Transcript 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.

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
NIH Data Sharing Policy
NIH believes that data sharing is essential for expedited
translation of research results into knowledge, products,
and procedures to improve human health.
The policy reaffirmed the principle that data should be
made as widely and freely available as possible while
safeguarding the privacy of research participants, and
protecting confidential and proprietary data.
NIH Bioinformatics Initiatives

NIH GWAS - Genome Wide Association Study

caBIG
Thethese
Cancer
Biomedical
Informatics
Grid
The
goal- of
initiatives
is to
build infrastructure
and
networks
to
facilitate
data
sharing,
integration,
 BIRN - The Biomedical Informatics Research Network
and interoperability.
 CTSA - Clinical and Translational Science Awards

NIH Blueprint Neuroimaging Informatics
Softwares are open source and free to download.

NCBC - National Centers for Biomedical Computing
NIH 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
- 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.
- dbGaP
- NBIA, Rembrandt
 Impact
and benefit of sharing tools
–
2 case studies
NIH Blueprint – NITRC

NITRC - Neuroimaging Informatics Tools and
Resources Clearinghouse: A web site and a
community

NITRC helps research laboratories to share their NIHfunded 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 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 - 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.
Cohort
IRB#
IRB#
CRIMSON
Cohort Table
i2b2 CRC
Rule Set
Samples Located
Study
CMV
IRB#
Workbench
Criteria Engine
Anon1
Anon2
Anon3
[..]
Picklist
(Accession#s)
Query
Holding Tank:
7-30 day rolling window of
all clinical accessions
Sample
Shipments
Workflow
Engine/LIMS
Accessioning
Honest Broker
MRN
(If consented)
Subject ID
(Study-specific)
Crimson Patient ID Crimson Sample ID
(Not MRN#)
(Not Acc#)
Cost and Throughput Comparison


Before Crimson
Study desires 10,000
samples for epidemiologic
analyses

samples
Throughput of 5-10
samples/month
– 120 years to collect 10K with
current process.
Avg cost for collection: $89/sample
– Costs for collection of 10K
Avg. cost/sample for the
study: $1,200
– $12,000,000 to collect 10K


After
Forwarded cohorts via i2b2
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 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 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 outcomes

Develop demonstration projects from China and
U.S. toward scientific data sharing

Share data standards

Share experience with electronic medical records