Re: [gpc-informatics] #162: PopMedNet node at UIOWA
#162: PopMedNet node at UIOWA --+-- Reporter: lv| Owner: prakashnadkarni Type: enhancement | Status: assigned Priority: major | Milestone: drn-basic-query Component: data-sharing | Resolution: Keywords:| Blocked By: 209 Blocking:| --+-- Changes (by dconnolly): * priority: minor = major -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/162#comment:7 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
RE: PopMedNet node at UNMC
If that is normal behavior, follow-up issue is … I got the query file downloaded (zip file) and try to unzip, I am not able to unzip I tried many ways to unzip), the system says that the *.zip is invalid. The file is oracle based query. Thanks. Ashok From: Verhagen, Laurel A [mailto:verhagen.lau...@mcrf.mfldclin.edu] Sent: Monday, February 09, 2015 9:52 AM To: Justin Dale; Mudgapalli, Ashok Cc: gpc-dev@listserv.kumc.edu Subject: RE: PopMedNet node at UNMC Justin is correct. Instructions are to download the queries, run locally, then upload. This is different than the first connectivity test. Thanks, Laurel From: gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Justin Dale Sent: Monday, February 09, 2015 9:41 AM To: Mudgapalli, Ashok Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu Subject: Re: PopMedNet node at UNMC We're seeing same screen when trying to edit the data model settings. I'm wondering if this is the intended behavior since these are all file distribution queries and we're supposed to open the file and run against the CDM through whichever mechanism we choose and then attach the results to the request? Not sure about all of this - suggest discussing in tomorrow's call. [Inline image 1] Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jd...@umn.edumailto:jd...@umn.edu On Mon, Feb 9, 2015 at 9:14 AM, Mudgapalli, Ashok ashok.mudgapa...@unmc.edumailto:ashok.mudgapa...@unmc.edu wrote: We were able install the Popmednet 5.0 version of the data mart client and connect to the PCORnet network. We are able to receive the “file distribution” query into our Data Mart client but unable to configure local Data Mart to execute the query for following reason. If you happen to know the solution or came across this issue please let me know. I sent an email to support team and waiting for the response. My local data mart is on Oracle. I did as follows: DataMart Client -- Settings - Edit -- highlighted our DataMart (C4-University of Nebraska Medical … -- Edit -- DataMart Settings dialog has [cid:image002.jpg@01D04450.F6445450] Clicked on Edit and it showed no model processor. [cid:image003.jpg@01D04450.F6445450] Ashok Mudgapalli, MS, Ph.D. Director of Research IT (Vice Chancellor for Research Office) Assistant Professor Genetics, Cell Biology, and Anatomy College of Medicine University of Nebraska Medical Center Omaha, NE 68198-7878 402-559-9072tel:402-559-9072 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edumailto:Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev 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 Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
PopMedNet node at UNMC
We were able install the Popmednet 5.0 version of the data mart client and connect to the PCORnet network. We are able to receive the file distribution query into our Data Mart client but unable to configure local Data Mart to execute the query for following reason. If you happen to know the solution or came across this issue please let me know. I sent an email to support team and waiting for the response. My local data mart is on Oracle. I did as follows: DataMart Client -- Settings - Edit -- highlighted our DataMart (C4-University of Nebraska Medical ... -- Edit -- DataMart Settings dialog has [cid:image001.jpg@01D04448.B8E40630] Clicked on Edit and it showed no model processor. [cid:image002.jpg@01D04448.B8E40630] Ashok Mudgapalli, MS, Ph.D. Director of Research IT (Vice Chancellor for Research Office) Assistant Professor Genetics, Cell Biology, and Anatomy College of Medicine University of Nebraska Medical Center Omaha, NE 68198-7878 402-559-9072 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
RE: PopMedNet node at UNMC
