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
