Pre-competitive data sharing between pharma and with academia

As part of NIH's Public-Private Partnership Program, a meeting was held in Washington, DC (4/28/2011) that brought together many from industry (particularly the pharmaceutical companies) and academia around the idea of pre-competitive data sharing for opportunistic acceleration of discovery pipelines while remaining respectful of privacy and property. i2b2 serves as the foundational platform proposed for this effort, in its implementation within TransMart. It will remain to be seen whether the governance and competitive concerns can be managed successfully in this initiative triggered by Eric Perakslis.

Modeling Disease Activity in RA

Karlson et al.,

Discussed the current "standard of care" for disease activity (DAS28) for which there is a straightforward calculation. Can we estimate a highly correlated measure using NLP on the clinical record? This will require extracting temporal relations (e.g. activity AFTER anti-TNF therapy). With regard to the disease activity/state itself, we will start by identifying four states: Remission, Low, Moderate, HIgh (also Indeterminate if the note is unclear or too short) which will first have to be identified by our "gold standard" reviewers and annotations (using Knowtator).

Several machine learning approaches to predicting the DAS28 using NLP were reviewed.

Cerner adopts the i2b2 model

This is an interesting piece of news seen on a mailing list. We were surprised to see this announcement regarding Cerner using i2b2 for its clients. As we do not have any relationship with Cerner in this regard, the precise nature of the implementation and its license are not clear. Nonetheless, for those of us working on secondary use of healthcare data using i2b2, this is another signal that our community is growing.

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Cerner i2b2 Node - Enabling Research Illumination

A client session of this Illumination is scheduled for Wednesday, April 20, 2011 12:00 PM CT.

Description of Session

The Cerner i2b2 node is a Cerner-hosted solution that improves the performance of i2b2 and facilitates secure data collaborations across multiple institutions. I2b2 (Informatics for Integrating Biology and the Bedside) is a National Center for Biomedical Computing. The informatics initiative is funded as a cooperative agreement with the National Institutes of Health (NIH). Using the Cerner i2b2 node, clients can perform cohort discovery queries on a de-identified dataset, save the query results, access patient identifiers for the saved query with IRB approval, and partner with other participating organizations to share data for cohort discovery queries. The service uses proprietary tools to map client data and improve i2b2 performance. The Cerner-hosted model reduces client investment in IT infrastructure, support, and maintenance

Benefits:

• Data mapping and security capabilities improve performance of i2b2

• Cerner-hosted model facilitates inter-institutional research

• Eliminates costs related to data mapping, security, system maintenance and IT infrastructure

Registration

To register for the session, click the link below. You will need a Cerner.com user name and password.

https://applications.cerner.com/members/illuminations/IllumDetails.aspx?illumid=4158

NLP

Guergana Savova led a discussion on the annotation tool, with a focus on functional status (e.g. SF 36). Pete Szolovits provided ongoing commentary on the applicability to specific UMLS relations to these annotations.

Diabetes and CVD

Stan shaw led a discussion of inflammatory markers in the diabetes population.

i2b2 EAC

March 24th, External Advisory Committee came to Boston for a visit.

The EAC is constituted of:

Daniel Masys (chair), Vanderbilt University

Elmer Bernstam, University of Texas at Houston

Lisa Cannon-Albright, University of Utah

Peter Tarczy-Hornoch, University of Washington, Seattle

George Hripczak, Columbia University

NIH representative: Valerie Florance, NLM project officer

Very productive meeting with useful directional advice from the EAC.

i2b2 All Hands Meeting

Eric Perakslis PhD presented his work on i2b2 in the J&J context and beyond with tranSMART. Interestingly, this i2b2 instance is hosted on the Amazon EC2 cloud. He had the temerity to run a live demo which worked flawlessly. Good Karma! Also the involvement of tranSMART with the Innovative Medicines Initiative in Europe with significant uptake by pharmaceutical industry (i.e. GSK/ECLIPSE, AstraZeneca, Pfizer, Novartis) was intriguing and encouraging.

His slide show is available here.

Other i2b2 business reviewed including the very success i2b2/NCBO tutorial last week at AMIA in San Francisco and the other SHRINE implementations that are occurring nationally.