Justin is correct. Instructions are to download the queries, run locally, then upload. This is different than the first connectivity test. Thanks, Laurel From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Justin Dale Sent: Monday, February 09, 2015 9:41 AM To: Mudgapalli, Ashok Cc: gpc-dev@listserv.kumc.edu Subject: Re: PopMedNet node at UNMC We're seeing same screen when trying to edit the data model settings. I'm wondering if this is the intended behavior since these are all file distribution queries and we're supposed to open the file and run against the CDM through whichever mechanism we choose and then attach the results to the request? Not sure about all of this - suggest discussing in tomorrow's call. [Inline image 1] Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jd...@umn.edumailto:jd...@umn.edu On Mon, Feb 9, 2015 at 9:14 AM, Mudgapalli, Ashok ashok.mudgapa...@unmc.edumailto:ashok.mudgapa...@unmc.edu wrote: We were able install the Popmednet 5.0 version of the data mart client and connect to the PCORnet network. We are able to receive the “file distribution” query into our Data Mart client but unable to configure local Data Mart to execute the query for following reason. If you happen to know the solution or came across this issue please let me know. I sent an email to support team and waiting for the response. My local data mart is on Oracle. I did as follows: DataMart Client -- Settings - Edit -- highlighted our DataMart (C4-University of Nebraska Medical … -- Edit -- DataMart Settings dialog has [cid:image004.jpg@01D0444E.0259ECD0] Clicked on Edit and it showed no model processor. [cid:image005.jpg@01D0444E.0259ECD0] Ashok Mudgapalli, MS, Ph.D. Director of Research IT (Vice Chancellor for Research Office) Assistant Professor Genetics, Cell Biology, and Anatomy College of Medicine University of Nebraska Medical Center Omaha, NE 68198-7878 402-559-9072tel:402-559-9072 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edumailto:Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev __ 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 Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: PopMedNet node at UNMC
We're seeing same screen when trying to edit the data model settings. I'm wondering if this is the intended behavior since these are all file distribution queries and we're supposed to open the file and run against the CDM through whichever mechanism we choose and then attach the results to the request? Not sure about all of this - suggest discussing in tomorrow's call. [image: Inline image 1] Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jd...@umn.edu On Mon, Feb 9, 2015 at 9:14 AM, Mudgapalli, Ashok ashok.mudgapa...@unmc.edu wrote: We were able install the Popmednet 5.0 version of the data mart client and connect to the PCORnet network. We are able to receive the “file distribution” query into our Data Mart client but unable to configure local Data Mart to execute the query for following reason. If you happen to know the solution or came across this issue please let me know. I sent an email to support team and waiting for the response. My local data mart is on Oracle. I did as follows: DataMart Client à Settings - Edit à highlighted our DataMart (C4-University of Nebraska Medical … à Edit à DataMart Settings dialog has Clicked on Edit and it showed no model processor. Ashok Mudgapalli, MS, Ph.D. Director of Research IT (Vice Chancellor for Research Office) Assistant Professor Genetics, Cell Biology, and Anatomy College of Medicine University of Nebraska Medical Center Omaha, NE 68198-7878 402-559-9072 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #210: Query by BMI percentile among children.
#210: Query by BMI percentile among children. -+- Reporter: bokov| Owner: gkowalski Type: enhancement | Status: assigned Priority: major| Milestone: cohort- Component: data-stds| char1 Keywords: BMI pediatric-cohort obesity-cohort | Resolution: Blocking: 33 | Blocked By: -+- Comment (by bokov): Responding on the TRAC ticket because this affects everyone working on this. It looks like the lookup table has ages in half-months except the two bounding ages-- 24 months and 240 months. Actually, it's weirder-- the real upper bound is 240.5 months. The intent seems to be that each actual age get binned to a round number. Not accounting for this this is a bug in the SQL scripts I sent. Attaching the patched scripts. Briefly, VISAGE is now calculated as `ROUND((ob.start_date - pd.birth_date)/30.4375)` instead of `ROUND((ob.start_date - pd.birth_date)/15.21875)/2` and at the end of `cdc_lookup.sql` the 240 montha age is dropped, and all the other ages except 24 are shifted upward by 0.5. On 02/09/2015 10:44 AM, Alex Bokov wrote: Wow, hadn't noticed that for some crazy reason the ages in the table I sent are all in half-months! Logging in right now to see what's going on, will respond shortly. On 02/09/2015 10:22 AM, Phillip Reeder wrote: We have 30k, of 300k, observations with a visage that are even numbers that were not in the bmi percentiles table. Is there a new file that has these even numbers? