STU 3 Ballot
TerminologyThis page is part of the FHIR Specification (v1.6.0: STU 3 Ballot 4). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions 
. Page versions: R5 R4B R4 R3 R2
| FHIR Infrastructure Work Group | Maturity Level: N/A | Ballot Status: STU 3 |
This specification includes support for the provision of a terminology service - that is, a service that lets healthcare applications make use of codes and value sets without having to become experts in the fine details of the code system, value set and concept map resources, and the underlying code systems and terminological principles. A server that supports all the functionality described here can be described as a "FHIR Terminology Service", and SHALL conform to the terminology server conformance statement. Note that servers can declare that they provide terminology services in their conformance statement:
<Conformance xmlns="http://hl7.org/fhir"> <!-- snip --> <instantiates value="http://hl7.org/fhir/Conformance/terminology-server"/> <!-- snip --> </Conformance>
Generally, SSL SHOULD be used for all production health care data exchange. Even though terminology servers do not generally handle patient information directly, hackers may still be able to infer information about patients by observing the codes and concepts that the terminology service is asked about, so encryption is still recommended.
A terminology server may choose not to authenticate the clients/users in any fashion, but can do so in order to limit or account for usage. For a value set maintenance server that allows terminologies to be edited, some form of authorization and/or authentication would be appropriate. This specification does not require any particular approach to security.
A FHIR terminology service is simply a set of functions built on the definitions provided by a collection of CodeSystem, ValueSet and ConceptMap resources, with additional inherently known terminologies providing support.
The terminology service builds on the basic principles for using terminologies in FHIR. Implementers should be familiar with:
In addition, implementers should be familiar with the operations framework. Further useful information about terminologies may be found in:
. Note: "namespace" is used differently here from the way it is used by IHTSDO (see discussion here)In order to be used with a value set, code systems and their content must be defined somewhere. They can be defined explicitly using the code system resource, or they can be defined elsewhere, and then used in a value set by quoting the correct system url. The FHIR specification defines a set of namespaces for commonly encountered code systems, and defines how some work with FHIR (e.g. SNOMED CT, LOINC, RxNorm). These code systems are often large, and have many internally defined properties that are part of their formal definitions. The code systems resource is not an appropriate way to distribute the contents of these code systems; the standard FHIR code system resource simply represents the properties of the code system. Instead, these terminologies provide their own distribution formats, and it is assumed that the content of these code systems are externally known to the terminology server.
Most useful terminology servers will make one or more of these external code systems available for use within the value sets that they manage. The list of additional terminologies that a terminology server supports beyond those defined in its value sets is published to clients by referencing code system resources in the server's Conformance Statement.
{
"resourceType" : "Conformance",
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/conformance-supported-system",
"valueUri" : "http://loinc.org"
}]
}
This extension is added to the root Conformance Statement.
When a terminology server exposes an external code system, it makes a set of services available internally that serve the operational interfaces below. The internal server depends on the following logical information for a terminology:
The FHIR specification itself defines these things for common terminologies (including SNOMED CT, LOINC, RxNorm), and provides the CodeSysten infrastructure for supporting typical relatively simple small code systems.
Implementers Note: Implementers interested in working with existing published terminologies for which the CodeSystem infrastructure is not suitable should discuss their needs with HL7 to get the list above extended.
Note: A terminology service may choose to expose additional external code system specific related functionality such as summation, or structured search, but these services are outside the scope of the FHIR terminology service.
For some of the operations below, it can be useful to perform them across all value sets known to the system. For example, $expand using a text filter, and searching all value sets at once. A special value set is defined that means "all value sets known to the server":
http://hl7.org/fhir/ValueSet/@all
Technically, this value set automatically imports all the existing value sets on the server. Note that this URL has no fixed meaning - its interpretation is server specific. This URL can only be used as a parameter to the operations described on this page.
The terminology service uses the code systems and value set resources defined on the system - both the implicit ones associated with the external code systems and those explicitly available at the /CodeSystem and /ValueSet endpoints - to serve the operational interface defined below. As code systems and value sets are created, updated or deleted, the outcomes of the operational services change. A terminology server should validate incoming resources, and ensure integrity of the terminology services. Typically, servers provide a test and production environment, but there is no explicit notion of this in the interface itself.
