FHIR Chat · CodeableConcept request

Stream: clinFHIR

Topic: CodeableConcept request

Bob Milius (Mar 16 2017 at 15:15):

I have another request/question, this time re CodeableConcept entries. Right now it looks like I can either enter something that is looked up and expanded, or the text value if not coded. I'd like to be able to enter my own coding. From what I can tell a CodeableConcept should allow me to add something like this for the Sequence.referenceSeq.referenceSeqId:

<coding>
    <system value="http://www.ebi.ac.uk/ipd/imgt/hla/"/>
    <version value="3.23"/>
    <code value="HLA00001"/>
 </coding>
 <text value="HLA-A*01:01:01:01"/>

Is there any way of entering this manually in clinFHIR?

David Hay (Mar 16 2017 at 16:09):

Hi Bob - what you need to do is actually create a profile on the resource you're building that binds the specific element to the ValueSet that, in turn, references that CodeSystem (in the example that would be the CodeSystem than has the system identifier of http://www.ebi.ac.uk/ipd/imgt/hla/
I've gone some way towards supporting that in CF - but it does need a terminology server that does understand that system. Do you know if there are any available?

If not, then there are alternatives that we can use to 'mock it up' for the purposes of example. Basically what we do is to create a CodeSystem resource that has some of the concepts in it (CF does have such a builder), then create the profile referencing that CodeSystem (via a ValueSet).

If you can either locate an existing ValueSet, or give me some sample data I'll have a go at it... (I'll also need to know what resource & element you are modifying)

Bob Milius (Mar 16 2017 at 16:54):

Thanks, David, for replying so quickly. @Joel Schneider is working on a terminology service for HLA nomenclature, but unfortunately there aren't any for DNA reference sequences. http://www.ebi.ac.uk/ipd/imgt/hla/ is one source for HLA sequences, but there are many others (e.g., RefSeq, genome assemblies, etc). There a long list of genetic authorities in http://build.fhir.org/terminologies-systems.html (scroll down to Code Systems for Genetics). Perhaps our work group (Clinical Genomics) needs to spend some effort working with these groups to develop them. In the meantime, I've been creating resource instances by hand with examples like the above (for this and other places in the ClinicalGenomics 'owned' resource and profiles.

The ValueSet for all DNA reference sequences would be huge. For HLA, there are just over 16000 alleles, so creating a ValueSet for that might be manageable, but I'm not sure about maintaining it (it gets updated every 3 months)

David Hay (Mar 16 2017 at 17:09):

Yeah - creating a sample would be reasonably straightforward, but doing it for real will be much harder!

Joel Schneider (Mar 16 2017 at 23:28):

I've got a relevant CodeSystem and ValueSet loaded into our STU3 HAPI test server, but am unable to add a server in clinFHIR because the Url field in the _Add new server_ dialog is greyed out..

Joel Schneider (Mar 16 2017 at 23:36):

Incidentally, a bundle containing that (preliminary) HLA Nomenclature CodeSystem and ValueSet is also available for download, here: https://s3.amazonaws.com/nmdp-fhir-terminology/fhir-imgt-hla-terminology-bundle.xml

So, it would be possible to load that bundle into another terminology server.

It presently uses a different code system url, and doesn't recognize HLA accession numbers as alternate designations for HLA allele names. However, for example, sending an application/fhir+json POST request such as the following to http://fhirtest.b12x.org/baseDstu3/ValueSet/$validate-code should succeed:

{
    "resourceType" : "Parameters",
    "parameter" : [
        {
            "name" : "url",
            "valueUri" : "http://hla-who.b12x.org/value-set/hla-who-nomenclature"
        },
        {
            "name" : "code",
            "valueCode" : "HLA-A*01:01:01:01"
        },
        {
            "name" : "system",
            "valueUri" : "http://hla-who.b12x.org/hla-who-nomenclature"
        },
        {
            "name" : "version",
            "valueString" : "3.26.0"
        }
    ]
}

David Hay (Mar 17 2017 at 23:28):

Hi Joel - did you press the 'check server' button? when adding a new server it required a valid conformance (CapabilityStatement) resource to be returned... (Also note that it requires a trailing '/' in the url, I need to fix that)...

Joel Schneider (Mar 18 2017 at 02:16):

I pressed all the checkboxes, but it still didn't enable editing of the Url.
Screen-Shot-2017-03-17-at-9.07.04-PM.png

Joel Schneider (Mar 18 2017 at 02:28):

Aha. At the suggestion of another user, I tried typing into the Url field and was able to enter data there.

The greyed-out text made me think the Url field was disabled. If it could be changed to an italic font and/or the text could be made selectable, I think that would give a visual cue indicating the field is editable.

David Hay (Mar 18 2017 at 03:43):

Ah - that's the standard 'placeholder' attribute font. Maybe replacing the url with a message like 'enter url here' would be more intuitive!

Jayashree Surnar (Mar 21 2017 at 05:33):

in scenariobuilder codeable conpets for Questionnaire and questionnaireResponse also not working. for server Public HAPI STU3 server
unable to choose the dataTypes for some of the fields.

David Hay (Mar 21 2017 at 20:40):

which datatypes?

Jayashree Surnar (Mar 22 2017 at 04:00):

hello David Hay , Q (Questionnaire.item.option.valueCoding), and QR (QuestionnaireResponse.item.answer.valueCoding), previoulsly these are not working, but now working fine.

sometimes working fine, sometimes not working. don't know why?

Last updated: Apr 12 2022 at 19:14 UTC

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FHIR Chat · CodeableConcept request · clinFHIR