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Facilitate Scientific Data Sharing by Sharing Informatics Tools and Standards. Second Meeting of the Board on Research Data and Information September 24, 2009. Belinda Seto and James Luo National Institute of Biomedical Imaging and Bioengineering National Institutes of Health. - PowerPoint PPT Presentation
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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