A value set describes a set of rules for what codes or concepts are considered to be in the value set. These rules might be simple (e.g. a direct list of codes from a specified version of a code system), or they might be quite complex (e.g. all codes with a particular property from an unspecified version of a code system).
A FHIR enabled application can simply ask a terminology server to figure out all the details, and return it a list of the current codes in the value set. This is known as "expanding" the valueset. As a summary, the client passes the server the following information:
The server returns a value set that contains the current list of codes that meet the filter criteria (or an OperationOutcome with an error if the expansion fails). Note that some value sets expand to many thousands of codes, or even an infinite number, and for these, the server SHOULD return an error code too-costly. In these cases the client can try again with a more specific text filter to reduce the number of codes returned - this may result in a valid expansion.
For further information, consult the definition of the operation.
The $expand operation has support for paging - for a client to retrieve a big expansion in a set of partial views, in order to present the most optimal user experience. The client specifies both an offset and a count - how many codes per page, and where in the sequence to start. The return expansion specifies the number of concepts in the expansion, and the offset at which this partial view starts. Note that all expansions SHOULD include the total code count, but the offset element SHALL only exist when paging is being used. Expansions that are hierarchical trees of concepts are not subject to paging and the server simply returns the entire expansion.
Some example uses for the expansion operation:
Examples
Expanding a value set that is already registered on the server as "23", with a text filter of "abdo":
GET [base]/ValueSet/23/$expand?filter=abdo
Expanding a value set that is specified by the client (using JSON):
POST [base]/ValueSet/23/$expand
[other headers]
{
"resourceType" : "Parameters",
"parameter" : [
{
"name" : "valueSet",
"resource" : {
"resourceType" : "ValueSet",
[value set details]
}
}
]
}
The server responds with a value set (this example in XML):
HTTP/1.1 200 OK
[other headers]
<ValueSet xmlns="http://hl7.org/fhir">
<!-- the server SHOULD populate the id with a newly created UUID
so clients can easily track a particular expansion -->
<id value="43770626-f685-4ba8-8d66-fb63e674c467"/>
<!-- no need for meta, though it is allowed for security labels, profiles -->
<!-- other value set details -->
<expansion>
<!-- when expanded -->
<timestamp value="20141203T08:50:00+11:00"/>
<contains>
<!-- expansion contents -->
</contains>
</expansion>
</ValueSet>
A system can ask a terminology server to return a set of information about a particular system/code combination using the lookup operation. The server returns information for both display and processing purposes. The client passes the server the following information:
The server returns some or all of the following information:
The recommended display for the code is a text representation of the code that the terminology server recommends as the default choice to show to the user, though a client may choose out of the other designations if it has reason to.
If the client does not ask for any particular properties to be returned, it is at the discretion of the server to decide which properties to return.
Examples
Looking up a code in a code system:
GET [base]/CodeSystem/loinc/$lookup?code=1963-8
Note that the logical id "loinc" is not a reliable identifer across systems; each server assigns logical ids to code system resources however it sees fit. A more reliable query is this:
GET [base]/CodeSystem/$lookup?system=http://loinc.org&code=1963-8&property=code&property=display&property=designations
Lookup the code system using a Coding (this example in XML):
POST [base]/CodeSystem/$lookup
[other headers]
<Parameters xmlns="http://hl7.org/fhir">
<parameter>
<name value="coding"/>
<valueCoding>
<system value="http://loinc.org"/>
<code value="1963-8"/>
</valueCoding>
</parameter>
</Parameters>
The server responds with a set of information (JSON this time):
HTTP/1.1 200 OK
[other headers]
{
"resourceType" : "Parameters",
"parameter" : [
{
"name" : "name",
"valueString" : "LOINC"
},
{
"name" : "version",
"valueString" : "2.48"
},
{
"name" : "display",
"valueString" : "Bicarbonate [Moles/volume] in Serum"
},
{
"name" : "abstract",
"valueString" : "false"
}
]
}
The following properties are defined:
| Name | Usage |
| system | The name of the code ssystem |
| version | The version of the code system used for the look up operation |
| display | The recommended display for the code, if one is known |
| definition | The definition for the code |
| designation | Other designations for the code |
| lang.X | Designations in language X (where X is an IETF Language code, see BCP-47 |
| parent | Parent codes for this code (for code systems with a defined heirarchy) |
| child | child codes of this code (for code systems with a defined heirarchy) |
In addition, any property codes defined by the code system (CodeSysem.property.code) can be used.
