i2b2 implemented over smart-on-fhir - blogs...

Partners (Shawn Murphy)AP-HP (Christel Daniel)

i2b2 implemented over SMART-on-FHIR

Mike Mendis & Nicolas Paris

October 5, 2017

1/9

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

2/9

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


3/9

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 !


4/9

i2b2-FHIR Design


5/9

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


6/9

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)


7/9

i2b2-FHIR Demo


8/9

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


9/9

Conclusion

i2b2-FHIR opens new area:I Data FederationI Data Variety

→ Work in progress to release in future i2b2 version


Thank you

Core i2b2 www.i2b2.org/softwareFHIR API https://github.com/parisni/i2b2-fhir-search

FHIR i2b2 https://github.com/mikemendis/i2b2-fhir-search

i2b2 implemented over smart-on-fhir - blogs...

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