Stream: IG creation
Topic: SNOMED Errors in qa.html
Saul Kravitz (Oct 13 2021 at 19:18):
Unable to find code 1156506007 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/**20210301**); The code "1156506007" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1156506007) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1156506007'
Unable to find code 1156530009 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/**20210301**); The code "1156530009" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1156530009) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1156530009'
Unable to find code 1149099005 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210301); The code "1149099005" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1149099005) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1149099005'
These codes are in the published version July 2021...should they be available? Looks like the terminology server is working from the March release....
Lloyd McKenzie (Oct 13 2021 at 20:22):
@Rob Hausam
Rob Hausam (Oct 13 2021 at 20:48):
I'm going to look at it soon (within the next hour or so). Had to check something else first. @Saul Kravitz @Lloyd McKenzie
Rob Hausam (Oct 14 2021 at 13:13):
@Saul Kravitz As with the LOINC issue, it took me a while to get to this, but all three of these SNOMED CT codes do validate correctly on tx.fhir.org using both the default version of SNOMED CT (with no edition or version specified) and also the US edition specified (the version portion of the string seems to be being ignored for some reason!). The version of the US edition that is loaded on the server is 20210901 (and only one version of the US edition is loaded, whereas there are multiple versions loaded for the International edition). But the bottom line is that all of these codes seem to be validating correctly directly on the terminology server, so again I suspect that what you are seeing may be an issue with your txcache?
Saul Kravitz (Oct 14 2021 at 14:53):
@Rob Hausam Here is a code that is in the July build that the official IG build process complains about:
https://browser.ihtsdotools.org/?perspective=full&conceptId1=1149099005&edition=MAIN/2021-07-31&release=&languages=en
Here are all of the terminology woes from http://build.fhir.org/ig/HL7/fhir-mCODE-ig/branches//splitlocationqualifier/qa.html
Terminology_PassThrough_TX_Message
fsh-generated/resources/Bundle-mcode-patient-bundle-jenny-m.json The code "97509-4" is not valid in the system http://loinc.org; The code provided (http://loinc.org#97509-4) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://loinc.org#97509-4'
fsh-generated/resources/Bundle-mcode-patient-bundle-jenny-m.json The code "97509-4" is not valid in the system http://loinc.org; The code provided (http://loinc.org#97509-4) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://loinc.org#97509-4'
fsh-generated/resources/Bundle-mcode-patient-bundle-jenny-m.json Unable to find code 1156506007 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210301); The code "1156506007" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1156506007) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1156506007'
fsh-generated/resources/Bundle-mcode-patient-bundle-jenny-m.json Unable to find code 1156530009 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210301); The code "1156530009" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1156530009) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1156530009'
fsh-generated/resources/Bundle-mcode-patient-bundle-jenny-m.json Unable to find code 1156506007 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210301); The code "1156506007" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1156506007) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1156506007'
fsh-generated/resources/Bundle-mcode-patient-bundle-jenny-m.json Unable to find code 1156530009 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210301); The code "1156530009" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1156530009) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1156530009'
fsh-generated/resources/Observation-binet-stage-group-A.json Unable to find code 1149099005 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210301); The code "1149099005" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1149099005) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1149099005'
fsh-generated/resources/Observation-cancer-disease-status-improved.json The code "97509-4" is not valid in the system http://loinc.org; The code provided (http://loinc.org#97509-4) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://loinc.org#97509-4'
fsh-generated/resources/Observation-cancer-disease-status-jenny-m.json The code "97509-4" is not valid in the system http://loinc.org; The code provided (http://loinc.org#97509-4) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://loinc.org#97509-4'
fsh-generated/resources/Procedure-radiotherapy-treatment-summary-chest-wall-jenny-m.json Unable to find code 1156506007 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210301); The code "1156506007" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1156506007) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1156506007'
fsh-generated/resources/Procedure-radiotherapy-treatment-summary-chest-wall-jenny-m.json Unable to find code 1156530009 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210301); The code "1156530009" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1156530009) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1156530009'
fsh-generated/resources/StructureDefinition-mcode-cancer-disease-status.json The code "97509-4" is not valid in the system http://loinc.org; The code provided (http://loinc.org#97509-4) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://loinc.org#97509-4'
fsh-generated/resources/StructureDefinition-mcode-cancer-disease-status.json
Rob Hausam (Oct 18 2021 at 20:52):
@Saul Kravitz When I build the IG locally I'm not seeing the same errors:. The SNOMED CT errors that I'm getting are like:
Bundle.entry[6].resource.ofType(Procedure).extension[3].extension[1].value.ofType(CodeableConcept).coding[0] (l612/c22) error
Unable to find code 1162782007 in http://snomed.info/sct (version http://snomed.info/sct/731000124108/version/20210901); The code "1162782007" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#1162782007) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#1162782007'
and I find this related line in FSH which may be the source (or one of them - there are multiple instances):
input/fsh/VS_Radiotherapy.fsh:* SCT#1162782007 "Three dimensional external beam radiation therapy (procedure)"
The code '1162782007' is not valid in either the current SNOMED CT International or US editions. The closest related code that I've found is:
118641002 |Three dimensional treatment planning for external beam radiation therapy (procedure)|
Do you know what the correct code should be?
Saul Kravitz (Oct 18 2021 at 21:11):
@Rob Hausam
It looks like the publisher is now running off of version/20210901 (the error messages above indicate verson/20210301), which should resolve all of the issues for codes that are published (like the ones I noted -- 1156506007, 1156530009, and 1149099005.
re SCT#1162782007 "Three dimensional external beam radiation therapy... yes, I got a bit a head of myself... That will be released in January....
thx...
Rob Hausam (Oct 18 2021 at 21:22):
Yes, that seems to be the case. So looks like things are going in the right direction. :)
Last updated: Apr 12 2022 at 19:14 UTC
