The proposal for event-oriented datasets wasn't sidelined; it was completed in Oct 2015:
#228 closed enhancement (fixed) refine DataBuilder output for traditional analysis (UTHSCSA-CIRD/datafinisher) https://informatics.gpcnetwork.org/trac/Project/ticket/228 "Between datafinisher, edc_summary and analysis techniques such as the breast cancer dataset (#356), we are meeting the immediate requirements of our customers. It would be interesting to explore the overlap between the datafinisher and the BC techniques, but it's not clear anyone can justify the time. If there is GPC business that isn't addressed by these techniques, let's open a more focussed ticket." The needs of the SAS PROCs used in the PCORnet distributed research network are met by building a CDM datamart at each site. But exchanging datasets is out of its scope. Some of the CDM tables turn out to be fairly researcher-friendly, so within GPC we're also using those as the basis of inter-site data exchange in the case of breast cancer diagnoses and procedures. https://informatics.gpcnetwork.org/trac/Project/ticket/448 -- Dan ________________________________________ From: Campbell, James R [[email protected]] Sent: Saturday, July 09, 2016 2:24 AM To: Dan Connolly Cc: Kowalski, George; Phillip Reeder; French, Tony; [email protected]; McClay, James C Subject: Re: DataBuilder installation instructions I believe that Alex was proposing data extract utilities from i2b2 that produced event-oriented (as opposed to time-oriented) datasets ready for the researcher to analyze statistically. I was referring to the SAS PROCs that PCORI is using to distribute queries across network sites, reflecting that while i2b2 is easy to use in order to identify patient/encounter sets, it is not so friendly for specifying and extracting the datasets that the statistician needs for analysis. As far as proprietary is concerned, a useful question for our GPC network data managers would be: what is the statistical tool bench of choice for their analytical work? Jim James R. Campbell MD [email protected] Office: 402-559-7505 Secretary: 402-559-7299 Pager: 402-888-1230 > On Jul 8, 2016, at 5:14 PM, Dan Connolly <[email protected]> wrote: > > Which proposal was sidelined? > > And which PCORI procedures are there for sending data between sites? My > understanding is that PCORnet keeps data local at sites. > > The databuilder is agnostic to R vs. SAS. It's python (and java) and SQL. > > I expect building a SAS dataset from a sqlite file is straightforward (via > CSV perhaps); I'm not interested to persue it. I don't invest in proprietary > technology unless I am compelled to. > > -- > Dan > > ________________________________________ > From: Campbell, James R [[email protected]] > Sent: Friday, July 08, 2016 3:07 PM > To: Kowalski, George > Cc: Dan Connolly; Phillip Reeder; French, Tony; [email protected]; > McClay, James C > Subject: Re: DataBuilder installation instructions > > I may misunderstand the current DataBuilder functionality but I would > rejuvenate the proposal that Alex tried to present at hackathon 2 that was > sidelined. I would also try to align our data extraction utilities with > PCORI procedures and ask for development that would allow for extraction of > SAS data sets of requested clinical data that are ready for analysis on that > platform. Our researchers do not use R and are not about to learn new skills > to suit our purpose. > Jim > > James R. Campbell MD > [email protected] > Office: 402-559-7505 > Secretary: 402-559-7299 > Pager: 402-888-1230 > >> On Jul 8, 2016, at 10:39 AM, Kowalski, George <[email protected]> wrote: >> >> MCW is in. I’d prefer a docker instance. >> >> In the mean time I’ve developed a separate tool to extract all the data for >> a query into a sqlite file. >> >> https://github.com/MCW-BMI/i2b2Exporter >> >> It does not just take the concepts requested in the query as databuilder >> does , but all associated concepts for the query. >> >> G >> >> >> George Kowalski >> Biomedical Informatics Software Engineer >> Clinical & Translational Science Institute >> Medical College of Wisconsin >> 9200 West Wisconsin Avenue, Suite L722A >> Milwaukee, Wisconsin USA 53226 >> 414.805.7318 (office) / [email protected]<mailto:[email protected]> >> >> >> From: <[email protected]> on behalf of Dan Connolly >> <[email protected]> >> Date: Thursday, July 7, 2016 at 2:54 PM >> To: Phillip Reeder <[email protected]>, "French, Tony" >> <[email protected]>, "[email protected]" >> <[email protected]> >> Subject: RE: DataBuilder installation instructions >> >> Yes, I'd like that. Interested sites, please do chime in. >> >> I'll try to figure out details. >> >> I tend to use the normal Tuesday call slot for such things; perhaps it could >> start at 11:30 or something. We'll see. >> >> -- >> Dan >> ________________________________ >> From: Phillip Reeder [[email protected]] >> Sent: Thursday, July 07, 2016 12:53 PM >> To: Dan Connolly; French, Tony; [email protected] >> Subject: Re: DataBuilder installation instructions >> Dan, >> Any chance someone from your site could go through the install of the >> current version so that other sites could be on the most recent version? >> I know we, at UTSW, would like to get to a more recent version as well. I >> know you have made numerous changes and enhancements in the past year that >> we would like to have. Maybe we could schedule an installathon and get a >> bunch of people up to the latest version? Would other sites be interested? >> >> Phillip >> >> From: >> <[email protected]<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>> >> on behalf of Dan Connolly >> <[email protected]<redir.aspx?REF=Q1HPM7XGpVog9uReo0Fi62hTciKe6gZrDzYtwzGs1qQETABEoKbTCAFtYWlsdG86ZGNvbm5vbGx5QGt1bWMuZWR1>> >> Date: Thursday, July 7, 2016 at 11:10 AM >> To: "French, Tony" >> <[email protected]<redir.aspx?REF=Qj1yzHStiwpKhM0Nfa84xQflx-JkcYQMYMEy0hQd_6IETABEoKbTCAFtYWlsdG86YWRmcmVuY2hAcmVnZW5zdHJpZWYub3Jn>>, >> >> "[email protected]<redir.aspx?REF=pNh1vDjJti-nD9aNPMpgnVIvXOKsAs399Z_-3bk3iEoETABEoKbTCAFtYWlsdG86R1BDLURFVkBMSVNUU0VSVi5LVU1DLkVEVQ..>" >> >> <[email protected]<redir.aspx?REF=pNh1vDjJti-nD9aNPMpgnVIvXOKsAs399Z_-3bk3iEoETABEoKbTCAFtYWlsdG86R1BDLURFVkBMSVNUU0VSVi5LVU1DLkVEVQ..>> >> Subject: RE: DataBuilder installation instructions >> >> That's pretty much the main installation documentation, still. And that it >> is out of date is a known problem: >> >> * #335: problem: DataBuilder VM deployment outdated by migration of middle >> tier to jboss >> <redir.aspx?REF=l02ArUG3YbclGkb9YkfVT16GJ9tWpKyq6Cu_b5DnFNoETABEoKbTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvMzM1> >> I suggest you report details of the errors you're getting; perhaps there are >> easy fixes to the documentation that will get you going. >> >> Be sure to include the exact revision hash of the code you're trying to use; >> if you checked out the current code from the >> heron_extract<UrlBlockedError.aspx> repository, you might have better luck >> with an older version (such as rev 1b8a53f78be0 from Nov 2014, available in >> heron_extract.zip<redir.aspx?REF=MQLAqihRp1HMw4GwABGrrORljLijDE8LTVk97voAqBQETABEoKbTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC9hdHRhY2htZW50L3dpa2kvQnVpbGRlclNhZ2EvaGVyb25fZXh0cmFjdC56aXA.>). >> >> -- >> Dan >> ________________________________ >> From: >> [email protected]<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1> >> >> [[email protected]<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>] >> on behalf of French, Tony >> [[email protected]<redir.aspx?REF=Qj1yzHStiwpKhM0Nfa84xQflx-JkcYQMYMEy0hQd_6IETABEoKbTCAFtYWlsdG86YWRmcmVuY2hAcmVnZW5zdHJpZWYub3Jn>] >> Sent: Thursday, July 07, 2016 10:56 AM >> To: >> [email protected]<redir.aspx?REF=pNh1vDjJti-nD9aNPMpgnVIvXOKsAs399Z_-3bk3iEoETABEoKbTCAFtYWlsdG86R1BDLURFVkBMSVNUU0VSVi5LVU1DLkVEVQ..> >> Subject: DataBuilder installation instructions >> We are working on getting DataBuilder installed in our environment. I found >> the BuilderSaga<UrlBlockedError.aspx> article for installing it into an i2b2 >> demo VM. Is that the best guide to reference for installing it into an >> actual working environment or are there step by step manual instructions >> available anywhere? >> >> I have tried following the screencast to install using the latest i2b2 demo >> VM but have already ran into several errors. Does anyone have a historical >> link to i2b2vmware-1703a.zip ? >> >> >> >> Thanks, >> Tony >> >> >> Tony French | Software Development Manager >> Tools and Shared Resources >> Center for Biomedical Informatics >> [cid:[email protected]] >> 1101 West Tenth Street >> Indianapolis, IN, 46202 >> Tel 317-274-9087 | Fax: 317-274-9305 >> Twitter: @Regenstrief | >> Facebook.com/regenstriefinstitute<UrlBlockedError.aspx> >> www.regenstrief.org<UrlBlockedError.aspx> >> >> Confidentiality Notice: The contents of this message and any files >> transmitted with it may contain confidential and/or privileged information >> and are intended solely for the use of the named addressee(s). Additionally, >> the information contained herein may have been disclosed to you from medical >> records with confidentiality protected by federal and state laws. Federal >> regulations and State laws prohibit you from making further disclosure of >> such information without the specific written consent of the person to whom >> the information pertains or as otherwise permitted by such regulations. A >> general authorization for the release of medical or other information is not >> sufficient for this purpose. >> If you have received this message in error, please notify the sender by >> return e-mail and delete the original message. Any retention, disclosure, >> copying, distribution or use of this information by anyone other than the >> intended recipient is strictly prohibited. >> >> >> ________________________________ >> >> UT Southwestern >> >> >> Medical Center >> >> >> >> The future of medicine, today. >> >> >> _______________________________________________ >> Gpc-dev mailing list >> [email protected] >> http://listserv.kumc.edu/mailman/listinfo/gpc-dev > > 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 [email protected] http://listserv.kumc.edu/mailman/listinfo/gpc-dev
