Hi Jim, Yes, that's correct. We have a conversion table that holds the necessary conversions from local units to the standard units as dictated by the metadataxml and LOINC. Happy to discuss as well - I'll send another note off this chain to organize that unless it would be valuable to discuss on the Dev call.
The March QA is next on our priority list, and after that we will be able to work on the SNOMED test. I don't anticipate starting on that work until next week at the earliest. Thanks, Nate Apathy Solution Manager: i2b2 | [email protected] | 816.201.2785 -----Original Message----- From: Campbell, James R [mailto:[email protected]] Sent: Monday, March 30, 2015 11:09 PM To: Apathy,Nate Cc: <[email protected]>; Hickman, Hubert B; Campbell, Walter S; Munns, Michael B Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms Nate Yes, I am referring to metadata agreed from H2. When we rolled out metadataxml, we had to tweak some units but I matched those reported in our i2b2 to UCUM reference and tailored to our lab reports. Are you saying that you are comparing Regenstrief to local us=nits and compiling a lexicon of conversions into the metadataxml? I would be interested to discuss by call at your convenience ETA for SNOMED test load? Jim James R. Campbell MD [email protected] Office: 402-559-7505 Secretary: 402-559-7299 Pager: 402-888-1230 > On Mar 30, 2015, at 4:03 PM, "Apathy,Nate" <[email protected]> wrote: > > Hi Jim, > > Can you clarify what you mean by the "GPC lab metadata"? Are you referring to > the CMH: LOINC hierarchy on Babel that we decided upon during Hackathon II? > We are working on a project now to normalize our units, as coded LOINC is a > poor predictor of the actual units used in the lab setting for those tests. > We haven't developed a script to build metadataxml; rather we have a > reference table with 27,864 LOINC codes and their associated metadataxml per > the LOINC standard units in the multiaxial hierarchy. We do a lookup on that > table to pull the metadata in to our client lab ontologies, but as you can > probably surmise by now we ran in to a lot of issues initially with > mismatched units that made the metadataxml basically useless unless the units > matched exactly. That is what precipitated the unit normalization project. > There are several upstream data source issues that depend on other teams and > need to take place before that project can be completed, so we are targeting > the creation of t hat curated LOINC ontology with standard units by the end of April. > > Thanks, > > Nate Apathy > Solution Manager: i2b2 | [email protected] | 816.201.2785 > > -----Original Message----- > From: Campbell, James R [mailto:[email protected]] > Sent: Friday, March 27, 2015 11:54 PM > To: <[email protected]>; Apathy,Nate > Cc: Hickman, Hubert B; Campbell, Walter S; Munns, Michael B > Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms > > Nate > So, if I understand, you had calculated or developed metadataxml for all the > entries in the GPC lab metadata? Wow, I did not understand that from > Hackathon2 and we would love to get a copy of your java code to supplement > our metadata browsing tools. Did you develop a java-based computation of > metadataxml from the LOINC release record? We have considered that but have > not had time. > I thought we might be providing an enhancement to your metadata build but I > agree entirely that it seems irrelevant. > Jim > > James R. Campbell MD > [email protected] > Office: 402-559-7505 > Secretary: 402-559-7299 > Pager: 402-888-1230 > >> On Mar 27, 2015, at 1:11 PM, "GPC Informatics" <[email protected]> wrote: >> >> #158: usable view of LOINC lab terms >> -------------------------+---------------------------- >> Reporter: rwaitman | Owner: nateapathy >> Type: enhancement | Status: assigned >> Priority: major | Milestone: data-domains3 >> Component: data-stds | Resolution: >> Keywords: | Blocked By: >> Blocking: | >> -------------------------+---------------------------- >> >> Comment (by nateapathy): >> >> We reviewed the metadata included in the UNMC LOINC hierarchy and >> found >> 922 with metadata XML applied. We compared those leaf terms to our >> current hierarchy and found 622 that overlapped with the 71,000+ >> terms that are in our base hierarchy (the majority of which is hidden >> on Babel). All of our metadata XML matched the data you had for >> yours, only with a few semantic differences in naming conventions for tests >> within the metadata panel. >> >> Since there is not a major material difference between these two sets >> of metadata, I'm inclined to direct the group to the information I >> shared in >> [https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:2 >> 0 comment20] on this thread. That comment includes a link to the base >> multiaxial hierarchy from Regenstrief and the Java code we use to >> transform that into our base LOINC hierarchy that was agreed upon as >> the GPC hierarchy during Hackathon II. >> >> Let me know if there are any next steps or additional questions we >> need to answer or clarify before we can close this ticket. >> >> -- >> Ticket URL: >> <http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:28 >> > gpc-informatics <http://informatics.gpcnetwork.org/> >> Greater Plains Network - Informatics > > 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. > > CONFIDENTIALITY NOTICE This message and any included attachments are from > Cerner Corporation and are intended only for the addressee. 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