Thanks for the suggestions, Alex; I incorporated pretty much all of them. On code sharing... I have a long list of warts in the HERON code that I'd like to fix to make it more portable and modular (the agenda now has a list of some of them), but to date, we haven't managed to commit the necessary resources. I asked Russ whether to re-consider this at HackathonTwo, and he said yes, it's important for phase 2.
Reviewing my August comment on portable ETL for Epic<https://informatics.gpcnetwork.org/trac/Project/ticket/71#comment:9>, we did talk about that: It's possible that having a truly portable Epic ETL will become a priority as/when we take on GPC phase 2 partners. In discussions around ​HeronProjectTimeline#Aug2014Planning<https://informatics.kumc.edu/work/wiki/HeronProjectTimeline#Aug2014Planning>, other items took priority, as new partners appear to be 4 to 6 months away at the earliest. Meanwhile, we just did another "yellow sticky" ​<https://informatics.kumc.edu/work/wiki/HeronProjectTimeline#Aug2014Planning>HeronProjectTimeline<https://informatics.kumc.edu/work/wiki/HeronProjectTimeline> update thru June (to appear), and portable ETL still isn't scheduled. On the other hand, phase 2 doesn't actually start until well after June, so perhaps things will come together by then after all. -- Dan ________________________________ From: [email protected] [[email protected]] on behalf of Alex Bokov [[email protected]] Sent: Friday, January 09, 2015 12:11 PM To: [email protected] Subject: Re: HackathonTwo: detailed agenda 10:15 for 1:45: Morning Session 2 1. Breast Cancer Survey Finder File<https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonTwo#bc-finder-wp1> led by Kansas/UIOWA 2. informatics support for ALS, Obesity cohort surveys<https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonTwo#survey-dev> ...in the obesity cohort survey let's include a more thorough assessment of obstacles to implementing BMI percentiles, and what we have learned so far about what is needed for i2b2 to fully support the needs of the cohort queries. On 01/08/2015 12:16 PM, Dan Connolly wrote: 13:00 for 1:30: Afternoon Session 1 * * GPC Ontology v1, aka milestone:data-domains2<https://informatics.gpcnetwork.org/trac/Project/milestone/data-domains2> * GPC Demographics #67<https://informatics.gpcnetwork.org/trac/Project/ticket/67>, #186<https://informatics.gpcnetwork.org/trac/Project/ticket/186> * GPC Diagnoses #63<https://informatics.gpcnetwork.org/trac/Project/ticket/63>, #90<https://informatics.gpcnetwork.org/trac/Project/ticket/90>, #91<https://informatics.gpcnetwork.org/trac/Project/ticket/91> * GPC Vitals #23<https://informatics.gpcnetwork.org/trac/Project/ticket/23> * GPC Meds. #78<https://informatics.gpcnetwork.org/trac/Project/ticket/78> * Cancer Tumor Registry #185<https://informatics.gpcnetwork.org/trac/Project/ticket/185> Let's aside time to making sure everyone understands how ontologies are supposed to work in i2b2, and how multiple ontologies can be made to point to the same entries in the CONCEPT_DIMENSION table. Another reason that we're finding data alignment challenging is that people don't share Heron code. So, rather than just giving up, why not talk through... 1. What are people's obstacles to using Heron code? Would sites use more of it if it wasn't an all-or-none commitment? 2. How can Heron code be better modularized so that there is a clean, documented way to incorporate (and merge changes to) bits and pieces of it in your ETL process without copy-pasting stuff by hand each time you want to incorporate an ETL feature that another site implemented? 3. What conventions can we come up with that permit incorporation of site-specific code that doesn't benefit KUMC be done in a manner that does not impact KUMC or add to their workload or risk? Fri, Jan 23 * 16:00:00 for 2:15: Afternoon Session 2 * Infrastructure discussion * CDM ETL and DRN Query, cont.<https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonTwo#gpc-drn> * Encounters design #155<https://informatics.gpcnetwork.org/trac/Project/ticket/155>, #120<https://informatics.gpcnetwork.org/trac/Project/ticket/120> How about, as part of the infrastructure discussion, comparing notes on performance improvements-- where to look for problems on ETL tasks that gobble up temp space or run forever.
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