i2b2 webclient i2b2 Glowing Bear tranSMART · i2b2 webclient i2b2 Glowing Bear tranSMART ... Application Programming Interface RI: Resource Interface EXT: EXTension IRCT-EXT Data

i2b2 webclient i2b2

Glowing Bear tranSMART

forked i2b2 webclient MedCo

Clinical Research SystemsFront Ends

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i2b2

Glowing Bear tranSMART

MedCo

Clinical Research SystemsFront End

IRCTPIC-SURE API

HTTP REST API Client Side Server Side

Client

Data Source 2

Data Source 2 API

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PIC-SURE: Patient-centered Information Commons: Standardized Unification of Research ElementsIRCT: Inter-Resource Communication ToolHMS-DBMI: Harvard Medical School - Department of Biomedical Informatics[1]: Alex AT Bui, John Darrell Van Horn, NIH BD2K Centers Consortium, et al. “Envisioning the future of big data biomedicine”. In: Journal of biomedical informatics 69 (2017), pp. 115–117.

Data Source 1Data Source 1 API

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[1]: Shawn N Murphy et al. “Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)”. In: Journal of the American Medical Informatics Association 17.2 (2010), pp. 124–130.[2]: Elisabeth Scheufele et al. “tranSMART: an open source knowledge management and high content data analytics platform”. In: AMIA Summits on Translational Science Proceedings 2014 (2014), p. 96.

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[1]: J. L. Raisaro et al. “MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data”. In: IEEE/ACM Transactions on Computational Biology and Bioinformatics (2018), pp. 1–1. issn: 1545-5963. doi: 10.1109/TCBB.2018.2854776.

IRCT(PIC-SURE) i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API

KeycloakOpenID Connect API

API call

JWKS retrieval

Interoperability Layer Clinical Research SystemsFront End

Glowing BearCrypto Module

Interoperability Module

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[1]: Hail, an open-source, scalable framework for exploring and analyzing genomic data: https://github.com/hail-is/hail

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[1]: Nat Sakimura et al. “OpenID Connect Core 1.0 incorporating errata set 1”. In: The OpenID Foundation, specification (2014).

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[1]: Glowing Bear, a modern cohort selector for i2b2 tranSMART: https://glowingbear.app/

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"where": [ { "field": { "pui": "/resource/study/Age/", "dataType": "INTEGER" }, "predicate": "CONSTRAIN_VALUE", "fields": { "OPERATOR": "GT", "CONSTRAINT": "20" }} ]

where part: constraints on data

field: path and type of query term queried(obtained from tree)

predicate used on query term

fields: additional input to predicate}}

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IRCT-CLPIC-SURE API

HTTP REST API Client Side Server Side

Client IRCT-API IRCT-RI Data Source

IRCT: Inter-Resource Communication ToolCL: Communication LayerAPI: Application Programming InterfaceRI: Resource InterfaceEXT: EXTension

IRCT-EXT

Data Source API

xStep

HTTP REST API

Client Side

Server Side

API call

JWKS retrieval

IRCTPIC-SURE API

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API





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4

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6

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i2b2

tranSMART 17.1

tranSMART API v24 6

6

6

2 3

1. User Login2. GB Initialization3. Query Construction4. Query Submission5. Query Translation6. Query Processing7. Result Storage8. Result Display

Back End SystemGlowing Bear

LegendJWT: JSON Web Token

HTTP Request Client SideServer Side

Keycloak

(1) Get JWT

(2) HTTP Request, with JWT

(3) Get public key

Cached Request

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{ "alg": "RS256", "typ": "JWT", "kid": "eTFrdyrNxXLNHI7p0Ywybc7z1SBHTEcqWcMTybtdvQY"}

● …{ "exp": 1523454086, "iat": 1523453186, "iss": "http://localhost:8081/auth/realms/master", "aud": "glowing-bear", "nonce": "N0.28573339803406971523453198656", "resource_access": { "account": { "roles": [ "role1", "role2" ] } }, "preferred_username": "test", "email": "[email protected]"}

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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval



Interoperability ModuleImplementation

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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval




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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval


Glowing BearInteroperability

ModuleImplementation

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Crypto Module

IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval




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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval




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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval




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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval




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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval




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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval




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IRCT i2b2

tranSMART 17.1

PIC-SURE API

HTTP REST API

tranSMART API v2

Client Side

Server Side

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API

i2b2 API


API call

JWKS retrieval




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IRCTPIC-SURE API

MedCoNode 1

MedCoNode 2

...

MedCoNode n

i2b2 API





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5

6

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78

xStep

HTTP REST API

Client Side

Server Side

API call

JWKS retrieval

1. User Login2. GB Initialization3. Query Construction4. Query Submission5. Query Translation6. Query Processing7. Result Storage8. Result Display

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i2b2 webclient i2b2 Glowing Bear tranSMART · i2b2 webclient i2b2 Glowing Bear tranSMART ... Application Programming Interface RI: Resource Interface EXT: EXTension IRCT-EXT Data

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