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

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

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

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?

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.

CBM and Specimen Resource Locator

Sharing Data on the Grid – caTissue Suite vs. CBM

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

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

NIH SRL Participants and CBM Challenge Participants

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

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

CBM Experience - University of Colorado Cancer Center Michael Ames

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

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

CBM Experience – Washington University - caTissue Rakesh Nagarajan

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

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

iGoogle Gadget – Querying the CBM Grid Node iGoogle Application Queries and used GridPortlet Using “My Gadgets” http://www.neatdev.com/cabig/gadget.xml Aggregating Data from the Grid: UCCC Washington University

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 http://www.google.com/ig 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: http://www.neatdev.com/cabig/gadget.xml The Specimen Counts should appear on your iGoogle homepage.

Specimen Counts

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

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: http://tmxstorefront.hcc.musc.edu/

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

BIRT (in the works)

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

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

What we have today Artifact Links Description CBM with Value Domains.EAP UML Model : https://ncisvn.nci.nih.gov/svn/common_biorepository_model/trunk/caCORE_SDK/models/CBM%20with%20Value%20Domains.EAP https://ncisvn.nci.nih.gov/svn/common_biorepository_model/trunk/caCORE_SDK/models/CBM%20with%20Value%20Domains.xmi EA Model (with Permissible values, and XMI version CBM. SQL MySQL Database https://ncisvn.nci.nih.gov/WebSVN/filedetails.php?repname=common_biorepository_model&path=%2Ftrunk%2Fdatabase%2FCBM.sql Database to be used for ETL; Now has the NCI Concept Code and NCI-Concept name HTML view of EA model: https://ncisvn.nci.nih.gov/svn/common_biorepository_model/trunk/html_documentation/index.htm 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)

Anatomic Source

Specimen Type

Diagnosis

Preservation Type

Mappings

Where we are headed: Specimen Resource Locator http://biospecimens.cancer.gov/locator From 2002 to December 2009, ~14,000 queries looking at static-based SRL Q1 2011 – 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

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 21090 data types, etc.) Position to be first Specimen Management Service Set component

How to Participate View CBM Wiki (Latest information): https://wiki.nci.nih.gov/display/TBPT/Common+Biorepository+Model+%28CBM%29 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

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!

CBM Challenge (Fall 2010)

Extra Slides

Key CBM Sites: CBM Site (Latest Information): https://cabig.nci.nih.gov/workspaces/TBPT/CBM/ CBM 1.0Beta Grid Test Package (May 2010) – email and links will be found on CBM website CBM Latest Model (Interactive Enterprise Architect version, IE browser): https://ncisvn.nci.nih.gov/svn/common_biorepository_model/trunk/html_documentation/index.htm Find CBM 1.0Beta Test Nodes! The service is deployed to the  Training Grid. Here is the service URL: http://portal.training.cagrid.org/web/guest/discovery Then search for a service using “Name” field - with name “CBM”: CBM Site for Vendor/Community Comments: https://cabig-kc.nci.nih.gov/Biospecimen/forums/ Find “Common Biorepository Model” – Discussions Forum

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

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 http://portal-demo.training.cagrid.org/cagridportlets/xml/form. This form returns links to XML files, which contain data retrieved from multiple servers. 3

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

Key TBPT/NCI Sites: The Specimen Resource Locator (website) http://biospecimens.cancer.gov/locator caBIG® Tissue Banks & Pathology Tools Workspace: https://cabig.nci.nih.gov/workspaces/TBPT OBBR – Office of Biorepositories and Biospecimen Research: http://biospecimens.cancer.gov OBBR & NCI Best Practices http://biospecimens.cancer.gov/practices/

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

BIRT (in the works)

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

CBM Challenge (DEC 2009 Update) June 2009 - 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

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: https://ncisvn.nci.nih.gov/svn/common_biorepository_model/trunk/caCORE_SDK/models/CBM 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.