Mapping FHIR to OMOP CDM - FHIR DevDays · Sohrab Hejazi, Azadeh Nassirian Technical University of...
Transcript of Mapping FHIR to OMOP CDM - FHIR DevDays · Sohrab Hejazi, Azadeh Nassirian Technical University of...
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November 20-22, Amsterdam | @HL7 @FirelyTeam | #fhirdevdays | www.devdays.com
Mapping FHIR to OMOP CDM
SeyedSohrab Hejazi
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Using FHIR as an Intermediate Platform
FHIR Clinical
Datawarehouse
transMART
OMOP
cBioPortal
XNAT
i2b2
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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.
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OMOP Major Components and Tables
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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)
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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
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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
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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.
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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)
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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)
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www.devdays.com
Sohrab Hejazi, Azadeh Nassirian
Technical University of Dresden
Institute of Medical Informatics and Biometry