Stream: IG creation
Topic: cdcrec code errors in US Core
Eric Haas (Dec 01 2020 at 05:52):
similar to this stream we are using VSAC for race and ethnicity codes. however there are several errors in examples that have cropped up. The codes and code systems(oids) have not changed:
INFORMATION: Patient/child-example: Patient.extension[1].extension[0].value.ofType(Coding): Code System URI 'http://cts.nlm.nih.gov/fhir/cs/cdcrec' is unknown so the code cannot be validated
ERROR: Patient/child-example: Patient.extension[1].extension[0].value.ofType(Coding): The code provided (http://cts.nlm.nih.gov/fhir/cs/cdcrec#2186-5) is not in the value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837, and a code from this value set is required: CodeSystem uri 'http://cts.nlm.nih.gov/fhir/cs/cdcrec' is unknown (from http://tx.fhir.org/r4)
== /scratch/ig-build-temp-CDMML3/repo/input/examples/patient-example.json ==
INFORMATION: Patient/example: Patient: Validate resource against profile http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
ERROR: Patient/example: Patient.extension[0].extension[3].value.ofType(Coding): The Coding provided (urn:oid:2.16.840.1.113883.6.238#1586-7) is not in the value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.1.11.14914, and a code is required from this value set. (error message = Not in value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.1.11.14914)
ERROR: Patient/example: Patient.extension[0].extension[4].value.ofType(Coding): The Coding provided (urn:oid:2.16.840.1.113883.6.238#2036-2) is not in the value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.1.11.14914, and a code is required from this value set. (error message = Not in value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.1.11.14914)
ERROR: Patient/example: Patient.extension[1].extension[0].value.ofType(Coding): The Coding provided (urn:oid:2.16.840.1.113883.6.238#2135-2) is not in the value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837, and a code is required from this value set. (error message = Not in value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837)
ERROR: Patient/example: Patient.extension[1].extension[1].value.ofType(Coding): The Coding provided (urn:oid:2.16.840.1.113883.6.238#2184-0) is not in the value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.877, and a code is required from this value set. (error message = Not in value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.877)
ERROR: Patient/example: Patient.extension[1].extension[2].value.ofType(Coding): The Coding provided (urn:oid:2.16.840.1.113883.6.238#2148-5) is not in the value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.877, and a code is required from this value set. (error message = Not in value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.877)
== /scratch/ig-build-temp-CDMML3/repo/input/examples/patient-infant-example.json ==
INFORMATION: Patient/infant-example: Patient: Validate resource against profile http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
ERROR: Patient/infant-example: Patient.extension[1].extension[0].value.ofType(Coding): The Coding provided (urn:oid:2.16.840.1.113883.6.238#2186-5) is not in the value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837, and a code is required from this value set. (error message = Not in value set http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837)
note I changed the code system to http://cts.nlm.nih.gov/fhir/cs/cdcrec to see if that was the issue but it was not.
note also this is one of the few time these vsac link actually resolves to an actual valueset for me ( although maybe I logged in during the session)
Grahame Grieve (Dec 01 2020 at 05:57):
did you clear the txCache?
Eric Haas (Dec 01 2020 at 06:17):
using the autobuild...
Eric Haas (Dec 01 2020 at 06:18):
not commiting the cache
Lloyd McKenzie (Dec 01 2020 at 15:38):
You should always commit the cache - saves hammering on the terminology server
Eric Haas (Dec 01 2020 at 18:04):
not building locally
Eric Haas (Dec 01 2020 at 18:04):
only with autobuild see why here
Eric Haas (Dec 01 2020 at 18:36):
cleared cache as described here
Grahame Grieve (Dec 02 2020 at 03:35):
I can't reproduce this. It may have been fixed by the things I already did, but... why? Anyhow, lets see if it continues to happen after the next release
Grahame Grieve (Dec 02 2020 at 03:43):
oh turns out I can now that I have updated the US core source. (Really though I had...)
Grahame Grieve (Dec 02 2020 at 03:43):
but I agree with the validator on this one. I think you have the wrong system URI
Grahame Grieve (Dec 02 2020 at 03:43):
given what the value set says
Eric Haas (Dec 02 2020 at 16:17):
@Gay Dolin @Brett Marquard If the system has changed, then I don't think we should use VSAC, they are not the same. The OID has been used by C-CDA and since the beginning in US Core. Why did VSAC change it to <code>http://cts.nlm.nih.gov/fhir/cs/cdcrec</code>???
