For the "why" of this Hackathon please see the Rationale and Detailed Objectives page.
Date and Time
December 1st - December 5th
Starting with breakfast everyday at 8AM
Countway Library at Harvard Medical School
10 Shattuck Street
Boston, MA 02115
Conference Room 319A
- Michael McDuffie (BCH / CBMI HMS , Boston)
- Michael Mendis (i2b2 Partners, Boston)
- Lori Phillips (i2b2 Partners, Boston)
- Gustavo Lopes (The Hyve / IMI / TraIT, The Netherlands)
- Florian Guitton (Imperial College, London, UK)
- Terry Weymouth (University of Michigan, Ann Arbor)
Design and code an approach to reintegrate i2b2's cohort discovery and ontology management code.
- Personal introductions
- Intro to tranSMART Architecture for Michael / Lori (McDuffie)
- Intro/history to i2b2 (Mendis)
- Presentation on current API direction (Gustavo)
- Discuss best way to run i2b2 alongside tranSMART
- API Discussion
- Set obtainable goals for rest of hackathon
- API Discussion
- Hacking with morning and evening status updates
- Explicit plan for followup work
- Discuss future work in both projects
- Working i2b2 1.7 Demo (Public demo may be enough)
- Working i2b2 1.7 instance with minimal number of cells running against a local tranSMART DB, with the schema from i2b2 1.7 copied over to replace any overlapping schema held by tranSMART.
- Working development version of 1.2 on a new branch on our laptops
- Environment to test our integrated code
- JIRA / Wiki (Probably use tranSMART Foundation's)
- Develop complex test data sets to exercise i2b2 use cases, like dates and modifiers
Main points of discussion
- Identify compulsory i2b2 components that we need to stand up alongside tranSMART in order to achieve or goals (i.e. which cells)
- (some background; basic i2b2 documentation)
- Outline software interface between i2b2 and tranSMART
- User interface to take advantage of these components for ontology representation
- User interface to take advantage of these components for cohort generation
- Temporal queries (i2b2 1.7 functionality)
- Any other functionality we identify in our discussions
- i2b2 plugins and tranSMART compatibility
- Discuss future of both projects and how we can keep the code from getting too far away from each other
A. Create communication layer between tranSMART and i2b2 using XML messaging.
B. Create UI components for generating Ontology tree and conducting cohort discovery. This should be modular/abstract enough to allow for the easy addition of interface components that correspond to new i2b2 services.
C. (Reach Goal) Start work on a new communication layer that will allow the streaming of data from CRC to external applications like tranSMART.
Minimum Success Criteria
A. Display ontology tree communicating with the the i2b2metadata services.
B. Create complex query using nodes from tree plus options for
- Logical operators (AND/OR boxes)
C. Use the patient sets created above for Summary Statistics and Advanced Workflows.