I admit I have only looked at lab in detail, but it is missing ~60 rows added in 3.1. Also the “zz Version” row says 2.1. I notice medications also says 2.1.
My mistake, on a closer look I see you have included the modifiers in our trees. The import tool I was using set m_exclusion_cd to the empty string instead of null, which was breaking it. I’ll make a note in my issues list that you might want to add a warning about this to any README / documentation you have. The more philosophical question is whether your new trees should also have the modifiers. I’d suggest so, for the relevant ones, and it would be easy to do by just changing the applied_path and add an exclusion code (for the parent folder) to the existing modifiers. This would make them fully compatible with our PCORnet transform. On the other hand, I agree they are used inconsistently and infrequently, so if that’s a lower priority we can work with that. … As an aside, one of our sites just informed me ICD-10 added a ton of new diagnosis codes in the newest release. Are you / are you interested in maintaining that tree as well? My (perhaps mistaken) understanding is that the ICD-10 tree is quite standardized so we wouldn’t run into the implementation differences we saw in Labs and Meds… Thanks! Jeff Jeffrey Klann, PhD Instructor of Medicine, Harvard Medical School Director, SCILHS Query Core From: "Campbell, James R" <campb...@unmc.edu> Date: Wednesday, April 4, 2018 at 8:59 AM To: Jeffrey KLANN <jeff.kl...@mgh.harvard.edu>, Shawn MURPHY <snmur...@partners.org> Cc: "Campbell, Walter S" <wcamp...@unmc.edu>, "Pedersen, Jay G" <jay.peder...@unmc.edu>, "Narayana, Yeshwanth R" <yeshwanth.naray...@unmc.edu>, "Estiri, Hossein" <hest...@mgh.harvard.edu>, Matthew JOSS <mj...@partners.org>, GPC STANDARDS <gpc-dev@listserv.kumc.edu> Subject: Re: SNOW SHRINE metadata Jeff We definitely sought out and used 3.1b as root; why do you say version 2? There is virtually no agreement on the use of your modifiers in GPC and some sites recommend stripping them from the release. We, for one, do not use the structures you imply in OBSERVATION_FACT deployment in order to populate CDMV3.1-4. I am torn as to how we treat them in publication. At the request of Medical College of Wisconsin, we added 80 or so labs to our ontology and Yesh is just now deploying to our release site so check with him and he will assure we have our 20180330 release. Jim ________________________________ From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu> Sent: Tuesday, April 3, 2018 8:16 PM To: Campbell, James R; Murphy, Shawn N. Cc: Campbell, Walter S; Pedersen, Jay G; Narayana, Yeshwanth R; Estiri, Hossein; Joss, Matthew A. H. Subject: Re: SNOW SHRINE metadata Non-UNMC email This is great! I’m making a list of detailed suggestions that will need to be addressed before it can be used in production in ARCH, but the content looks really good. I’ll put my issues in a Google Doc and share it with all of you. I’m going to try to get your new labs table running at our Partners ARCH site and if that works we’ll deploy it in the network! My major suggestion is about your distribution. I really like how you’re making it backward compatible with our ontology by only appending to it. I’d suggest that you use that approach and distribute your work only as patches / add-ons to our ontology, at least until ours is finished being developed, instead of releasing a full table version, for a couple reasons. One, we will be changing the core ontology (but not the terminology trees) to support CDM v4 in the coming months and it would make versioning difficult for you to maintain something sync’ed with ours. Also, you seem to have forked from v2, not 3.1b. Finally, your version breaks the modifiers. If you release as patches you avoid having to keep track of all this. If we decide to stop developing the ontology at the end of 2018 we could revisit this. What do you think? You may certainly reference our work in publication. Your current acknowledgement is fine (except that you spelled Harvard wrong <g>) but please add a link to our GitHub (https://github.com/ARCH-commons/arch-ontology) so folks can see the development history. Also it is released under the i2b2 license so my understanding is that yours must be also, or something compatible. Thanks! Jeff Jeffrey Klann, PhD Instructor of Medicine, Harvard Medical School Director, SCILHS Query Core From: "Campbell, James R" <campb...@unmc.edu> Date: Saturday, March 31, 2018 at 1:34 PM To: Jeffrey KLANN <jeff.kl...@mgh.harvard.edu>, Shawn MURPHY <snmur...@partners.org> Cc: "Campbell, Walter S" <wcamp...@unmc.edu>, "Pedersen, Jay G" <jay.peder...@unmc.edu>, "Narayana, Yeshwanth R" <yeshwanth.naray...@unmc.edu> Subject: SNOW SHRINE metadata Jeff Shawn We have completed our build of SNOW SHRINE_20180331 i2b2 metadata and plan to publish this with strict versioning control on our website. (https://www.unmc.edu/pathology/informatics/tdc) I enclose a mock-up of our download page which will require the user to have a UMLS account to obtain the material. Based upon our last discussion, we have obtained SCILHS 3.1b and expanded your metadata as follows: 1) Laboratory has a new expanded LOINC concept set with common panel codes and about 1500 commonly used lab tests 2) Medications has appended a comprehensive (all historical RXNORM and NDC code) metadata set indexed by ingredient and organized alphabetically. The VA schema you built remains and we have agreement with NLM that we can count on support for VA Therapeutic and Physiologic classification going forward even though NDF-RT is defunct. 3) Diagnoses with addition of SNOMED CT conditions/problems We will be publishing both FULL and DELTA releases six monthly with updates for all ONC terminologies and will probably have a FIXES release in a few months with some additional lab requests. I want to ask your permission to reference your work in publication and ask what you would like for acknowledgement on the download page? 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. If you have received this e-mail by mistake, please delete it and immediately contact the sender. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. 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