One way to determine whether a code is in a value set is to expand the value set (as described above), and then look at the returned codes to see if the code is in the expansion. However this is not an efficient way to test whether a code is valid, and for some value sets (e.g. with infinite number of members), it cannot work. Instead, a FHIR terminology server provides a "validate-code" operation. The client passes the server the following information:
The server returns a true/false indicating whether the code/concept is valid, and a list of errors and warnings associated with it. The server should also return an appropriate display for the concept for use in a UI context.
Note that if the server is passed a CodeableConcept, the server is able to check whether any of the codes are valid against the value set, and also check whether multiple codings are allowed and/or the codings provided are consistent with each other.
Every code system has an implicit value set that is "all the concepts defined
in the code system" (CodeSystem.valueSet). For some code systems, these value set URIs are defined
in advance (e.g. for LOINC, it is http://loinc.org/vs).
However for some code systems, they are not known. Clients can refer to these implicit
value sets by providing the URI for the code system itself.
Examples
Simple validation of a code/system against a known value set:
GET [base]/ValueSet/23/$validate-code?system=http://loinc.org&code=1963-8&display=test
Validate a CodeableConcept against a client specified value set (this example in JSON):
POST [base]/ValueSet/$validate-code
[other headers]
{
"ResourceType" : "Parameters",
"parameter" : [
{
"name" : "coding",
"valueCodeableConcept" : {
"coding" : {
"system" : "http://loinc.org",
"code" : "1963-8",
"display" : "test"
}
}
},
{
"name" : "valueSet",
"resource": {
"resourceType" : "ValueSet",
[etc]
}
}
]
}
The server responds with validation information (JSON this time):
HTTP/1.1 200 OK
[other headers]
{
"resourceType" : "Parameters",
"parameter" : [
{
"name" : "result",
"valueBoolean" : "false"
},
{
"name" : "message",
"valueString" : "The display \"test\" is incorrect"
},
{
"name" : "display",
"valueString" : "Bicarbonate [Moles/volume] in Serum"
}
]
}
To test whether code A subsumes code B, perform a $subsumes operation. The client passes the server the following information:
If the client passes Codings, it is allowed to use system values that are different from the system in which subsumption testing is to be performed. In this case, the server SHALL return an error unless the relationships between the code systems is well defined.
If the concepts can be compared, then the server returns an outcome code:
| equivalent | Concepts A and B are equivalent |
| subsumes | Concept A subsumes Concept B |
| subsumed-by | Concept A is subsumed by Concept B |
| not-subsumed | Concepts A and B are not related by any subsumption relationship |
Examples
Test whether a SNOMED CT Concept 399211009 (History of myocardial infarction) is subsumed by 22298006 (Myocardial infarction):
GET [base]/CodeSystem/$subsumes?system=http://snomed.info/sct&codeA=3738000&codeB=235856003
Or using Codings:
POST [base]/CodeSystem/$subsumes
[other headers]
<Parameters xmlns="http://hl7.org/fhir">
<!-- Subsumption testing - use SNOMED CT rules -->
<parameter>
<name value="system"/>
<valuUri value="http://snomed.info/sct"/>
</parameter>
<!-- Australian distribution -->
<parameter>
<name value="version"/>
<valuString value="http://snomed.info/sct/32506021000036107/version/20160430"/>
</parameter>
<parameter>
<name value="codingA"/>
<valueCoding>
<system value="http://snomed.info/sct"/>
<code value="3738000"/>
</valueCoding>
</parameter>
<parameter>
<name value="codingB"/>
<valueCoding>
<system value="http://snomed.info/sct"/>
<code value="235856003"/>
</valueCoding>
</parameter>
</Parameters>
Server response:
HTTP/1.1 200 OK
[other headers]
{
"resourceType" : "Parameters",
"parameter" : [
{
"name" : "outcome",
"valueCode" : "subsumes"
},
]
}
It is also possible to validate a set of concepts against their relevant value
sets by using the $validate-code operation in a Batch
interaction.