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/210#comment:15 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit -+--- Reporter: mish | Owner: dconnolly Type: enhancement | Status: assigned Priority: minor| Milestone: cohort-char1 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+--- Changes (by dconnolly): * owner: bokov = dconnolly * priority: major = minor -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/178#comment:14 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
RE: [gpc-informatics] #228: DataBuilder output not directly analyzable
That excerpt regards the CDM; presumably the CDM is sufficiently directly analyzable for PCORI needs. And we're not using the DataBuilder to build the CDM. The complete, longitudinal data bit is about claims data, I believe; i.e. milestone 7.7 Approaches to enhance the completeness and comprehensiveness of longitudinal data capture are developed and submitted to PCORI (RC 3) Which leaves helping researchers deal with DataBuilder output; this is a goal I personally support, but I don't know of any gpc-dev obligations or due dates in this area. -- Dan From: Alex Bokov [alex.bo...@gmail.com] on behalf of Alex Bokov [bo...@uthscsa.edu] Sent: Monday, February 02, 2015 2:29 PM To: gpc-dev@listserv.kumc.edu; Dan Connolly Cc: Matthew Hoag; Vincent Leonardo Subject: Re: [gpc-informatics] #228: DataBuilder output not directly analyzable This is the only ticket I could find that directly addresses the following PCORI phase-I goal (emphasis mine): * Organization of patient data mapped to the PCORnet Common Data Modelhttp://www.pcornet.org/resource-center/pcornet-common-data-model/ (CDM), including the extent to which complete, longitudinal data on one million patients is or will be available for research; fill out the required table; ability to efficiently respond to an SAS query generated through PopMedNethttp://www.popmednet.org/ Data that is representable as a table that has the characteristics described in the ticket is trivially exportable to SAS as a CSV file. The hard part is making it representable as this type of table in the first place. In addition, this ticket addresses the practical goal of giving the researchers we (UTHSCSA) are encouraging to apply for PCORI funding data that is actually usable without their statisticians messing around with SQLIte. On 02/02/2015 02:16 PM, GPC Informatics wrote: Note I more or less stopped tracking milestone:data-agg1. I wonder what priority to give this ticket. More in due course... ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: survey-redcap-als Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by dconnolly): In section 5.0 Data management and case report forms of the protocol (attached to #208): The following EMR data will be included for analysis: age, gender, race, ethnicity, living situation, occupation, and years of education. I don't know where living situation, occupation, and years of education are expected to come from. They're not on the current survey draft, and they're not in any of the currently planned GPC ontologies. In section 6.0 Biostatistical Approach: Outcome Measures, Data Analysis and Power: ... Basic descriptive statistics will be used to describe the overall ALS clinic cohort: including basic demographics (age, gender, race, ethnicity, living situation, occupation, years of education) and functional burden as identified by survey response (clinical diagnosis, and functional status). -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:31 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Feb 10 gpc-dev agenda
