Stream: nordics
Topic: code systems
Jens Villadsen (May 17 2020 at 20:40):
NPU (https://en.wikipedia.org/wiki/NPU_terminology) as codesystem is used in Denmark and I expect elsewhere also. Could you northern colleagues confirm that NPU is also used among you? @Mikael Rinnetmäki @Espen Stranger Seland @Viktor Jernelöv.
Jens Villadsen (May 17 2020 at 20:41):
As a side question, I read in an article that 'most of northern europe' uses NPU. Does that include the Netherlands @René Spronk ?
Mikael Rinnetmäki (May 18 2020 at 04:42):
I believe NPU is used exclusively in Denmark, Norway, and Sweden.
Mikael Rinnetmäki (May 18 2020 at 04:43):
Espen Stranger Seland (May 18 2020 at 05:55):
We have "Norsk laboratoriekodeverk" which is based on NPU, but I'm not sure how much of NPU is used.
https://ehelse.no/kodeverk/laboratoriekodeverket
René Spronk (May 18 2020 at 06:43):
I haven't heard of it before, I'm fairly sure it's not in use in the Netherlands. Either units are a total mess (systems do whet they want, as is mostly the case in Hl7v2 lab messages), or it'll be UCUM. There is some ongoing work to create patyient-friendly translations for code systems such a sSNOMED, but I haven't heard about an effort to do so for units.
Oskar Thunman (May 19 2020 at 11:16):
I can confirm this is used in Sweden. Lot's of local extensions, last time I checked, but it's derived from NPU.
Mikael Rinnetmäki (Jun 06 2020 at 12:50):
The codes used in Finland can be found at https://www.kommunforbundet.fi/social-och-halsovard/informationshantering/nomenklaturer-och-klassifikationer/nomenklatur-laboratorieundersokningar
Jens Villadsen (Nov 15 2021 at 12:29):
@Petter Wolff / @Daniel Karlsson (@Espen Stranger Seland / @Øyvind Aassve / @Michael Johansen ) - I took the time this weekend to build a conversion tool that transforms the entire NPU CVS tables and converts it into a FHIR CodeSystem. Do you know if I can publish the codesystem - eg. in a new IG on https://github.com/hl7nordic - and who should I ask doing so?
Jens Villadsen (Nov 15 2021 at 12:30):
It's roughly 28.000 codes
Jens Villadsen (Nov 15 2021 at 12:32):
I'll open source the tool that does it as well
Jens Villadsen (Nov 15 2021 at 19:46):
source is -> https://github.com/trifork/fhir-xsv-translator
Espen Stranger Seland (Nov 16 2021 at 07:18):
The terms are here, I belive it's OK as it's part of an IG.
https://www.ehelse.no/kodeverk/laboratoriekodeverket/_/attachment/download/7be637dd-578e-43e0-9c92-7980cff9c715:2eb46000bd7c4bbebc07c1f3631ef14409f11911/NPU%20-%20_Vilk%C3%A5r%20for%20bruk%20(PDF).pdf
We should also follow up our contact with Helle and @Jostein Ven on how we can help each other.
Jens Villadsen (Nov 16 2021 at 08:31):
@Espen Stranger Seland any good suggestions for the name of the IG?
Jens Villadsen (Nov 16 2021 at 08:32):
"Common Nordic terminology"?
Jens Villadsen (Nov 16 2021 at 08:33):
And do we have other content for it
Espen Stranger Seland (Nov 17 2021 at 07:13):
Good question. What about something that can be a start on a (future) Nordic terminology service? This is, also a focus on mapping and not only common code systems.
Jens Villadsen (Nov 17 2021 at 22:42):
@Espen Stranger Seland well anything as a resource in the IG can be hosted on any FHIR server
Jens Villadsen (Nov 17 2021 at 23:19):
@Grahame Grieve news flash - the IGpublisher aint necessarily totally thrilled building IG's with CodeSystems that have +28.000 entries ... it gets through, but it takes time
Jens Villadsen (Nov 18 2021 at 00:05):
@Espen Stranger Seland and others - NPU is now available here: http://build.fhir.org/ig/hl7nordic/common-nordic-terminology/branches/main/CodeSystem-npu.html
Jens Villadsen (Nov 18 2021 at 00:05):
wait for it in the browser as that site contains ALL of NPU ...