Example
A request to validate 2 concepts from a CDA document, with OIDs for value set identifiers:
POST [base]
[other headers]
{
"ResourceType": "Bundle",
"type": "batch",
"entry": [{
"request": {
"method": "Get",
"url": "ValueSet/$validate-code?system=http://loinc.org&code=2324-4&uri=urn:oid:1.2.3.4.6"
}
},
{
"request": {
"method": "GET",
"url": "ValueSet/$validate-code?system=http://snomed.info/sct&codes=22298006&uri=urn:oid:1.2.3.4.7"
}
}]
}
The server responds with a series of validation outcomes (JSON this time):
HTTP/1.1 200 OK
[other headers]
{
"ResourceType": "Bundle",
"type": "batch-response",
"entry": [{
"resource": {
"resourceType": "Parameters",
"parameter": [{
"name": "result",
"valueBoolean": "false"
},
{
"name": "message",
"valueString": "'2324-4' is not a valid LOINC code"
}]
}
},
{
"resource": {
"resourceType": "Parameters",
"parameter": [{
"name": "result",
"valueBoolean": "false"
},
{
"name": "message",
"valueString": "The concept is not in the specified value set (\"Organisms\")"
},
{
"name": "display",
"valueString": "Myocardial infarction"
}]
}]
}
A client can ask a server to translate a concept from one value set to another. Typically, this
is used to translate between code systems (e.g. from LOINC to SNOMED CT, or from a HL7 V3 code to
a HL7 V2 code). The client calls the translate operation and passes the following parameters:
The client passes either a concept map, or the value sets for the source and destination context. If there is no concept map, then the server may determine the appropriate map to use from context provided in the value sets. If there is no particular context, the appropriate value sets would be the value sets for the entire coding system at question (e.g. from http://snomed.info/sct to http://loinc.org/vs). The server performs the translation as it is able based on the concept maps that it knows about. If no single mapping can be determined then the server returns an error. Some servers may require a concept map to use for the translation.
Example
Translate from FHIR Composition status to HL7 v3 Act Status (based on
this defined concept map:
GET [base]/ConceptMap/$translate?system=http://hl7.org/fhir/composition-status &code=preliminary&valueSet= http://hl7.org/fhir/ValueSet/composition-status &target=http://hl7.org/fhir/ValueSet/v3-ActStatus
The server responds with validation information:
HTTP/1.1 200 OK
[other headers]
{
"resourceType" : "Parameters",
"parameter" : [
{
"name" : "result",
"valueBoolean" : "true"
},
{
"name" : "outcome",
"valueCoding" : {
"system" : "http://hl7.org/fhir/v3/ActStatus",
"code" : "active",
}
}
]
}
It is also possible to translate a set of concepts against their relevant value
sets by using the $translate operation in a Batch
interaction.
Example
A request to translate 2 concepts from a CDA document, with OIDs for value set identifiers:
POST [base]
[other headers]
{
"ResourceType": "Bundle",
"type": "batch",
"entry": [{
"resource": {
"ResourceType": "Parameters",
"parameter": [{
"name": "concept",
"valueCodeableConcept": {
"system": "http://loinc.org",
"code": "2324-4"
}
},
{
"name": "target",
"valueUri": "urn:oid:1.2.3.4.6"
}]
},
"request": {
"method": "POST",
"url": "ConceptMap/$translate"
}
},
{
"resource": {
"ResourceType": "Parameters",
"parameter": [{
"name": "concept",
"valueCodeableConcept": {
"system": "http://snomed.info/sct",
"code": "22298006"
}
},
{
"name": "target",
"valueUri": "urn:oid:1.2.3.4.7"
}]
},
{
"request": {
"method": "POST",
"url": "ConceptMap/$translate"
}
}]
}
The server responds with a series of translation outcomes:
HTTP/1.1 200 OK
[other headers]
{
"ResourceType": "Bundle",
"type": "batch-response",
"entry": [{
"resource": {
"resourceType": "Parameters",
"parameter": [{
"name": "result",
"valueBoolean": "false"
},
{
"name": "message",
"valueString": "'2324-4' is not a valid LOINC code"
}]
}
},
{
"resource": {
"resourceType": "Parameters",
"parameter": [{
"name": "result",
"valueBoolean": "true"
},
{
"name": "outcome",
"valueCodeableConcept": {
"coding": {
"system": "http://example.com/codesystems/example",
"code": "xxxx"
}
}
}]
}
}]
}
The 5 operations Expand, Lookup, Validate, subsumes, and Translate account for most operational requirements associated with terminology use. However there is one difficult but important use case that they do not address, which is integrating terminologically based logic into application searches.
