Facilitate Scientific Data Sharing Facilitate Scientific Data Sharing by Sharing by Sharing

Informatics Tools and StandardsInformatics Tools and Standards

Belinda Seto and James Luo

National Institute of Biomedical Imaging and Bioengineering

National Institutes of Health

Second Meeting of the Board on Research Data and InformationSeptember 24, 2009

NIH Data Sharing PolicyNIH Data Sharing Policy

NIH believes that data sharing is essential for expedited NIH believes that data sharing is essential for expedited translation of research results into knowledge, products, translation of research results into knowledge, products,

and procedures to improve human health.and procedures to improve human health.

NIH believes that data sharing is essential for expedited NIH believes that data sharing is essential for expedited translation of research results into knowledge, products, translation of research results into knowledge, products,

and procedures to improve human health.and procedures to improve human health.The policy reaffirmed the principle that data should be The policy reaffirmed the principle that data should be made as widely and freely available as possible while made as widely and freely available as possible while safeguarding the privacy of research participants, and safeguarding the privacy of research participants, and

protecting confidential and proprietary data. protecting confidential and proprietary data.

The policy reaffirmed the principle that data should be The policy reaffirmed the principle that data should be made as widely and freely available as possible while made as widely and freely available as possible while safeguarding the privacy of research participants, and safeguarding the privacy of research participants, and

protecting confidential and proprietary data. protecting confidential and proprietary data.

NIH Bioinformatics InitiativesNIH Bioinformatics Initiatives

NIH GWAS - Genome Wide Association Study

caBIG - The Cancer Biomedical Informatics Grid

BIRN - The Biomedical Informatics Research Network

CTSA - Clinical and Translational Science Awards

NIH Blueprint Neuroimaging Informatics

NCBC - National Centers for Biomedical Computing

The goal of these initiatives is to build infrastructure The goal of these initiatives is to build infrastructure and networks to facilitate data sharing, integration, and networks to facilitate data sharing, integration, and interoperability.and interoperability.

The goal of these initiatives is to build infrastructure The goal of these initiatives is to build infrastructure and networks to facilitate data sharing, integration, and networks to facilitate data sharing, integration, and interoperability.and interoperability.

Softwares are open source and free to download.Softwares are open source and free to download.Softwares are open source and free to download.Softwares are open source and free to download.

NIH Bioinformatics InitiativesNIH Bioinformatics Initiatives

NIH GWAS - Genome Wide Association Study - dbGaP

caBIG - The Cancer Biomedical Informatics Grid - NBIA, Rembrandt

BIRN - The Biomedical Informatics Research Network

CTSA - Clinical and Translational Science Awards

NIH Blueprint Neuroimaging Informatics - NITRC

NCBC - National Centers for Biomedical Computing - i2b2

The above trans-NIH infrastructures, tools and standards were presented at 3rd US-China Roundtable on Scientific Data Cooperation.

Impact and benefit of sharing tools

– 2 case studies

NIH Blueprint – NITRCNIH Blueprint – NITRC NITRC - Neuroimaging Informatics Tools and

Resources Clearinghouse: A web site and a community

NITRC helps research laboratories to share their NIH-funded neuroimaging tools and resources.

– To provide the neuroimaging informatics tools and resources to the neuroimaging research community at large

– To provide opportunities for public comment regarding neuroimaging informatics tools and resources by the neuroimaging research community at large

NITRC identifies software, data sets and other resources developed under NIH grants useful to the greater community and encourages their developers to share them.

NITRC ResultsNITRC Results Within 1.5 years since its first release, NITRC has

– hosted 220 tools and resources

– more than 53% of the tools on NITRC are new tools that have not been previously shared online.

– built a community of 6,000 unique visitors per month

– 1,077+ registered users (11% non-English)

– with 42,000 downloads

With an average tool development grant of $350,000 it is estimated that if 6% of the tools on NITRC today are utilized by another research laboratory instead of that laboratory requesting new government funding, this project will have more than paid for itself.

NCBC - i2b2NCBC - i2b2

The i2b2 (Informatics for Integrating Biology and the Bedside) is designed to address is that of creating a comprehensive software and methodological framework to enable clinical researchers to accelerate the translation of genomic and “traditional” clinical findings into novel diagnostics, prognostics, and therapeutics.

Criteria Engine

Picklist(Accession#s)

Samples Located

Workflow Engine/LIMSHolding Tank:

7-30 day rolling window ofall clinical accessions

Cohort Table

Crimson Patient ID(Not MRN#)

Subject ID(Study-specific)

Crimson Sample ID(Not Acc#)

MRN(If consented)

i2b2 CRC

SampleShipments

Honest Broker

WorkbenchAnon1Anon2Anon3

[..]

Accessioning

CMV

Query

StudyRule SetIRB#

IRB#

CohortIRB# CRIMSON

Cost and Throughput ComparisonCost and Throughput Comparison

Before Crimson Study desires 10,000

samples for epidemiologic analyses

Avg. cost/sample for the study: $1,200– $12,000,000 to collect 10K

samples

Throughput of 5-10 samples/month– 120 years to collect 10K with

current process.

After Forwarded cohorts via i2b2

Avg cost for collection: $8-9/sample– Costs for collection of 10K

samples: $85,000

Avg throughput: – 4-600 samples/month (1

Crimson node)– 1000+ with 2 Crimson nodes

operational.– Collection of controls in <1 year– Experimental samples in 1.5 - 4

years.

Looking ForwardLooking Forward

Outcomes of 3rd US-China Roundtable meeting

– Dr. Huixiong John Zhang, University of Electronic Science and Technology of China (UESTC):

Interest in leveraging NIH bioinformatics infrastructure and initiatives, e.g. caBIG, BIRN, CTSA, NCBC (i2b2), etc. to facilitate data sharing

– Dr. Xuan Dong, First Hospital of Chiang Zhou City:

Identified two MRI imaging data sets and time series neuro-physiological data sets for consideration for sharing.

NBIA will be used as the tools to share the image data.

PhysioNet will be used as the tools to share the neuro-physiological data

Looking ForwardLooking Forward

Met with Drs. Yixue Li and Lei Liu, Shanghai Center for Bioinformation Technology and discussed potential collaborations on data and standards sharing:

– Clinical research informatics and sharing of standards (including HL7, IHE, DICOM, etc.)

– Medical imaging, data sharing and decision support.

– GWAS informatics and database, data analysis, data standards.

Driving toward tangible outcomesDriving toward tangible outcomes

Develop demonstration projects from China and U.S. toward scientific data sharing

Share data standards

Share experience with electronic medical records