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

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

Deployment Package Base deployment package (current version includes Oracle Data Patch) For Linux/Unix: uctions.docx For Windows: ows.zip uctions_windows.docx

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

Patches Oracle Date Patch for caGrid Services Empty Objects Patch for caTissue Suite Annotation API Gleason Score Patch for caTissue Suite Pathology Annotation for SCG API and its caGrid Service cats_pcbin_participant API war fix – Customizing UMichigan war at respective sites – Following instructions from TBPT KC

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

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?

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?

Current Status - Queries

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