A typical example of this is a user that wants to find any observations for male patients over the age of 50 who attended a particular clinic within a particular 2 week period, with a diagnosis of gout, and who had an elevated serum creatinine.
In this case, both "diagnosis of gout" and "serum creatinine" involve value set and/or subsumption queries (e.g. against SNOMED CT and LOINC respectively). This search has to be executed by some logical processing engine that knows how to find patient related in a given persistence store. Often, this is some kind of SQL query, though many other technological choices are available. However this is done, the challenge with an operation like this is to integrate the terminological knowledge into a search execution that also covers other relationships expressed in the search criteria.
One approach to this problem would be to using the expand operation above, so that the system executing the search could generate expansions, and then search for these expansions. This has a couple of problems:
An alternative approach is to generate a subsumption closure table ,
which lists all the possible relationships, and allows for rapid execution of these kind of queries. However this has other problems:
This is the main reason why most systems do not support post-coordination or other forms of coded expressions.
In FHIR, this problem is solved by building a closure table on the fly as new codes are seen. This technique leaves the FHIR terminology server responsible for the terminological reasoning, and the client responsible for the closure table maintenance. To the client, it doesn't matter whether the concept is post-coordinated or not. Here's a description of how the process works:
The $closure operation takes 2 parameters:
The operation returns a concept map which has a list of mappings that represent new entries to make in the closure table.
The closure table can be resynchronized by passing an additional "version" parameter, which is a value taken from the version in one of the delta responses. This is a request to replay all the mapping changes since that delta was sent.
Before it can be used, a closure table has to be initialised. To initialise a closure table, POST the following to [base]/ConceptMap/$closure:
{
"resourceType" : "Parameters",
"parameter" : [{
"name" : "name",
"valueString" : "[name]"
}]
}
A successful response is a 200 OK from the server, with an associated ConceptMap:
{
"resourceType": "ConceptMap",
"id": "[name]",
"version": "0",
"name": "Closure Table [name] Creation",
"status": "active",
"experimental": true,
"date": "2015-12-20T23:10:55Z"
}
If there is an error – usually involving the closure name, the server returns a HTTP status 400 with an operation outcome:
{
"resourceType": "OperationOutcome",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>invalid closure name \"invalid-id!\":</p></div>"
},
"issue": [
{
"severity": "error",
"details": {
"text" : "invalid closure name \"invalid-id!\""
}
}
]
}
What closure names are valid is at the discretion of the server.
