1. PSBIN caTissue Suite and caB2B 04/09/2012 Baris Suzek Andy Helsley Suhas Khot Dave Mulvihill

2. Acknowledgements UCLA – Andy, Buddy Michigan - Radhika OHSU - Fred MSKCC - Ravi Baylor – Stephen, Heidi UWash – Xenia, Paul Northwestern - Dong UCSF – Sudeep Dana Farber - Paul

3. Deployment Package Base deployment package (current version includes Oracle Data Patch) For Linux/Unix: http://pir.georgetown.edu/~suzek/PSBINcaGridServiceDeployment.zip http://pir.georgetown.edu/~suzek/PSBINcaGridServiceDeployment_Instr uctions.docx For Windows: http://pir.georgetown.edu/~suzek/PSBINcaGridServiceDeployment_wind ows.zip http://pir.georgetown.edu/~suzek/PSBINcaGridServiceDeployment_Instr uctions_windows.docx

4. Data Loader Package A OHSU/UCLA development to import/export data – Community project caRuby Fixed as of 3/15/2012 – Updated the annotation service API clients – Fixed tiny.java for GleasonScore.XScore and GeneralHealthAnnotation.ageAtDiagnosis Another iteration of fixes 4/4/2012 – Focusing on data problems; how to handle empty values? E.g. Gleason Score

5. Patches Oracle Date Patch for caGrid Services http://pir.georgetown.edu/~suzek/oracle_patch.zip Empty Objects Patch for caTissue Suite Annotation API http://pir.georgetown.edu/~suzek/PatchingcaTissueSuiteAnnotationAPIs.docx Gleason Score Patch for caTissue Suite Pathology Annotation for SCG API and its caGrid Service http://pir.georgetown.edu/~suzek/PatchingPathologyAnnotationSCG.docx cats_pcbin_participant API war fix – Customizing UMichigan war at respective sites – Following instructions from TBPT KC

6. Current Status – Deployments UCLAMichiga n OHSUMSKCCBaylorUWashNorthwesternUCSFDana Farber Base Pkg Done ? Planned Oracle Date Done N/ADoneN/A Done? Empty Object Done In progress Done ? Planned Gleas on Score Done In progress Done ? Planned cats_p cbin Done N/ADone Planned?DonePlanned Query from UCLA caB2B Done Pending firewall DonePending firewall Done?Pending firewall Planned Data load Planne d DonePlannedIn progress PlannedDonePlanned

7. Current Status - Queries #0: Give me all participants #1: Which frozen tissue samples are available for black or African American men who were diagnosed after 2005 and had a pre-treatment PSA > 10? – PSA (LabAnnotation.result) is not numeric so instead of numeric comparison option to use equal with PSA #2: Which samples are available for men diagnosed over age 60 with clinical tumor stage T2a or T2b and biopsy gleason total > 6? – Tertiary Score is used for Gleason total; the data loader loads the total to this data element #3: Which samples are available for men with biospy gleason 3+4 or 4+3 (primary+secondary) who had neoadjuvant hormone therapy?

8. Current Status - Queries #4: Which samples are available for men who had surgery before 2007, were over 65 years old at the time of surgery, and had prostatectomy gleason > 3 (in either primary or secondary gleason)? #5: Which samples are available for men who had a prostatectomy with Gleason total <6, surgical margins uninvolved by invasive carcinoma, absent extra prostatic extension, and absent lymphatic invasion? #6: Which samples are available for men who had adjuvant hormone therapy or adjuvant radiation therapy?

9. Current Status - Queries

10. Next Steps caB2B – Enhancements/features – Demo Data loads – UCLA, Baylor, MSKCC, OHSU, UWash, UCSF, Dana Farber caGrid deployments – Northwestern, Dana Farber