1. Common Biorepository Model (CBM) : Specimen Searches Across Real Specimen Collection Data
caBIG® Tissue Banks &
Pathology Tools Workspace
TBPT F2F
Houston, Texas
November 3, 2010

2. Agenda Progress on CBM Challenge with CBM 1.0 Beta
CBM Use at the University of Colorado Cancer Center
CBM Use at the Medical University of South Carolina Hollings Cancer Center
CBM Use at Washington University St. Louis and caB2B Querying
Model, Next Steps and Discussion

3. Common Biorepository Model (CBM): Update
Anna Fernandez, PhD
TBPT Workspace
November 3, 2010

4. Why CBM? (1/2)
Clinical research often uses only locally obtained specimens due to limited ability to search for specimens outside an institution.
The ability to aggregate similar specimens from various sites will expand the validation of pathology research findings and thus, more quickly impact patient care.
caGrid allows for data from caBIG-compatible systems to be connected across the sites
Has a CQL querying language that allows for interrogation of model metadata to navigate and find information about the data on the “grid node”
caTissue Suite allows individual specimen level queries on caGrid
How can we get, at minimum, all biorepository systems to share SUMMARY LEVEL information about their specimens, if many use different vendor systems and/or institute-developed solutions?

5. Why CBM? (2/2)
A CBM serves as a simple information model for interfacing with systems by sharing key summary-level specimen information, enabling a single search across multiple biorepositories/banks.
Biorepository software vendors and NCI stakeholders (tissue bank personnel, researchers) convened to develop a CBM undergoing final development stage.
The goal is to reduce the time and effort required by researchers to locate biorepositories with needed specimens.
Researchers will be able to search via the OBBR’s Specimen Resource Locator to identify specimen resources to fit their research needs.

6. CBM and Specimen Resource Locator

7. Sharing Data on the Grid – caTissue Suite vs. CBM

8. Common Biorepository Model Specimen Management Services
Compatibility Path
Compatibility
Functionality
Bronze
caGrid Services
Common Biorepository Model
Specimen Management Services

9. ITERATIVE Development PROCESS with CBM Community
CBM Challenge (Fall 2010)
ITERATIVE Development PROCESS with CBM Community

10. NIH SRL Participants and CBM Challenge Participants

11. Path to CBM 1.0 (to 2009)
June - Aug
December
November
Dec - Jan
Internal NCI Revisions
2009
Feb-May
Updated version
CBM 0.93,
Review with Stakeholders; engage more vendors
CBM Vendor Participants Accept CBM Challenge (14)
SRL Stakeholders define initial vocabulary terms desired, initial Silver Level Review Feedback incorporated into CBM 0.95
Sept-Nov
Vendor workshop developed CBM 0.9
2008
CBM 0.95 Service files generated (Grid-KC, with simple data set from caTissue ETL);
CBM vendors ready to begin looking at service docs

12. Path to CBM 1.0 (2010) Jan-April June July-Oct Nov 2010
CBM Participants Mapping to REAL Collections:
UCCC, using .NET service connected to home-grown system
Hollings Cancer Center –AIM TissueMetrix
WashU-caTissue
Jan-April
June
CBM 1.0Beta -Oct
All terms in caDSR,
Mapping to terms with SNOMED, ICD-9/10 synonyms,
Corrections to model based on June feedback
July-Oct
Nov
CBM Vendors Stand up Grid with Test Data (IMS, 5AM, caTissue-WashU (early ETL), AIM)
FreezerWorks testing code
Daedalus, Healthcare IT, Westat, GenoLogics , Ocimum Biosolutions, LabVantage looking at code, ready when vendors ready
UCCC interested in testing
CBM 1.0Beta-May – Service Files Generated for early testers; new term curation started in NCI Thesaurus
2010
2011: CBM 1.0 ECCF-SAIF Compliant, caBIG Compatible Service

