i2b2 webclient i2b2 glowing bear transmart · i2b2 webclient i2b2 glowing bear transmart ......
TRANSCRIPT
i2b2 webclient i2b2
Glowing Bear tranSMART
forked i2b2 webclient MedCo
Clinical Research SystemsFront Ends
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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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"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
KeycloakOpenID Connect API
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability Module
1
4
5
6
6
78
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability ModuleImplementation
➔
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability ModuleImplementation
➔
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability ModuleImplementation
➔
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability ModuleImplementation
➔
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability ModuleImplementation
➔
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability ModuleImplementation
➔
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
KeycloakOpenID Connect API
API call
JWKS retrieval
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability ModuleImplementation
➔
IRCTPIC-SURE API
MedCoNode 1
MedCoNode 2
...
MedCoNode n
i2b2 API
KeycloakOpenID Connect API
Interoperability Layer Clinical Research SystemsFront End
Glowing BearCrypto Module
Interoperability Module
1
2 34
5
6
6
6
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