caTissue 2.0

Architectural and Semantic Challenges

June 10th, 2011

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Agenda

• Background• Team, laundry

• Challenges• Dynamic Extensions• Technology Stack• caGrid Query• Federated Instance-level Authorization

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Background: Team

• NCI/SAIC Leadership• Ian Fore: NCI Program Manager• Brent Lander: SAIC COTR

• Project Leadership by Washington University• PIs: Rakesh Nagarajan, Mark Watson• PM: George Bijoy

• Development by Persistent Systems• Led by Srikanth Adiga and Harsha Gokhale

• Development by SemanticBits• Led by Patrick McConnell and Denis Krylov

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Background: The Laundry List

• caGrid user integration• GridGrouper integration• caGrid writeable API• Biospecimen ordering• Standard operating procedures• MAGE-TAB export• CTRP/COPPA integration• Subject management/registration integration (ala C3PR and

services)• Technology stack upgrade and BDAification• GSID service (separate effort) and integration• CBM (Common Biorepository Model) migration

George, please reviewand edit.

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Dynamic Extensions

• Require the capture of different data elements or different value domains• Has to happen FAST - not in 3 months or 3 weeks - in 3 days• We are here to facilitate research, not hinder it• Research generates new data NOW (>=80% of PIs)• Researchers want to reuse other researchers DEs NOW

• Use cases• Add a class, or four; add an attribute, or ten

• How we do it• Extend model in particular areas: Participant, Specimen

Collection Group, Specimen• Save the new extension as XMI• Regenerate data model, API via caCORE

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Technology Stack

CBIIT Tech Stack

JBoss 5.1.xJava 1.6

caGrid 1.3.xcaCORE (missing)

caGrid 1.3 Tech Stackhttp://cagrid.org/display/knowledgebase/caGrid+Software+Compatibility+Table

JBoss 4.0.5GAJava 1.5

caCORE 4.0/.1.1/.2/.3

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caGrid Query

• Temporal Query• Find patients younger than three years at the time they were

registered to the collection protocol• Find out the age of the participants as of today• Find all the specimens that are to be collected today

• Generate caGrid query service for DEs• Create via click of the button in caTissue• Requires enhancements to Introduce?

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Federated Instance-level Authorization

• Many, many caBIG applications leverage instance-level security in a common way• Protocol/Study/Collection Protocol• Experiment• Organization• Organization + Study (Subject)

• This is true across CTMS, TBPT, and LS• GridGrouper is too generic• We need a common way to reference these common

instances across organizations