Hi All, A shorter email from me:
It seems the real value will be something like this: 1) Pooling together the ontologies that are available so we all aren't too duplicative. This just means that we would have the opportunity to download the ontologies of others that send in their i2b2 ontology tables so that we could save the work ourselves. The problem is that it would also be nice to have a prescribed way to update them, this is tougher. 2) Having an approach to the ontologies that need a license. CPT4 comes to mind immediately. 3) Many of the approaches will be most helpful with some example data to show exactly how the data is represented and queried under that ontology so people can decide if this is the right approach for them. This seems especially important with different modifier approaches. 4) The ontologies will give up a good bottom-up way to compare different ways of populating i2b2 such that transformations into mini-sentinel and OMOP will be guaranteed to have the right data elements available in an i2b2 instance, and an ontology could be attached to specific transformation. Each of these could use a lot more discussion, but have reached the limit of my attentions span for now. Thanks, Shawn. From: Russ Waitman [mailto:[email protected]] Sent: Friday, April 11, 2014 5:36 PM To: Dan Connolly Cc: John Steinmetz; James R Campbell; Steve Fennel; Michael Kahn; Murphy, Shawn N.; Lisa' 'Dahm; Paul Harris; [email protected]; Dan Masys; [email protected]; James C McClay; Thomas Campion; Nathan Graham; Klann, Jeffrey G.; Tamara McMahon; Brittany Zschoche; Churchill, Susanne E.; Michael J Becich; Alfredo Tirado-Ramos; Kenneth Mandl; Keith Marsolo; Umberto Tachinardi Subject: Re: Ontology build for i2b2 Hi Dan, Jim and everybody on GPC-dev and other select other CDRN people, Catching up on this email thread Jim and I were meeting with the PedsNet CDRN Michael Kahn, Tom, Brad Taylor, Shawn Murphy, Lisa Dahm at UCIrvine, Paul Harris at Vandy and others. We were telling them about how the GPC manages our terminology and informatics technical efforts. We showed them the GPC mailing list, wiki, babel etc. so they can understand what our network is doing and offered for people to follow along. I was kind of falling into a: "the GPC doing this" storytelling. But Michael Kahn thought there could be a window of opportunity to explore comparing our i2b2 approaches and feeding mini-sentinel or OMOP (Michael's used it I think for other big efforts in Colorado so it's important to him as it has some good analytics for his kind of work). This could be important for us as we want to develop a way for us to evolve a common approach to data interoperability and representations that might compliment mini-sentinel's evolutionary path, valuable repurposing of the FDA investment, and distributed analysis frame work. If were are all independent CDNR efforts, we lose opportunities to see if some of these complimentary i2b2 and OMOP approaches can coalesce. Perhaps discussions that include all 29 networks are too diffuse but if there were 2-4 i2b2 based efforts some synergies might emerge. I am not on the Disney call so it's hard for me to gauge. What we decided was that while we do have a current GPC technical and terminology call, there's too much on that agenda to derail the good GPC progress we are making within our network (though others could listen in). Jim pointed out establishing guiding principles is important and good to get laid down when then starting terminology or tooling discussions. So, it may be very "sharing" centric calls initially. I'll differ slightly from Jim in that I think it is important for GPC PCORNet for the terminology ontology people be grounded in tooling matters from the contractual timeline perspective. It seems reasonable to do a couple things: 1. Protect the current technical call and keep the agenda as is so the GPC continues on it's current tempo I think on reflection that it's important for both DanC and JimC to drive that call so I don't want terminology "split off" into a separate effort as I'd be concerned we lose the cross-pollination. 2. Set up a call led by JimC and the other CDRNs to talk about where we are with the other CDRNs wrt terminology mainly but touch upon some tooling things like babel. DanC might be stretched but I would think we could have Nathan or Matt represent. Similarly am stretched with many things in my head but just hope overall with all the people on the project we'll get generally pointed in the right direction and if we hit some bumps, all of us are good hearted and will persevere. I think Shawn's team may have sent out a doodle so we'll see how many can link up. 3. Depending on where things shake out, we could conceivably have Harvard, UCRex (possibly a PedsNet site on i2b2 like Keith at Cinci) ship their ontology to post on Babel for comparison. Nathan Graham (cc'ed explicitly) might be the conduit. Over time people could also run the KUMC concept path statistics scripts so we see how much data is sitting at each site in the terminology nodes. This wouldn't be 30-40 but more like the current GPC 10 plus initially 1-4. BTW, Alfredo says they have data now in San Antonio!!!! I also see we now have the CMH ontologies that Cerner will provide on Babel! 