Stream: terminology
Topic: code system URI determination ambiguity
Avi Kelman (Feb 14 2020 at 22:57):
Hi all, I need clarification about the instructions for determining which URI to use for a code system.
https://www.hl7.org/fhir/terminologies-systems.html provides an order of operations for determining the correct URI to use for a code system, but in some cases I find that there's ambiguity, because the instruction says to check the OID Registry first, but it doesn't specify which information is right to use from there and when to use it.
Using NCBITaxon as an example with immediate relevance, the OID registry has a Comp OID value for NCBI and status "Pending". Downloading the full External Coding System OIDs Excel Report, I see "http://www.ncbi.nlm.nih.gov/Taxonomy/" in the _description_ column but not in the _URL_ column. I also add that the terminologies-systems page has on it a note saying that the UMLS pattern may be the right choice according to one interpretation of "Until these code systems are registered" and "Pending".
So should the system URI be urn:oid:<yada>, http://www.ncbi.nlm.nih.gov/Taxonomy/, or http://www.nlm.nih.gov/research/umls/ncbi?
Does a status of "Pending" alter the instruction to refer to the OID Registry or how to use the information? Does a URI found outside of its designated column count?
Michael Lawley (Feb 15 2020 at 01:11):
I believe NCBITaxon has an OWL form which might also indicate an appropriate in-use URI? Something like http://purl.obolibrary.org/obo/ncbitaxon.owl
Avi Kelman (Feb 17 2020 at 04:04):
That could also be good, but https://www.hl7.org/fhir/terminologies-systems.html is explicit about working through the list of options in order, and the OID Registry is #1 on the list. It just doesn't say what to use from the registry.
Robert McClure (Feb 17 2020 at 18:00):
@Avi Kelman Your general question of "what identifier in FHIR do I use for externally defined code system X" is something the HL7 terminology Authority HTA is responsible for. They have been a bit bombarded with needs/requests but the process is to be found there once finalized. It would move things along if you identified the need to them and provided what you know wrt the code system(s) per the list here. If you need NCBITaxon start with that one when you ask for guidance. By that phrase do you mean specifically the owl representation noted here? if so, I suspect that literal url is the identifier. There is no OID for that specific ontology at the HL7 OID registry.
Avi Kelman (Feb 17 2020 at 18:56):
Your general question of "what identifier in FHIR do I use for externally defined code system X"
Ah. That's not my question. I guess I failed to clarify my needs, so let me try restating it differently. My question rephrased is "What is the unambiguous ordered sequence of observations that expert members have decided one should make to fulfill the ambiguous directive phrase 'working through' at the top of https://www.hl7.org/fhir/terminologies-systems.html in relation to the given ordered list of sources one should inspect for systems that have not been validated by the terminology authority?" Is the answer to just pick whatever I want willy nilly from the first source that satisfies finding anything anywhere inside?
If you need NCBITaxon start with that one when you ask for guidance.
I know that I have mentioned one specific system, but I would greatly prefer an answer that addresses the essence of the issue rather than just one example of its manifestation.
Avi Kelman (Feb 17 2020 at 19:19):
There is no OID for that specific ontology at the HL7 OID registry.
There is one "pending" according to https://www.hl7.org/oid/index.cfm?Comp_OID=2.16.840.1.113883.6.205
Michael Lawley (Feb 17 2020 at 21:59):
Since Jan 2005 no less
Avi Kelman (Jul 07 2020 at 20:52):
Following up on this because we still don't have any answer.
NCIT references 2.16.840.1.113883.3.26.1.1 (https://wiki.nci.nih.gov/pages/viewpage.action?pageId=7472532) but then the OID registry doesn't even have a field for entering reference URIs and https://www.hl7.org/fhir/terminologies-systems.html says to use URI fields and does not say to use OIDs. This is all very confusing for something that by rights should be very simple.
Last updated: Apr 12 2022 at 19:14 UTC
