Hi Michael, Excellent question! Unfortunately, I don't have a great answer for you. We chose to deviate from the CDM specification in order to get the queries to run. Our approach is included at the bottom of #381, comment 8<https://informatics.gpcnetwork.org/trac/Project/ticket/381#comment:8>. Let me know if you'd like more information on that.
On the Annotated Data Dictionary (ADD) submitted with the Data Characterization query output, the Technical Infrastructure tab specifically asked: "(4) All SAS file distribution queries will assume that fields are specified as noted in the CDM documentation. This is especially important for fields specified as SAS time or SAS date types. What technical approach have you taken to enable you to run SAS file distribution queries against your DataMart?" Similar to the Data Characterization work that UNMC completed in Phase 1 with PCORnet CDM v1, there will be a meeting to discuss the Empirical Data Characterization Report. (We expect that file this week!) I anticipate that we will discuss the time field question then. Prior to that meeting, James might be able to provide better guidance? Thanks, Laurel From: Michael Prittie [mailto:[email protected]] Sent: Tuesday, March 01, 2016 3:15 PM To: Verhagen, Laurel A; [email protected] Subject: Issue with time fields in PCORnet SAS Diagnosis Query results Hi Laurel, As you might know we're working on our i2b2 to PCORnet CDMv3 ETL here at KUMC (based on the SCHILS transform). While doing so, we ran into the same issues you listed in the ticket #381<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_381-23comment-3A8&d=BQMF-g&c=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs&r=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5&m=ykKr2fa7LSaAU_3vxkT80bMIUVSGRh1fV0OuD4zInr8&s=DiqxhnsNP4e3f-KPk1e_2-SUbr_Ijmo0uYNNamNlELc&e=>. Most were simple enough to correct, with the exception of the time field errors. The CDMv3 specification clearly states that time fields should be 5 character text fields (i.e. "HH:MM"), but the SAS code seems to expect numeric fields. Nathan and Dan suggested I reach out to you to see you handled this at Marshfield, and if you ever heard back from PCORI on this. Thanks! Michael Prittie Biomedical Informatics Software Engineer Division of Medical Informatics University of Kansas Medical Center ______________________________________________________________________ The contents of this message may contain private, protected and/or privileged information. If you received this message in error, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained within. Please contact the sender and advise of the erroneous delivery by return e-mail or telephone. Thank you for your cooperation.
_______________________________________________ Gpc-dev mailing list [email protected] http://listserv.kumc.edu/mailman/listinfo/gpc-dev