Brett Marquard (Dec 02 2020 at 17:22):
I am confused, the value set still includes the code system OID 2.16.840.1.114222.4.11.877 - see https://vsac.nlm.nih.gov/valueset/2.16.840.1.114222.4.11.877/expansion/Latest
Eric Haas (Dec 02 2020 at 17:41):
that is the HTML representation the downloadable fhir artifact does not.
Eric Haas (Dec 02 2020 at 17:44):
https://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837/$expand
which I assume is what the validator is using.
<?xml version="1.0" encoding="UTF-8"?>
<ValueSet xmlns="http://hl7.org/fhir">
<id value="2.16.840.1.114222.4.11.837"/>
<meta>
<versionId value="1"/>
<lastUpdated value="2012-10-25T12:28:31.000-04:00"/>
</meta>
<url value="http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837"/>
<version value="20121025"/>
<name value="Ethnicity"/>
<status value="active"/>
<date value="2012-10-25T12:28:31-04:00"/>
<publisher value="CDC NCHS"/>
<compose>
<include>
<system value="http://cts.nlm.nih.gov/fhir/cs/cdcrec"/> <!--- NOT THE OID! -->
<concept>
<code value="2135-2"/>
<display value="Hispanic or Latino"/>
</concept>
<concept>
<code value="2186-5"/>
<display value="Not Hispanic or Latino"/>
</concept>
</include>
</compose>
</ValueSet>
Eric Haas (Dec 02 2020 at 17:57):
also unable to download 2.16.840.1.114222.4.11.877 expansion directly assuming is intensional so I assume that is why using the vsac package for now. Maybe that is what the validator is basing this upon? @Grahame Grieve
Eric Haas (Dec 02 2020 at 18:05):
In the vsac package I see it as ;
resourceType: ValueSet
id: 2.16.840.1.114222.4.11.877
meta:
source: https://vsac.nlm.nih.gov/valueset/2.16.840.1.114222.4.11.877/expansion
url: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.877
version: C-CDA R2.1 2020-07-13
name: DetailedEthnicity
title: Detailed Ethnicity
...
compose:
include:
- system: http://terminology.hl7.org/CodeSystem/v2-0005 #<<<<< not an OID
version: "1.2"
concept:
- code: 2137-8
display: Spaniard
- code: 2138-6
...
Brett Marquard (Dec 02 2020 at 18:19):
Fun.
Eric Haas (Dec 02 2020 at 18:44):
(deleted)
Grahame Grieve (Dec 02 2020 at 19:44):
I can't find my APIKey and I can't find anywhere in the NLM web site that lets me get another one. I tried logging out but that didn't even work
Brett Marquard (Dec 02 2020 at 19:44):
I wish I used twitter - "FHIR Creator can't even find NLM key"
Brett Marquard (Dec 02 2020 at 19:45):
took me about 30 mins, I would tell you, but it will probably take me another 30 to find
Brett Marquard (Dec 02 2020 at 19:45):
faster this time -- log in here: https://uts.nlm.nih.gov/uts/
Brett Marquard (Dec 02 2020 at 19:46):
Grahame Grieve (Dec 02 2020 at 19:46):
found it. google knows, even if NLM don't
Grahame Grieve (Dec 02 2020 at 19:57):
this is the source that the publisher uses internally:
https://github.com/FHIR/packages/blob/master/packages/us.nlm.vsac/package/ValueSet-2.16.840.1.114222.4.11.837.json
https://github.com/FHIR/packages/blob/master/packages/us.nlm.vsac/package/ValueSet-2.16.840.1.114222.4.11.877.json
Eric Haas (Feb 26 2021 at 00:31):
@Grahame Grieve @Gay Dolin OK so here is the issue:
US Core and CCDA use the code system oid 2.16.840.1.113883.6.238 as the URI for the omb race valueset
when we try to use VSAC the valueset in the package uses the uri: http://cts.nlm.nih.gov/fhir/cs/cdcrec as I pointed out above. It does not use an oid. If we use VSAC then My assumption is that the instance validation will fail if the OID is 2.16.840.1.113883.6.238 is used instead of http://cts.nlm.nih.gov/fhir/cs/cdcrec because the VSAC package definition will be used - is that correct?
Also we are investigating how to change VSAC to use the same code system as both CCDA and FHIR. Would providing the OID as an alternative identifier in the codesystem change the validation. ( I am assuming no)
Last updated: Apr 12 2022 at 19:14 UTC