Espen Stranger Seland (Nov 18 2021 at 11:23):
Pretty long... Are there not any display names in "base" NPU like we have in the Norwegian NLK? I believe it's definitions in "display".
Jens Villadsen (Nov 18 2021 at 11:44):
@Espen Stranger Seland I don't see any display names in https://labterm.dk/Download/DownloadTable/NPUdefinitionEN211028.csv (from https://labterm.dk/download/Index1)
Espen Stranger Seland (Nov 18 2021 at 12:21):
Looking at NLK, it's mostly - but not always - the first part, i.e. "U—Acebutolol" before ';'for NPU01001, but that does not work as a rule for NPU01001 and NPU01002. Maybe it works better with the non-discuntinued codes.
Espen Stranger Seland (Nov 18 2021 at 12:25):
Another discussion is how to publish NLK and the Swedish/Danish counterparts, which combines NPU and national codes. As you see here, there are both NPUxxx and NORxxx. I don't think combining them with ValueSet is a good solution, but as a complete OR separate CSs.
Jens Villadsen (Nov 20 2021 at 14:47):
The national codes should be defined as their own code systems
Jens Villadsen (Nov 20 2021 at 14:47):
And then eventually combine them in eg. valuesets
Jens Villadsen (Nov 20 2021 at 14:50):
Anyways - @Daniel Karlsson / @Espen Stranger Seland - I've now added all the definitions (as codesystem - +28.000 entries) and all the lists (as 1259 valuesets). It seems like the amount of data in the codesystem is too much for the IG publication mechanism to finish @Grahame Grieve - which is fair I guess. Next step would be to add the codesystem to a TX server, while the valuesets could remain in the IG and define the national extensions and translations
Rob Hausam (Nov 21 2021 at 08:38):
@Jens Villadsen We've handled CodeSystem resources of this size in tx.fhir.org - for code systems such as ICD10, etc. Including NPU shouldn't be a problem.
Jens Villadsen (Nov 21 2021 at 10:15):
@Rob Hausam sure. The TX server can handle it. But the issue is that the Codesystem currently only is in the IG
Daniel Karlsson (Nov 21 2021 at 13:51):
Jens Villadsen said:
Anyways - Daniel Karlsson / Espen Stranger Seland - I've now added all the definitions (as codesystem - +28.000 entries) and all the lists (as 1259 valuesets). It seems like the amount of data in the codesystem is too much for the IG publication mechanism to finish Grahame Grieve - which is fair I guess. Next step would be to add the codesystem to a TX server, while the valuesets could remain in the IG and define the national extensions and translations
@Jens Villadsen thanks! I will have this confirmed by the NPU steering committee. I do however think we need a discussion about the properties and their semantics. E.g. perhaps we should follow LOINC's example in using STATUS=DEPRECATED rather then Active=false (for the cause of interoperability).
Daniel Karlsson (Nov 21 2021 at 14:16):
Questions... the concept.definition is not used, should concept.definition = short definition and display = short name, trivial name etc. (kortnavn, trivialnamn) in national renderings? Long definition is not in the published CSV, but in the future, there might be other sources than the published CSV which should be looked into.
Jens Villadsen (Nov 21 2021 at 14:58):
@Daniel Karlsson I've moved the short definition from display to definition now.
Jens Villadsen (Nov 21 2021 at 15:01):
Where do I find the short name/trivial name that should be added as display? I'm not familiar with any CSV's that contain the english version of the short name/trivial name.
Jens Villadsen (Nov 21 2021 at 15:02):
I suggest that national renderings using kortnavn trivialnamn should be defined in CodeSystem supplements
Jens Villadsen (Nov 21 2021 at 15:02):
Which can be easily constructed
Rob Hausam (Nov 21 2021 at 15:32):
@Jens Villadsen Right - my point was that we can change that if we (you) would like to do that.
Jens Villadsen (Nov 21 2021 at 15:33):
I definetly would like to change it, but it will only be with the accept of the NPU steering committee, obtained by @Daniel Karlsson
Jens Villadsen (Nov 21 2021 at 15:49):
@Daniel Karlsson can you point to an example where the status field is used in LOINC?
