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:20 >> 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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