13. CBM Experience - University of Colorado Cancer Center
Michael Ames

14. CBM Experience – Hollings Cancer Center -AIM
Bill Morgenweck,
Kevin Hooper

15. Where we are today, Tuesday Nov 3
UCCC has a node on the Training Grid – generated from a CBM service based on October 2010 CBM1.0Beta
ETL mapping done from MS-SQL to MS-SQL
Used CBM vocabulary
Using CBM1.0Beta-October EA model
Hollings Cancer Center – with Artificial Intelligence Tissue Metrix
ETL mapping from Oracle SQL to MySQL
Extensively used the CBM vocabulary (CBM1.0Beta October vocab)
Close to showing on the Grid – can query the Database
Using CBM1.0Beta-May service files
Washington University
Early caTissue Suite-CBM ETL scripts from April 2010 used (not complete mapping)
Using CBM1.0Beta-May service files and Database

16. CBM Experience – Washington University - caTissue
Rakesh Nagarajan

17. Query Common Biorepository Model (CBM): iGoogle App
Mukesh Sharma
Rakesh Nagarajan

18. Training Grid Portal has CBM Nodes: http://portal. training. cagrid

19. iGoogle Gadget – Querying the CBM Grid Node
iGoogle Application
Queries and used GridPortlet
Using “My Gadgets”
Aggregating Data from the Grid:
UCCC
Washington University

20. How to install the Specimen Counts Google Gadget (connecting to CBM test nodes on the caGrid)
Works best on Chrome and Firefox viewers
Go To
Click “add stuff”
Search for “My gadgets” and click to add this to your iGoogle Page
Install “My gadgets”, go back to your iGoogle page
Once installed, enter this address in the “add gadget” bar:
The Specimen Counts should appear on your iGoogle homepage.

21. Specimen Counts

22. Hollings Cancer Center/AIM http://tmxstorefront.hcc.musc.edu/
HCC
Normal Breast Tissue
HCC 52

23. Hollings Cancer Center : Number of cases by specimen
Waiting for Grid Connection – will be up soon (next few days?)
Specimens that will be exposed are reported here:

24. BIRT (Ex. June 2009) – open-source reporting tool
Tie into XML output of Grid Queries
Customize reporting
Could customize what is displayed

25. BIRT (in the works)

26. Lessons Learned as we continue…
Working with Vendors and multiple systems helps identify issues and iteratively improve
Mapping issues – are we all mapping to the same things
Testing with real data – when challenges are identified
Grid node testing – various environments/difficulties encountered helps documentation and potential muddy areas!
Extract-Transform-Load process – must be meticulous and all terms agreed on
Mapping Decisions are key in the process - Map to a code or map to an NCI preferred name?
All must subscribe to same version – or work out how to map against different versions
Through Real-testing is when we find this challenges – THANKS to the institutes testing with us in this Challenge

27. Fall 2010 Additions to help ETL
Tables added with the lists of values from the model
Can be directly accessed by ETL processes
Enforces integrity via foreign keys
Mapping table
Addresses mappings to
ICD9CM
ICD10
SNOMEDCT

28. What we have today Artifact Links Description
CBM with Value Domains.EAP UML Model :
EA Model (with Permissible values,
and
XMI version
CBM. SQL
MySQL Database
Database to be used for ETL; Now has the NCI Concept Code and NCI-Concept name
HTML view of EA model:
Able to navigate through EA model (w/o having EA on machine) – can walk through UML model
/cbm service files and Grid Deployment instructions
90% complete. Needs some testing of the /cbm
Files generated from running model through caCORE-SDK and Introduce (latest version)

