1/15/2014: All Hands Meeting:

Tim Miller, PhD (CS) from Guergana’s group presented his work on extracting and representing temporal relations from narrative text. And he focused on the “CONTAINS” relation which is useful in multiple ways which he illustrated across several use cases.

i2b2 phenotyping challenges

Plenge, Bickel, Weber, Kohane, McGaw, Liao

Discussed the effortful process required to train a NLP filter for a given phenotype. We

Currently:

Step 1: Experts galore: (clinical, NLP, modeling/statistics, programmers)

Step 2: Build study-specific data mart

Step 3: Extract information

Step 4: Define "Gold Standards" from the extracted knowledge

Step 5: Build filter algorithm and apply to study at hand

Step 6: Not remember very well and loss of institutional memory regarding phenotypes

We reviewed several alternative, more fully automated models.

All Hands Meeting

More than 20 participants. First, Kohane went over the outline of what i2b2 (v2) is going to focus on. Then reviewed recent AUG meeting and introduced Robert Plenge and Stanley Shaw who described the new DBP's of which they are PI.

i2b2 in Japan

As our Summer winds down, the various i2b2 core development teams are returning to Boston. Meanwhile our colleagues in Japan have been busy implementing their version of i2b2. Kudos!

New members of the i2b2 team

Brian Wilson (bioinformatics and statistical genetics) and Guergana Savova (natural language processing) both from the Mayo Institute have just joined the i2b2 team. Welcome to both!

AMIA Translational Summit

Shawn, Zak, Susanne, Vivian, Mike, and Griffin attended the AMIA Translational Informatics Summit 2010 in SF. There were several i2b2 events including a) a packed three and half hour tutorial b) an overview of i2b2 applications c) an evening AUG meeting. Lots of interest, good questions and interesting developments.

Open Source

A very insightful response from Fred Trotter. He lays down the options in a very nuanced and clear fashion. Much appreciated.

Widening the Use of Electronic Health Records Data for Research

A symposium hosted by the National Center for Research Resources (NCRR). Louise Ramm, Deputy Director of NCRR provided framing challenges and welcome. Zak Kohane introduced use cases, sources of and reviewed the false dichotomy between health-record based research and clinical trials..

Gary Gibbons provided a perspective of disease in the African-American population as an exemplar of a complex orphan disease in the sense that like rare orphan diseases, it is understudied and insufficiently treated. He also pointed out how in many parts of the country underserved minorities are located away from the academic health centers that have made the most inroads in the use of electronic health records.. Therefore, institutions such as Morehouse School of Medicine have their work cut out for them (and not a lot of resources) to integrate data from a large number of only lightly affiliated practices. That same challenge presents an opportunity to be even more impactful in an orphan disease of epidemic quality. Professor Gibbons also urged a broadening of the captured context beyond what is conventionally captured in a standard (brief) healthcare visit. Environmental variables that are highly penetrant, much more so than many genomic markers are poorly captures. He concluded by reviewing the current compelling information about pharmacogenomic differences, and population genetic risks and also the wide holes in our knowledge of these as they pertain to various groups within the USA.

Andrew Auerbach from UCSF addressed comparative effectiness research and its translation into "Health system innovation research" Described how much can be done with charge data, and how additional codified data types (e.g. medications) can further improve the quality of that data. Closed with a discussion of how the various stakeholders in using EHR data for research (.e.g NIH, Payors, health systems leaders, physicians, and patients) might be well aligned or not. Put us on notice that IRB's are unfamiliar about distributed query systems and/or grids and this is becoming at last an obstacle for many CER studies. Summarized several use cases such as optimal length of treatment of pneumonia? Can a patient-focused discharge checklist reduce risk for readmission?

Robert Plenge described his use of i2b2 and electronic health records for genotypic research and discovery of endophenotypes.
John Brownstein reviewed non-traditional public health research using institutional data and non-traditional, non-institutional healthcare data extraction and analysis.

i2b2 Academics Users Group—Natcher Building, NIH

Zak Kohane summarized some of the new i2b2-based projects that recently were announced including a South Carolina consortium (a GO grant funds the automated consent component), a pediatric rheumatology research network including 60 sites (NIH GO grant), Shawn Murphy is working with an imaging consortium to better integrate images into i2b2 instances (CTSA administrative supplement) using XNAT/BIRN infrastructure, and B.U. and U. Mass received a GO grant to study health disparities using i2b2 as infrastructure. Lynn Bry received a 2 year R01 under ARRA for the Crimson-i2b2 integration project.

