i2b2 implemented over smart-on-fhir - blogs...
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Partners (Shawn Murphy)AP-HP (Christel Daniel)
i2b2 implemented over SMART-on-FHIR
Mike Mendis & Nicolas Paris
October 5, 2017
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Cohort Discovery
I i2b2 is a key leader with 200 implementations worldwideI Tools federate multiple i2b2 instances (Shrine, Insite, TrinetX)I Analytic tools extend i2b2 (transmart) to handle genomicI Alltogether provides a 360◦view of patients and hospitals
→ Large scale cohort discovery needs i2b2 democratisation
AP–HP/Partners | i2b2 implemented over SMART-on-FHIR
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Improving i2b2
Panoramic View of Hospitals:
Data Federation ChallengeI ETL processes need a dedicated engineer teamI Different practices & terminologies used
Panoramic View of Patients:
Data Variety ChallengeI RDBMs based i2b2 star schema cannot handle every typesI Specialized technology emmerges faster than i2b2 adopt them
AP–HP/Partners | i2b2 implemented over SMART-on-FHIR
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Fast Healthcare Interoperability Resources
Data Variety ChallengeI FHIR is an Agile and RESTful Approach to Healthcare
Information ExchangeI FHIR covers most patients & hospitals concepts (clinical,
imaging, genomic, providers. . . )
Data Federation ChallengeI FHIR specifies both a Search & a Terminology Mapping APII EHR vendors massively adopt FHIR
→ Let’s make i2b2 part of the 50 SMART-on-FHIR apps !
AP–HP/Partners | i2b2 implemented over SMART-on-FHIR
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Implementation
Change made to CRC cellI New pm_cell_data entry to point to URL of FHIRI By using the project_path can configure to use different FHIR
API for different projectsI Easy to change without restarting i2b2I Limited to one FHIR API per project
Change made to PM cellI New class written that extends Panel ItemsI Any ontology item that begins with
FHIR is sent to the new classI The Item Code, constraint value and date contraints are sent to
the FHIR API
AP–HP/Partners | i2b2 implemented over SMART-on-FHIR
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Benchmarks
0
20000
40000
60000
8K 100K 200K 400K
Patient Set Size
Tim
e S
pent
(m
s)
Labels
FHIR Parsing
FHIR Generation
Database
5B physiological table
I FHIR generation stepbottleneck
I under the minuteI linear performances
→ Bridging the gap (i2b2 /specialized tech)
AP–HP/Partners | i2b2 implemented over SMART-on-FHIR
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Roadmap
Work done:I Ontology ModelI Querying FHIR APII Terminology MappingI Mixed star schema & FHIR API & No-SQL DBs
On the way:I Oauth2 securisationI Multiple FHIR endpointI Performance optimisationsI Release as a SMART-on-FHIR app
AP–HP/Partners | i2b2 implemented over SMART-on-FHIR
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Conclusion
i2b2-FHIR opens new area:I Data FederationI Data Variety
→ Work in progress to release in future i2b2 version
AP–HP/Partners | i2b2 implemented over SMART-on-FHIR