Epigenetics

Shaw, Kohane, Kasif, Plenge, Churchill, Liao, Murphy, Savova

Extensive discussions about which epigenetics marks are best captured from clinical discards and under what hypotheses.

Auto-immune CVD

Autoimmune CVD DBP

Murphy, Karlsson. Gainer, Shaw, Savova, Szolovits, Liao, Kohane, Churchill, Cai,

Discussed the NLP annotation pipeline (used by the "gold standard" annotators).

Discussed predictors of RA (by NLP and codified data) in patients who previously did not qualify as having RA.

CVD & DM DBP

Shaw, Savova, Liao, Churchill, Murphy, Gainer, Sordo, Kohane

Discussed how to learn lessons from other NLP CVD efforts that Guergana has been involved in (e.g. the eMERGE applications of her cTAKES framework). Discussed the addition of echocardiogram data.

Diabetes and Cardiovascular Disease

Gainer, Murphy, Shaw, Liao, Kohane, Churchill

Extensive discussion of which case cohort definition we will adopt for cardiovascular disease. Projected that discussion into the eventual endgame for molecular physiological characterization.

Specifics around EKG and echocardiogram reports reviewed.

Kickoff meeting of DBP #1

Ashwin (IBD) Ananthakrishnan, Philip L. De Jager (MS), Beth Karlson, Helena Canhão, Kat, Sordo, Guergana, Stan, Peter Szolovits, Robert Plenge, Raoul Guzman, Vivian Gainer, Xia Zongqi (Neuro-rheumatology), LJ Wei, Peter Szolovits, Tianxi Cai

The PI's described how they propose to build on the experience of the RA DBP to go into further depth into the phenotypes (around RA) and drug effects/efficacy and see how far we can go with EHR-derived phenotypes. Further, we will be studying the shared and differing pathotypes across a larger range of autoimmune diseases, namely including inflammatory bowel disease and multiple sclerosis (for which we have expert representation in this DBP). We also reviewed the imperative to identify subcohorts (based on combinations of clinical and genomic stratification) that have distinguishing therapeutic efficacy and/or adverse events.

New DBP: Diabetes and CVD

Present: Stan Shaw, Vivian Gainer, Margarita Sordo. Kat, Susanne Churchill, Ozlem, Zak, Guergana

The new DBP led by Stan Shaw addresses the epigenetics (DNA methylation, histone acetylation, histone methylation assayed using full genome-scale resequencing) of heart disease in the context of diabetes mellitus.

Kat reviewed the overall approach that we take in DBP's in defining cohorts through billing code,

Ozlem gave an update on the new de-identification pipeline.

We reviewed which fellow we might find to do some of the heavy lifting with Stan.

Technology updates

Kohane, Murphy, Weber, Churchill, Wilson. Mendis

Reviewed plugin architecture and convergence between web and Java client.

Reviewed "normals" project.

Planning for hands on i2b2 tutorial for AMIA NOW

Mendis, Wilson, Savova, Weber, Kohane, Churchill,

Discussed the content for a hands on tutorial for the upcoming AMIA NOW.

What's next

Discussed what might be the priority areas for i2b2 in Core 2 for the competitive re competition.

The RFA has not yet be announced so the discussion was, of necessity, wide-ranging.

i2b2 AUG prep

Shawn, Diane, Zak, Susanne, Griffin

Discussed provisioning new DBP's

Discussed the GO grants that other sites have obtained using i2b2 infrastructure.

Short term planning

Zak, Shawn, Griffin, Susanne

Committed to the details of AUG meeting at the CTSA

Reviewed additional hires required for ancillary i2b2

Discussed storage needs.

Review of Core 1 needs from Core 2

Murphy et al.

Reviewed data marts required for Core 1 activities

• Normals
• NLP
• Predictive medicine
• Relevance networks
• Inflammation as an underlying process across diseases (the systems approach)

Working on Web Client for PM Cell

Present: Shawn, Griffin, Susanne, Diane, Zak, Mike

Discussed a bare-bones web client for PM management.

Resource Allocation

Discussed allocation of analyst time in light of present and possible funding streams

Core 2

Discussed how to allocated new resources required for i2b2 collaborating grants (R01s and U01s).

Reviewing the Roadmap

Shawn Murphy led a discussion of the roadmap over the next year of i2b2.

2b2 Roadmap for 2009-2010

Release 1.4 = “Enterprise Ready i2b2”
Release Candidate targeted for September 2009

This release allows the entire set of patients from the enterprise to be exposed to the research community of the hospital while preserving patient privacy, providing the way for basic queries to funnel down to a set of patients interesting to the investigator. The chosen set of patients is matched to controls from the enterprise database and a project-specific mini-database is created. Major software enhancements of release 1.4 compared to release 1.3 include a hardening of the project management cell with a new, full featured client for managing enterprise users, a plug-in architecture for the data repository cell that allows complex server-side workflows, and streamlined project mini-database creation with processes to build sets of matched control patients for a given set of patients of interest.

Release 1.5 = “NLP Workflow Enabled i2b2”
Release candidate targeted for February 2010

This release allows the text notes that are contained in a project-specific mini-database, such as clinic notes of a patient or radiology reports, to be processed in a high throughput manner with natural language processing (NLP). Any NLP tool can fit into this workflow, because the i2b2 workbench serves as a means to flow notes to the workstation of the NLP expert, and once the expert has transformed the text into coded data, re-import the coded data back into the i2b2 hive. The i2b2 workbench will also provide a tool for basic natural language processing to be performed using a Support Vector Machine for people who have no experience with NLP. Major software enhancements of release 1.5 compared to release 1.4 include a hardening of the data import process, a coupling of ontology management with data import processing, and a tool for non-expert NLP users.

Release 2.0 = “Open repository i2b2”
Release targeted for July 2010

This version represents the beginning of an open repository management of i2b2 software. An open Concurrent Versions System (CVS) will allow the i2b2 community to submit changes to the software that will be considered for all new releases.

Ongoing SHRINE discussions

Shared Health Research Information Network is the i2b2 framework to allow federated queries across multiple healthcare systems that is now being adopted by several national efforts, even while we continue to define it.

Storage

Richter, Murphy, Keogh, Kohane

Reviewed the very significant infrastructural requirements for i2b2 instances and the multiple data marts that we are deploying. Brent has two interesting solutions at HP and Sun that we are exploring.He will report back in one month with the results.

Authentication

Murphy, McMurry, Kohane, Weber, McGow

Discussed some of the challenges of different namespaces for authentication across different i2b2 instances. All the more challenging with the proliferation of SHRINE implementations. Discussed different national solutions such as Shibboleth.