Susanne Churchill welcomed the group and noted that there is a consortium of European i2b2 users/implementors/refiners that are putting together a proposal for joint work across the European Union (for EU funding). She noted that the AUG now numbers over 100 and represents 30 healthcare/academic institutions including 5 internationally.

Shawn Murphy summarized several new developments including

• Release Candidate 1.4 to support the Enterprise including: analysis views, improved role-based access and auditing, replacement of Gridsphere with webservices and AJAX client, Microsoft Active Directory integration, obfuscation of results for privacy purposes.
• In the future, the distributions of i2b2 be via configurable VM's so that the functionality can be attached to local databases without requiring a full install. The full source code compile and install will still be available.
• Eclipse plug-in "store" where developers can contribute their own plug ins and where users can download the plugins they want.
• More support for derived data (e.g. to systematically return NLP concepts derived from the clinical notes

Lynn Bry described the Crimson system and how i2b2 discarded sample have far higher utilization rates than other samples (e.g. for biorepositories). She also described the Sample Ontology and how she is borrowing from WHO and SNOMED to standardization. The system includes an ontology manager to allow local ontology management and update samples. Also described are the IRB permissions data from RC 1.4. Will work towards multisite studies within the two year implementation time frame. Lynn described the Enterprise Master Specimen Index that tracks samples and patient relationships in various levels of identity (consented identified, de-identified, and anonymous samples).

Dan Housman and Peter Emerson from Recombinant were invited into the AUG for the discussion segment about sample management (because of the AUG's wish to keep companies at arm length) to discuss their own efforts in sample management. They made it clear that all their developments they are involved in will be contributed back to the i2b2 community as fully open source code.

Andy McMurry summarized the status of the distributed querying system called SHRINE that is now implemented at several Harvard-affiliated hospitals and several West Coast academic health centers (e.g. UCSF and UW) that is now fully IRB approved (at Harvard) for queries returning aggregate numbers (across demographics, laboratory results, medications and diagnoses). Andy also made a very clear several technical hurdles that were overcome including the ontology matching process (on the fly). Finally, he announced the availability of SHRINE code in a fully open source codebase.

i2b2 CICTR presented by Nick Anderson. They have been able to query muiti-institutional "anonymized PHI data". Application is in diabetes and cardiovascular disease. Described technical, governance, ontology and evaluation process that CICTR is driving. Nick described the heterogeneous systems that CICTR has to query across. Nick distinguished the need for high level institutional support which is a sine qua non requirement for success and the need for a broad range of paid technical personnel.

Keith Marsolo from Cincinnati's Children's reported on their Epic roll out and how that relates to their i2b2. Described their quality assurance efforts. Notes the challenge of the firehose and makes the acute observation that most investigators just want a spreadsheet and anything more complicated than that tends to get ignored. Keith also emphasized their goal to allow streamlined adding of research data to the clinical data. He makes the important point that "age at FACT" is essential for pediatric applications to allow them to be easily accessed in the i2b2 workbench. Keith mentioned using i2b2 for research databases for Eosinophilic esophagitis, and IBD.

Phil Reeder from UT Houston talked about medications mapping. It is a challenge and they have chosen to map to RxNorm and then manually had to map into SNOMED CT (perhaps their database was out of date). Started from an All Scripts database and had a semi-automated process. Notes that every year there are at least a 1000 new drugs (i.e. different packaging, pill sizes etc). Brought up the thorny (and annoying IMHO) of the proprietary mappings to standard vocabularies.