29. Anatomic Source

30. Specimen Type

31. Diagnosis

32. Preservation Type

33. Mappings

34. Where we are headed:
Specimen Resource Locator
From 2002 to December 2009, ~14,000 queries looking at static-based SRL
Q – SRL Developers will begin
CBM 1.0 documentation/service/test package will be developed (caBIG® Compliant ECCF/SAIF service)
SRL 2.0 Work will begin
Electronic web form = A web-based questionnaire based on CBM
Common Biorepository Model = through CBM challenge adoptees
SRL will provide names of biorepositories’ contacts that have specimens researchers are looking for.
Additional information will be obtained from direct interaction with contact
Material Transfer Agreements (collaboration, purchase, etc) – will then be discussed between researcher and biorepository
High level plan (as presented today): (5/14) Presented CBM v1.0 at ISBER conference Achieve silver-compliance for CBM Complete the database audit and clean-up Start website/database rebuilt Finalize architecture, project approval, and secure CBIIT resources
Database audit and clean-up next steps: Export and review existing data; use excel or access template Harmonize with CBM data model (the drop-down choices) Add in new biorepository resources; call to action for new lists Pre-requisite = an Excel or Access template to capture data in a CBM-like format Database next steps (detail): Export existing records from CBM Identify other possible new resources for including Using template each group adds in their data Individual templates combined into a single list and shared for review and approval

35. CBM 1.0Beta Next Steps in Testing
Work with our testing vendors to check if we can query them
Through querying, determine if the values are appropriate/expected
Helping with how Specimen Resource Locator will also be expecting data in
Test if .NET-based service is matching with the caCORE-SDK/Introduce version, in terms of querying paths
caTissue Suite ETL – continue testing with Washington University, to expose all the data types and thus, aggregate with the specimen information from other test sites
Incorporate feedback, more detailed instructions, guidance for ETL
CBM 1.0Beta – transfer to Specimen Resource Locator Development team
ECCF/SAIF documentation
Comply with the standards set up for new caBIG® services (ISO data types, etc.)
Position to be first Specimen Management Service Set component

36. How to Participate
View CBM Wiki (Latest information):
Review Model and vocabulary – how will it match with your biorepository data?
Test the service/mapping when final service files are released
ETL process can begin today
Contact TBPT
If you are using a CBM Participating Vendor system – let them know you are interested in testing/using CBM
Identify key projects in your institute that could have/will benefit from finding more specimens for their work – or finding uses for the specimens they currently hold

37. Acknowledgements Hollings Cancer Center
Artificial Intelligence in Medicine (AIM)
University of Colorado Cancer Center
University of Virginia (.NET service)
TBPT – CBM Team
Ian Fore, DPhil, NCI-CBIIT
Anna Fernandez, PhD, Booz Allen Hamilton
Libby Prince, Sapient Government Solutions
Andrew Breychak, Sapient Government Solutions
Ben Fombonne, Kelly Government
Beth DiGiulian, Booz Allen Hamilton
caGrid KC, special thanks to Joe George, Bill Stephens, & Justin Permar!
Tissue Banking Knowledge Center
Vendor Community
Biorepository community!

38. CBM Challenge (Fall 2010)

39. Extra Slides

40. Key CBM Sites:
CBM Site (Latest Information):
CBM 1.0Beta Grid Test Package (May 2010) – and links will be found on CBM website
CBM Latest Model (Interactive Enterprise Architect version, IE browser):
Find CBM 1.0Beta Test Nodes!
The service is deployed to the  Training Grid. Here is the service URL: Then search for a service using “Name” field - with name “CBM”:
CBM Site for Vendor/Community Comments:
Find “Common Biorepository Model” – Discussions Forum

41. caBIG iGoogle Gadget
Queries & displays NCI Common Biorepository Specimen Count Data
Developed by Booz Allen Hamilton

42. caBIG iGoogle Gadget Flowchart
PHP Page
caGRID.org
REST form
XML output 1 4 2
First, the caBIG iGoogle Gadget is added to an iGoogle Homepage. A Google Gadget is stored in an XML file which contains gadget metadata as well as HTML, CSS and Javascript.
When the iGoogle homepage loads, the Gadget makes an AJAX request to retrieve data from a PHP page hosted on an external server.
The PHP page makes several queries using the RESTful interface to cagrid.org, located at This form returns links to XML files, which contain data retrieved from multiple servers. 3