When the consumer (client) encounters a new code, it POSTs the following to [base]/ConceptMap/$closure:
{
"resourceType" : "Parameters",
"parameter" : [{
"name" : "name",
"valueString" : "[name]"
}, {
"name" : "concept",
"valueCoding" : {
"system" : "http://snomed.info/sct",
"code" : "22298006",
"display" : "Myocardial infarction"
}
}]
}
Note that this example only includes one concept, but more than one is allowed:
{
"resourceType" : "Parameters",
"parameter" : [{
"name" : "name",
"valueString" : "[name]"
}, {
"name" : "concept",
"valueCoding" : {
"system" : "http://snomed.info/sct",
"code" : "22298006",
"display" : "Myocardial infarction"
}
}, {
"name" : "concept",
"valueCoding" : {
"system" : "http://snomed.info/sct",
"code" : "128599005",
"display" : "Structural disorder of heart"
}
}]
}
The response varies depending on the conditions on the server. Possible responses: If the closure table has not been initialised: Return a 404 Not Found with
{
"resourceType": "OperationOutcome",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>invalid closure name \"[name]\":</p></div>"
},
"issue": [
{
"severity": "error",
"details": {
"text" : "invalid closure name \"[name]\""
}
}
]
}
If the closure table needs to be reinitialised: Return a 422 Unprocessable Entity with
{
"resourceType": "OperationOutcome",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>closure \"[name\" must be reinitialised</p></div>"
},
"issue": [{
"severity": "error",
"details": {
"text" : "closure \"[name]\" must be reinitialised"
}
}
]
}
The server should only send this when it’s underlying terminology conditions have been changed (e.g. a new version of SNOMED CT has been loaded). When a client gets this, it’s only choice is to initialise the closure table, and process all the codes in the closure table again (the assumption here is that the system has some external source of ‘all the codes’ so it can rebuild the table again). If the concept(s) submitted are processed ok, but there’s no new concepts, or no new entries in the table, return a 200 OK with :
{
"resourceType": "ConceptMap",
"id": "[name]",
"version": "[version]",
"name": "Updates for Closure Table [name]",
"status": "active",
"experimental": true,
"date": "2015-12-20T23:12:55Z"
}
If there’s new entries in the closure table, the server returns a 200 OK with:
{
"resourceType": "ConceptMap",
"id": "b87db127-9996-4d0c-bda9-a278d7a24a69",
"version": "[version]",
"name": "Updates for Closure Table [name]",
"status": "active",
"experimental": true,
"date": "2015-12-20T23:16:24Z",
"element": [{
"codeSystem": "http://snomed.info/sct",
"code": "22298006",
"target": [{
"codeSystem": "http://snomed.info/sct",
"code": "128599005",
"equivalence": "subsumes"
}]
}]
}
Notes
Given the way that the closure operation functions, it’s possible for a client to lose a response from the server before it is committed to safe storage (or the client may not have particularly safe storage). For this reason, when a client is starting up, it should check that there has been no missing operations. It can do this by passing the last version (from the Concept Map response) it is sure it processed in the request:
{
"resourceType" : "Parameters",
"parameter" : [{
"name" : "name",
"valueString" : "[name]"
}, {
"name" : "version",
"valueString" : "3"
}]
}
That’s a request to return all the additions to the closure table since version 3. The server returns its latest version in the concept map, along with anything added to the closure table since version 3 (not including version 3)
Notes:
The client uses the result of the closure operation to maintain a closure table. Simplistically, it might look like this:
| Scope | Source | Target | |
| patient-problems | http://snomed.info/sct|22298006 | http://snomed.info/sct|128599005 | |
| patient-problems | http://snomed.info/sct|24595009 | http://snomed.info/sct|90560007 | |
| obs-code | http://loinc.org|14682-9 | http://loinc.org|LP41281-4 |
The client can then use a table like this as part of its general search conditions. Using the example from above: "Find any observations for male patients over the age of 50 who attended a particular clinic within a particular 2 week period, with a diagnosis of gout, and who had an elevated serum creatinine." This query could be done, for instance, with an SQL query like this:
Select * from Observations, Patients, Encounters, Conditions, Observations as Obs2 where
Observations.patient = Patients.Key and Patients.Age > 50 and
Observations.encounter = Encounters.Key and Encounter.clinic = [key]
and encounter.date >= [date] and encounter.date <= [date] and
Conditions.patient = Patients.Key and Conditions.code
in (select Source From ClosureTable
where Scope = "patient-problems" and Target = "http://snomed.info/sct|90560007") and
Obs2.patient = Patients.Key and Obs2.value > 0.19 and Obs2.code
in (select Source From ClosureTable
where Scope = "obs-code" and Target = "http://loinc.org|LP41281-4")
Note that in real clinical systems, tables are usually far more structured than this example implies, and the query is correspondingly more complex. The closure table would usually be normalised - this example is kept simple to demonstrate the concept.
© HL7.org 2011+. FHIR STU3 Ballot (v1.6.0-9663) generated on Thu, Aug 11, 2016 17:07+1000. QA Page
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