Ralph Zottola and Edward Westrick described the effort at U. Mass (data sourced from Meditech system, REDcap EDC, biorepository, EMPI, Allscripts, and departmental systems) where they are up to 2,000,000 patients. Edward described the managed care network (1000 physicians) that plugs into U. Mass and how quality measures inform the discussions and bargaining with payors. Reviewed different measures including HEDIS, patient experience, was well as the increasingly important Relative Resource Utilization (Efficiency). Demonstrated how knowing what is going on in the healthcare institution allows for a sober and leveraged discussion with payors. The healthcare system approached the medical school and settled on i2b2 and they already have seen that they can accurately forecast their performance and to provide a feedback loop (with financial incentives) to healthcare providers. Ralph pointed out that the fact that clinical operations are using i2b2 is also causing an improvement in the quality of the data being delivered to the data marts.

Iain Sanderson and Jihad Obeid. Iain started by describing a very comprehensive Informatics Initiatives in South Carolina. They have a unified IRB with a goal of clinical trials across the state. There is both a scientific and a funding motivation in this. There are three informatics initiatives have dovetailed (CTSA biomedical informatics, HSSC IT business plan, and a GO grant on consent). This has resulted in the South Carolina Integrated Platform for Research (SCIPR) that uses i2b2 for the clinical research data warehouse. In the process they are adopting a wide range of open source solutions including Sun Microsystems' JavaCaps. Iain reports that the data sharing agreements between the 6 centers across HSSC are under way and likely to result in an MoU in short order. Iain also described the beginnings of the consent management/gathering system, the permissions ontology and documenting the different consent processes at the institutional members of the HSSC. Finally, Iain discussed how personal patient health portals may be used to provide the patient-facing part of the network.

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.

Nice overview of the i2b2 data model and ontologies

by a third party.

Rheumatoid Arthritis Detection Strategies—All Hands Meeting

Elizabeth Karlsson discussed multiple epidemiological approaches to identifying patients at risk for rheumatoid arthritis.

Webcast on i2b2 by Griffin Weber

Nicely done and very informative.

http://www.recomdata.com/www/resources/i2b2_Webinar.wmv

Revving the German i2b2 Engine

We recently received news from our informatics colleagues in the German medical research organization (TMF) regarding impressive strides they have made in adopting and adapting the i2b2 codebase. Much of this work has been done under the supervision of Hans-Ulrich Prokosch with his amazingly productive colleague Sebastian Mate. I paraphrase here a recent missive:

First, Sebastian simplified the installation process such that, based on his installation script, they can now set up a new i2b2-installation in less than half an hour. Further, he has already built up a comprehensive Erlangen specific ontologies (urology cancer data items: ICD-10-GM, ICD-O, ICPM, TNM-Codes, Grading, Study Codes, Patient Scores, patient age groups, gender etc).

They have also imported more than 800.000 patient records from their hospital data warehouse, mainly with demographic data, and ICD-codes, procedure codes, gender and age and a second smaller subset with patients from their newly established urology cancer documentation application which is part of their hospital information system.

In their evaluation project for TMF, Sebastian has analyzed the TMF pseudonymisation module and established it as a first preprocessing step before loading data records into the i2b2 hive. All their data within i2b2 are now fully pseudonymized.

View Larger Map

Labs, labs everywhere

Turns out that there are 11,000 distinct laboratory types at Partners Healthcare System alone. The ontological mapping challenge is non-trivial but fortunately can be made scaleable by having every source system provide a mapping into standard such as LOINC.

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.

i2b2 Academics Users Group Meeting

Because of fears of the swine flu, most of the Boston i2b2 team decided not to fly to Seattle. Instead NIck Anderson graciously allowed us to hold the meeting by web meeting technology.

Nice write up of the meeting by Connected-Science

Mapping i2b2 Implementations

This is a nice variant of the Healthmap application. Please let me know if you think your center was erroneously included or omitted.

SHRINE discussions

Andy McMurry, Griffin Weber, and Shawn Murphy led a discussion regarding how the business rules of sharing across distinct HIPAA entities affect the details of the registration/authentication process for distributed queries.

All Hands Meeting

Roy Perlis disclosed that his MDD/Drug efficacy R01 docking with i2b2 had been funded.

Relevance Network software by Vlad has been adopted by several sites.

Discussed the various ARRA opportunities.