43. caBIG iGoogle Gadget Flowchart
PHP Page
caGRID.org
REST form
XML output 1 4 3
Using the links obtained in the previous step, these XML files are retrieved and summed within the PHP page. The PHP page then outputs this summary data in XML format.
The caBIG iGoogle Gadget’s AJAX request is completed as the XML data output by the PHP page is retrieved. A Javascript callback function parses the summary XML and outputs it to the screen.
Selecting a different option within the caBIG iGoogle Gadget does not make another AJAX request, but instead locally re-parses the already retrieved XML summary data. 2

44. Key TBPT/NCI Sites:
The Specimen Resource Locator (website)
caBIG® Tissue Banks & Pathology Tools Workspace:
OBBR – Office of Biorepositories and Biospecimen Research:
OBBR & NCI Best Practices

45. BIRT (in the works) – open-source reporting tool
Tie into XML output of Grid Queries
Customize reporting
Could customize what is displayed

46. BIRT (in the works)

47. caBIG® Tissue Banks & Pathology Tools Workspace
CBM Next Steps
caBIG® Tissue Banks &
Pathology Tools Workspace
caBIG® TBPT
National Cancer Institute

48. CBM Challenge (DEC 2009 Update)
June Challenge announced to use CBM to expose data on the caGrid – Vendor & Cancer Centers (biorepositories) involvement
Fall 2009 – A CBM with caGrid artifacts ready for testing
Winter 2010 –First set of vendors have incorporated a CBM into their systems and can expose test data on the caGrid
Fall 2010 – First set of cancer centers (biorepositories) have deployed CBM at their site and are exposing real data on the caGrid
End of 2010/2011 – Researchers demonstrate real-world cases of successful research with biospecimens located via CBM
2009
2010
Vendor Commitment to identify resources/timeline for CBM testing in their product
NCI-CBIIT releases initial
Documentation, SW artifacts and
tools for vendors to start testing
Vendors/caTissue/NCI-CBIIT pass test suite on test-data.
Biorepositories commitment to expose their own biorepository data using CBM-ready SW
Biorepositories with Vendors/caTissue successfully expose real data on the caGrid
NCI SRL 2.0 Ready to query for specimens across caGrid via CBM
Cancer Centers identify projects that will use CBM in specimen search
Researchers report out on research impact using CBM
Identify future publications using specimens located through CBM
ITERATIVE Development PROCESS with CBM Community

49. Where We’ve Been
In December, we had released a .95 version of the model. We had identified several vendors of specimen management systems who were willing to look into implementing the model. The model had been taken through a wide variety of NCI internal reviews
1.2 What does CBM 1.0Beta entail?
This is the latest iteration of the CBM model to provide sites for testing and provide feedback on. In this version:
The vocabularies that describe the specimen types, diagnoses types, etc. have been incorporated into the NCI Thesaurus (required for caBIG® semantic interoperability) and are fixed for at least 1 year (until May 2011 or later).
caBIG compatibility for this version is still under evaluation, as NCI is re-defining compatibility terms under Services-Aware Interoperability Framework (SAIF) and sub-framework—the Enterprise Conformance and Compliance Framework (ECCF).
This is the version NCI would like institutes (vendors and biorepostories) to start testing and provide feedback on:
Establish grid nodes from COTS and custom systems
CBM 1.0Beta EA model can be found at: with Value Domains.EAP
1.3 Which CBM version should I use?
The CBM 1.0Beta version has the vocabulary lists fixed for the near future – at a minimum for August 2011.
CBM 0.95 (released for community feedback in December 2009) had some errors in the model, and NCI did not have a final vocabulary list. The purpose for CBM 0.95 was to allow the CBM community to look at the model and try to instantiate a test grid service, as the same steps would have to be taken with subsequent releases.
CBM 1.0Beta has some additional bug fixes and allows for advanced queries.
CBM 1.0Beta will be used to develop a “TEST SUITE” for validation (expected no later than Dec 2010).
We advise you to use this version and this vocabulary list to start ETL process against your vendor or home-developed management system. We do not expect significant changes as NCI goes through caBIG® certification.