FHIR Chat · Terminology search

Hi -- I am new to the list, so please forgive any flubs in my message. Is there a mechanism to search for any item across all value sets matching all or part of a search string? All the functions I've found in the documentation (and all the tools I've found online) seem to require first identifying a specific code system and/or a specific value set. For example, let's say I want to find all values that start with "pulse" across all available value sets, regardless of code system. Is that possible in the FHIR APIs? Or... is there a resource (other than "Google") that enables such a search against an online FHIR terminology server (or the FHIR standard itself)? I am aware of tools that specifically search a single code system (e.g. SNOMED-CT or LOINC) -- but I'm looking for the capability to search across all value sets (either for that server, or all example value sets in the FHIR standard), regardless of underlying code systems.

Thanks!

Jon

René Spronk (Aug 11 2020 at 17:15):

A terminology that has been designed according to 'best practices' will have meaningless mnemonics as codes, as such a search method that's based on dealing with them like strings mostly doesn't make a lot of sense. Other than introducing a new search parameter on your FHIR server (or: on your terminology server) I'm not aware of a way to deal with the kind of search you're looking for.

Jon Handler (Aug 11 2020 at 17:33):

Thanks René! I should have asked about being able to search on the textual description of a value. So, if I want to find every code across every value set (regardless of code system) associated with a textual description that starts with (or contains) "pulse" -- is that possible?

Grahame Grieve (Aug 12 2020 at 01:24):

you can search for text using a value set, and the value set http://hl7.org/fhir/ValueSet/@all covers all value sets

Grahame Grieve (Aug 12 2020 at 01:24):

I'm not sure how many servers support that

Jon Handler (Aug 12 2020 at 02:56):

Wow -- thanks so much Graham! It doesn't appear that most servers support it, but really good to have gotten your guidance on how it would be done. I might not be doing the query right. Just trying to be able to search the descriptions of all values across all value sets, like, "show me all values across all value sets with a description that starts with "penicillin". I assumed http://hl7.org/fhir/ValueSet/@all ?description:text=penicillin might do it, but I'm getting errors on every server I've tried. <sigh> It's tough to be a newbie at something. :)

Grahame Grieve (Aug 12 2020 at 02:56):

should work on tx.fhir.org

Jon Handler (Aug 12 2020 at 04:04):

Thanks Grahame -- I am probably doing something wrong, but I can't make it work on tx.fhir.org. I get an error that @ is an invalid character.

Jon

Grahame Grieve (Aug 12 2020 at 04:37):

I'll add it to my list of things to look into

René Spronk (Aug 12 2020 at 05:47):

@Jon Handler yes, one can search the text associated with a code, by using the :text modifier. See http://build.fhir.org/search.html#token , example GET [base]/Observation?code:text=pulse

René Spronk (Aug 12 2020 at 06:08):

Ah. Your search is 'just' a search for codes (on a terminology server) that have a certain text in their description. That's addressed by Grahame's comment.

Grahame Grieve (Aug 18 2020 at 04:37):

did you try escaping the @?

Grahame Grieve (Aug 18 2020 at 04:42):

http://local.fhir.org:960/r4/ValueSet/$expand?text=text&url=http://hl7.org/fhir/ValueSet/@all = The code System "http://hl7.org/fhir/ValueSet/@all" has a grammar, and cannot be enumerated directly

Corey Smith (Sep 11 2020 at 14:17):

Hello all. I'm not sure if this is the right place for this. I'm using the validator to convert QuestionnaireResponse to a bundle of conditions and observations using a structuremap and it appears that tx.fhir.org is not responding. I'm getting this error: C:\fhir\sdohcc_gravity-master\sdohcc_gravity-master\HVS-structureMap>java -jar org.hl7.fhir.validator.jar source/SDOHCC_QuestionnaireResponse_HungerVitalSign_Example_1.json -transform http://hl7.org/fhir/us/sdoh-cc/StructureMap/SDOHCC-StructureMap-HungerVitalSignMapper-1 -version 4.0.1 -ig logical/ -ig map/ -log test.txt -output output/SDOHCC_Bundle_HungerVitalSign_Example_1.json
FHIR Validation tool Version 5.0.7-SNAPSHOT (Git# 6bc790d98b04). Built 2020-06-07T08:35:37.25+10:00 (96 days old)
Detected Java version: 1.8.0_201 from C:\Program Files\Java\jre1.8.0_201 on amd64 (64bit). 3616MB available
Arguments: source/SDOHCC_QuestionnaireResponse_HungerVitalSign_Example_1.json -transform http://hl7.org/fhir/us/sdoh-cc/StructureMap/SDOHCC-StructureMap-HungerVitalSignMapper-1 -version 4.0.1 -ig logical/ -ig map/ -log test.txt -output output/SDOHCC_Bundle_HungerVitalSign_Example_1.json
Directories: Current = C:\fhir\sdohcc_gravity-master\sdohcc_gravity-master\HVS-structureMap, Package Cache = C:\Users\corsmith\.fhir\packages
.. FHIR Version 4.0, definitions from hl7.fhir.r4.core#4.0.1
.. connect to tx server @ http://tx.fhir.org
Exception in thread "main" org.hl7.fhir.exceptions.FHIRException: Unable to connect to terminology server. Use parameter '-tx n/a' tun run without using terminology services to validate LOINC, SNOMED, ICD-X etc. Error = Error sending Http Request: Read timed out
at org.hl7.fhir.r5.context.SimpleWorkerContext.connectToTSServer(SimpleWorkerContext.java:258)
at org.hl7.fhir.validation.ValidationEngine.connectToTSServer(ValidationEngine.java:718)
at org.hl7.fhir.validation.ValidationEngine.setTerminologyServer(ValidationEngine.java:309)
at org.hl7.fhir.validation.ValidationEngine.<init>(ValidationEngine.java:339)
at org.hl7.fhir.validation.cli.services.ValidationService.getValidator(ValidationService.java:180)
at org.hl7.fhir.validation.Validator.main(Validator.java:175)
Caused by: org.hl7.fhir.r5.utils.client.EFhirClientException: Error sending Http Request: Read timed out
at org.hl7.fhir.r5.utils.client.ClientUtils.sendRequest(ClientUtils.java:326)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:235)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:219)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:210)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueGetResourceRequest(ClientUtils.java:146)
at org.hl7.fhir.r5.utils.client.FHIRToolingClient.getCapabilitiesStatementQuick(FHIRToolingClient.java:181)
at org.hl7.fhir.convertors.txClient.TerminologyClientR5.getCapabilitiesStatementQuick(TerminologyClientR5.java:94)
at org.hl7.fhir.r5.context.SimpleWorkerContext.connectToTSServer(SimpleWorkerContext.java:256)
... 5 more
Caused by: java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.socketRead(Unknown Source)
at java.net.SocketInputStream.read(Unknown Source)
at java.net.SocketInputStream.read(Unknown Source)
at org.apache.http.impl.io.AbstractSessionInputBuffer.fillBuffer(AbstractSessionInputBuffer.java:161)
at org.apache.http.impl.io.SocketInputBuffer.fillBuffer(SocketInputBuffer.java:82)
at org.apache.http.impl.io.AbstractSessionInputBuffer.readLine(AbstractSessionInputBuffer.java:276)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:138)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:56)
at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:259)