4. It's also seems Shawn and Jeff Klann at Harvard will actively start working on porting data from i2b2 into min-sentinel compliant SAS files and really liked the GPC pcori ontology build. That would be a big help for us and having stuff in a common place like babel may be a scratchpad that would help them do work that should help each CDRN that uses i2b2. 5. The same environment could help people like Michael Kahn evaluate i2b2 <-> OMOP. Or not.... there were free libations during this session so our judgement could have been slightly impaired leading to induced optimism. 6. Shawn thought an in-person meeting might be needed to really gel - perhaps he suffers from a rare neurologic disorder: GoToMeeting Syndrome where one loses reading comprehension when delivered via LCD due to chronic webinar exposure ala IKFC. - We will see how things go after the first call. Steve and I recently had the surreal experience of landing at O'Hare and walking to the Chicago Hilton for our GPC IRB meeting without ever leaving air conditioning. I felt like I was in an alternative airport bubble universe. The other thing I took away is that the i2b2 meeting July 10th and 11th will be proceeded by a July 9th PCORI focus. I'll be at Cornell on the 9th but could then come up via the train to be there on the 10-11th. Dan and others this may be one to not miss. Might be a very good opportunity to catch up on these issues and also to understand as NCBC funding ends if i2b2 will move to a more community centric model for governance of development. While I am writing this I just got an email from them about the agenda on July 9th and will cut and paste it below. Russ Waitman, PhD Director of Medical Informatics Assistant Vice Chancellor for Enterprise Analytics Associate Professor, Department of Internal Medicine University of Kansas Medical Center, Kansas City, Kansas 913-945-7087 (office) [email protected]<mailto:[email protected]> http://www.kumc.edu/ea-mi/ http://informatics.kumc.edu<http://informatics.kumc.edu/> http://informatics.gpcnetwork.org<http://informatics.gpcnetwork.org/> - a PCORNet collaborative On Apr 11, 2014, at 3:18 PM, Lyons, Jessica Carpenter <[email protected]<mailto:[email protected]>> wrote: Hi all, Please join us for an in-person SCILHS Workshop to take place in Boston on July 9th from 12:00 pm - 6:00 pm. This workshop will occur prior to the annual SHRINE conference scheduled to take place on July 10th-11th. During this meeting we plan on discussing the use of the network by investigators, including PPRNs. The agenda for this workshop is listed below. Please let me know by April 25th if you or other colleagues plan to attend and how many we should expect. Let me know if you have any questions. Take care, Jessica Agenda: 12:00 Working Lunch - Speakers TBD 1:00 SCILHS approach to CDRN-PPRN Collaboration Phase 1 1:30 PPRN-CDRN use cases (3 -10 minute talks) 2:00 Inter-CDRN collaboration 3:00 Breakout 1 - Longitudinal Data Breakout 2: Patient-Reported Outcomes Data 3:45 Breakout reports 4:00 Wrap-up/Next Steps 4:30 Meeting Adjourns 4:30 - 6:00 Reception ________________________________ From: [email protected]<mailto:[email protected]> [[email protected]<mailto:[email protected]>] on behalf of Campbell, James R [[email protected]<mailto:[email protected]>] Sent: Friday, April 11, 2014 8:53 AM To: [email protected]<mailto:[email protected]> Cc: Lebsack, Jason A; John Steinmetz Subject: Ontology build for i2b2 Last evening Russ and I were speaking with Michael Kahn(Pitt CDRN), Shawn Murphy(Partners) and Thomas Campion(NYC). They have an active interest in cooperating with us in developing and maintaining our ontologies/modifiers for i2b2. The deliverables would be an agreed set of metadata builds for all our i2b2 installations that would share ontological definitions across all our network sites (30-40). GPC-DEV has too many issues on the plate and tooling matters do not concern me for vocabulary/ontology preparation. I am breaking out a separate team which will be conducting calls with the three networks mentioned above with the goal of reaching agreement on features of standard ontologies. I would observe that Nathan (Wilson), Bonnie, Brad, Glenn and Aaron would seem to be those most likely interested based on past participation, but GPC members who are interested, please confirm back to me by separate email if you want to be included in these discussions. Jim 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. 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