Specimen Resource Locator II

1
Specimen Resource Locator II Specimen Reporting

• TBPT face to face meeting 10 Oct 2007
• Ian Fore, D.Phil., NCI CBIIT/OBBR

2
Rationale for a biospecimen resource locator

• Sharing of biospecimens a criterion used for
  evaluation of biospecimen resources
• Provision of a facility to support this
  recommendation
• FAQ for the OBBR
• What specimens do you have?
• Biospecimen resource Biorepository
• but also resources like CHTN which collect and
  distribute biospecimens but do not store them

3
Existing Specimen Resource Locator

• http//pluto3.nci.nih.gov/tissue/default.cfm
• Demo

4
Some statistics

• 43 Specimen Resources
• Live since Aug 2002

5
Office of Rare Diseases

• Overall very similar goals
• Some differences
• ORD voluntary
• Some obligation on NCI banks

6
Overall Plan

• Define objectives
• List use cases
• Review existing locator
• Understand overlap with Office of Rare Diseases

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Draft Objectives

• Provide a system to enable researchers to locate
  biospecimens of interest accompanied by the data
  necessary to conduct research
• Increase the usage in appropriate research of
  biospecimens donated by cancer patients
• Build on and learn from the experience gained
  with (specific issues to be identified) with the
  NCI Specimen Resource Locator
• The system should be caBIG compatible in order to
  integrate with the informatics infrastructure
  being established by NCI to support
  interoperability of cancer informatics

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Draft use cases

• Locate biospecimens
• Request existing biospecimens
• Request collection of biospecimens
• Register a biorepository
• Submit specimen data
• Update specimen data

9
Review of existing NCI Specimen Resource Locator

• Materials gathered
• Database description
• Access to database obtained

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Revised focus

• Additional information to include
• Specimen quality
• Currently limited to preservation type
• caBIG compatibility

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Relevant caBIG initiatives

• Define technical standard for interfacing with
  biorepository systems
• Demonstrate querying via caGrid
• Work with repositories to instantiate this
  interface
• Prostate SPOREs
• Developing querying across eleven institutions
• caTissue Suite 1.0
• Federated querying of caTissue instances

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How is the grid relevant to biorepositories?

• Aim is to enable interoperation of Tissue Banks
• Proposal
• Establish a simple standard for a web service to
  allow communication of summary level information
• Numbers and types of specimens
• Directory of banks offering this information
• Ability to query multiple banks
• Mapping to terminology

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Integrating data from repositories
Report aggregator
API
API
API
UML model
UML model
UML model
Service implementation
Service implementation
Service implementation
Local system
caTissue
Filemaker Pro
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How is the grid relevant to biorepositories?

• Aim is to enable interoperation of Tissue Banks
• Proposal
• Establish a simple standard for a web service to
  allow communication of summary level information
• Numbers and types of specimens
• Directory of banks offering this information
• Ability to query multiple banks
• Mapping to terminology
• Keep it simple

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This is complex!
16
This is simple
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Examples

• Prototype caBIG service developed
• Implementations against
• Direct database representation of the data model
• MySQL
• Filemaker Pro
• caTissue Core
• Extract, Transform and Load
• Planned
• ACSR database - Microsoft Access
• Colon specimen data - Kim Jessup - FileMaker Pro
• Implementations are lightweight
• Write object relational mapping
• An additional way to share data from caTissue

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Next steps

• Complete project initiation by Nov 16
• Stakeholders
• Scope
• Use cases
• Plan for technical implementation
• Resources
• Determine risks and plan accordingly
• Project plan
• Implement to follow plan

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Team

• NCI Team
• Ian Fore - co-chair - CBIIT
• Irina Lubensky co-chair - CDP
• Kim Jessup - CDP
• Paula Kim - Advocate
• Shannon Lemrow - DCCPS
• Sheila Taube - CDP
• Biospecimen resource community
• ?

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caBIG TBPT involvement

• Roles/stakeholders represented in caBIG
• Biorepository managers
• Requesters of biospecimens
• IT staff
• Volunteers