Here's the proposed agenda, i.e. the current draft of Feb 10 meeting noteshttps://docs.google.com/document/d/1qlxl7b1Xef1n6MMT1TAjRRYU9QtZtK4rwJMc8pZULiE/edit?usp=sharing. Discussion of the ALS survey plan is a major focus; we'll see how much of the rest we get to. 1. Convene, take roll, review records and plan next meeting * Meeting ID and access code: 817-393-381https://global.gotomeeting.com/meeting/join/817393381; call +1 (571) 317-3131 * meeting notes (#12https://informatics.gpcnetwork.org/trac/Project/ticket/12): previous notes OK? today's scribe: UIOWA * roll: all 10 DevTeamshttps://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams represented? * KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW * comments on the agenda? new/closed/reopened ticketshttps://informatics.gpcnetwork.org/trac/Project/timeline FYI: (several) * Next meeting: Feb 17. Scribe volunteer? 2. milestone:survey-redcap-alshttps://informatics.gpcnetwork.org/trac/Project/milestone/survey-redcap-als Feb 9??? * #208https://informatics.gpcnetwork.org/trac/Project/ticket/208 ALS survey planhttps://informatics.gpcnetwork.org/trac/Project/ticket/208 * #197https://informatics.gpcnetwork.org/trac/Project/ticket/197 REDCap data dictionary for ALS surveyhttps://informatics.gpcnetwork.org/trac/Project/ticket/197 3. milestone/bc-survey-cohort-defhttps://informatics.gpcnetwork.org/trac/Project/milestone/bc-survey-cohort-def Feb 23 * #110https://informatics.gpcnetwork.org/trac/Project/ticket/110 securely de-identify and re-identify patient datahttps://informatics.gpcnetwork.org/trac/Project/ticket/110 * #227https://informatics.gpcnetwork.org/trac/Project/ticket/227 Data QA for Breast Cancer Finder Filehttps://informatics.gpcnetwork.org/trac/Project/ticket/227 4. milestone:cohort-char1https://informatics.gpcnetwork.org/trac/Project/milestone/cohort-char1 due Feb 23 * Alex: I will send out revised Obesity Federated query materials. (#33) * #210 BMI percentile - ref design sketch with SQL from Bokov 22 Janhttp://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001116.html * significant status change from any site? (for KeyGoalTrackinghttps://informatics.gpcnetwork.org/trac/Project/wiki/KeyGoalTracking) 5. milestone:data-domains2 due Feb 23 * #216https://informatics.gpcnetwork.org/trac/Project/ticket/216 GPC Diagnosis modifiers in HERON - UNMC progress? * #199https://informatics.gpcnetwork.org/trac/Project/ticket/199 Medication Modifiers Reeder Feb 6 definitionshttp://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001194.html * March QA - ticket? milestone? * #67, #186 Demographics * #23 BMI * #185 tumor registry 6. milestone drn-basic-queryhttps://informatics.gpcnetwork.org/trac/Project/milestone/drn-basic-query due Feb 28 * How to run CDM queries via PopMednet? (Dale 9 Febhttp://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001200.html, #143) * #145 transform (ETL) GPC i2b2 data to PCORNet CDMhttps://informatics.gpcnetwork.org/trac/Project/ticket/145 * #120https://informatics.gpcnetwork.org/trac/Project/ticket/120 Encounter terms * #229 Enrollment * #182https://informatics.gpcnetwork.org/trac/Project/ticket/182 Complete LOINC standardization of CDM V1 and share metadata with GPC 7. Milestone: bc-tracker-wp2https://informatics.gpcnetwork.org/trac/Project/milestone/bc-tracker-wp2 Mar 2 * GPC REDCap #192https://informatics.gpcnetwork.org/trac/Project/ticket/192, #159https://informatics.gpcnetwork.org/trac/Project/ticket/159 * Federated login (#174) T. Mish -- Dan ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Popmednet status
So far, - I was able to receive the file query from PCORnet technical team on DM client (V 5.0) - Pulled the query file from DM Client and ran the query manually on SQL Developer. - I uploaded the query result file to DM Client response window and submitted to Network - Now I am waiting for network technical team's response - Looks like the request and response model is file based (I could be wrong) - Just a note, I was not able to run the query from inside DM Client since I was not able to configure it to talk our data source. I am not sure whether this is a bug or design by choice. If you are in similar situation, please let me know or you can post other comments too Thanks Ashok Mudgapalli, MS, Ph.D. Director of Research IT (Vice Chancellor for Research Office) Assistant Professor Genetics, Cell Biology, and Anatomy College of Medicine University of Nebraska Medical Center Omaha, NE 68198-7878 402-559-9072 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: survey-redcap-als Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Wendy sent a report on ALS comobidities and complications to John on Friday Feb 06, 2015. John provided the list of ICD-9 codes comorbidities related to Charlson comobidity index and Jeff provided the list of ICD-9 codes for more ALS relevant comobidities and complications (Wendy and Siya together completed the work). Cohort characterization for ALS cohort will stop for now to focus on the Breast cancer cohort. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:32 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