Rob Hausam (Nov 21 2021 at 22:37):
@Jens Villadsen Just to be clear (if it wasn't), my "we can change that" comment was in response to your statement that "the issue is that the Codesystem currently only is in the IG".
Jens Villadsen (Nov 22 2021 at 06:51):
Loud and clear :)
Daniel Karlsson (Nov 22 2021 at 08:29):
Jens Villadsen said:
Daniel Karlsson can you point to an example where the status field is used in LOINC?
https://www.hl7.org/fhir/loinc.html
Log in is needed for the LOINC terminology server.
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=67573-6
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=21176-3
tx.fhir.org:
https://tx.fhir.org/r4/CodeSystem/$lookup?system=http://loinc.org&code=67573-6
https://tx.fhir.org/r4/CodeSystem/$lookup?system=http://loinc.org&code=21176-3
Interesting that the value of "STATUS" property differs between the LOINC server and tx.fhir.org.
Jens Villadsen (Nov 22 2021 at 09:03):
@Daniel Karlsson I don't have a login to LOINC I'm afraid
Jens Villadsen (Nov 22 2021 at 09:04):
Do you know why the STATUS property aint a coded value?
Daniel Karlsson (Nov 22 2021 at 14:21):
Jens Villadsen said:
Do you know why the STATUS property aint a coded value?
Sorry, I don't. In practice it likely is a "coded-like" value.
Jens Villadsen (Nov 22 2021 at 20:11):
@Daniel Karlsson - right. Let me know when the steering committee is ready to let NPU be uploaded
Jens Villadsen (Nov 22 2021 at 23:07):
and the active field is now called 'STATUS' where active == 0 marks it as 'DEPRECATED'
Jens Villadsen (Feb 15 2022 at 07:36):
@Daniel Karlsson rebooting the NPU discussion again ... The NPU excel files which I've based the conversion on don't hold any nice names for the 1259 valuesets that are one of the conversion results (alll can be seen here: https://build.fhir.org/ig/hl7nordic/common-nordic-terminology/artifacts.html). Could you perhaps come with some clues to why the groupings exists without human readable names?
Espen Stranger Seland (Feb 15 2022 at 08:59):
The national versions (DK, SW, NO(=NLK)) have "nice" display names, also for the NPU "core".
Example, there is a "Norsk_bruksnavn" in the first CSV on this page:
https://www.ehelse.no/kodeverk/laboratoriekodeverket
Jens Villadsen (Feb 15 2022 at 09:29):
@Daniel Karlsson correct me of I'm wrong here but the lists (ValueSets) are not downloadable from here: https://www.npu-terminology.org/npu-database/ - only from here: https://www.labterm.dk/download/Index1 - and it seems like the only thing that could actual be a name of a list would be some date?
Jens Villadsen (Feb 15 2022 at 09:30):
@Espen Stranger Seland what key couples the "bruksnavn" to the list?
Espen Stranger Seland (Feb 15 2022 at 14:12):
Kode - Norwegian national codes start with NOR, else NPU. The "clean" NPU codes comes further down (ca line 1543).
As you see, some of the NOR codes are replaced with NPU codes (in the 'Erstattes av' column). So the list also holds history/deprecated/replaced codes.
Jens Villadsen (Feb 15 2022 at 14:33):
@Espen Stranger Seland I think you are misunderstanding my question. Let's try with an example: What would be a good name for the valueset of eg. https://build.fhir.org/ig/hl7nordic/common-nordic-terminology/ValueSet-14060.html
Espen Stranger Seland (Feb 15 2022 at 18:52):
@Jens Villadsen Not sure what these code sets are based on, I would presume only a large CodingSystem.
Jens Villadsen (Feb 15 2022 at 19:49):
@Espen Stranger Seland the 1259 valuesets are based on the npulist definitions listed on https://www.labterm.dk/download/Index1
Espen Stranger Seland (Feb 18 2022 at 15:13):
@Jens Villadsen I see. I have no knowledge about how these groups are used in NLK, just guessing it correlates to one of the colums we have (Komponent, System, Egenskapsart etc.).
Last updated: Apr 12 2022 at 19:14 UTC
