medicine, to link data and generate medical knowledge, and to develop and apply innovative IT solutions for a better, data-based healthcare delivery system.
• Sharing of data accross ten university hospitals for medical research
• FHIR to OMOP essential component in the Data Integration Center (DIC)
www.devdays.com
Sohrab Hejazi, Azadeh Nassirian
Technical University of Dresden
Institute of Medical Informatics and Biometry
