DSTU2 Ballot Source
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This specification includes support for the provision of a consumer level 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 value set resource, and the underlying code systems. A server that supports all the functionality described here can be described as a "FHIR Terminology Service", and SHALL conform to this conformance statement: [link to be provided].
Generally, SSL SHOULD be used for all production health care data exchange. Even though terminology servers do not directly handle patient information, 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.
Note to reviewers/implementers: can we? it would increase interoperability if we could bind to a particular approach. If we said, for the operations, SSL+server certs mandatory, use client certificates if you want to authenticate the clients, and to use Smart on FHIR for editing value sets and concept maps, is there any problems with that?
A FHIR terminology service is a simply a set of functions built on the definitions provided by a set of 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 may be found in:
In order to be used with a value set, a code must be defined somewhere. They can be defined as part of an inline code system definition, or they can be defined elsewhere, and then used in a value set by quoting the correct namespace. 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. Inline code systems in Value Set resources are not an appropriate way to define these code systems; FHIR does not provide a formal representation at all. Instead, these terminologies provide their own distribution formats, and it is assumed that they 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 (still to figure out how this works).
A server SHOULD publish the additional code systems that it supports through intrinsic knowledge using the http://hl7.org/fhir/StructureDefinition/conformance-common-supported-system extension:
{
"resourceType" : "Conformance",
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/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 Value Set infrastructure for supporting typical relatively simple small code systems.
Implementers Note: Implementers interested in working with existing published terminologies for which the Value Set 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 exploration, or structured search, but these services are outside the scope of the FHIR terminology service.
The terminology service uses the value set resources defined on the system - both the implicit ones associated with the external code systems and those explicitly available at the /ValueSet endpoint - to serve the operational interface defined below. As 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 would 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 the 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.
For further information, consult the definition of the operation. Note to reviewers/implementers: Open Issue for connectathons: is paging support required for the iterating through an 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/$expand?filter=abdo
Expanding a value set that is specififed by the client (using JSON):
POST [base]/ValueSet/23/$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 the following information:
The recommended display to 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.
Examples
Looking up a code/system :
GET [base]/ValueSet/$lookup?system=http://loinc.org&code=1963-8
Lookup using a Coding (this example in XML):
POST [base]/ValueSet/$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" : "designation",
"valueString" : "Bicarbonate [Moles/volume] in Serum"
},
{
"name" : "abstract",
"valueString" : "false"
},
{
"name" : "designation",
"part" : [
{
"name" : "value",
"valueString" : "Bicarbonate [Moles/volume] in Serum "
}
]
}
]
}
One of the ways 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" 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". For some code systems, these value set URIs are defined
in advance (e.g. for LOINC, it's 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/$validate?system=http://loinc.org&code=1963-8&display=test
Validate a CodeableConcept against a client specified value set (this example in JSON):
POST [base]/ValueSet/$validate
[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"
}
]
}
The Expand and Validate operations can be used to perform subsumption testing. To test whether code A subsumes code B, perform a validate specifying a value set built of all the codes that are subsumed by code A, and test whether code B is subsumed by it. Note that a server is allowed (and SHOULD, but is not required to) consider concept maps when doing subsumption testing. E.g. if A is a LOINC code, and it has a precise mapping to a SNOMED CT code that subsumes B, with an appropriate scope, then the server can indicate that this it is true that LOINC code A subsumes SNOMED CT code B.
In order to make it convenient to perform this subsumption testing, code systems that define subsumption hierarchies should define simple URLs to express a value set that includes all the codes subsumed by a code.
Examples
Test whether a Snomed Concept 399211009 (History of myocardial infarction) is subsumed by 22298006 (Myocardial infarction):
GET [base]/ValueSet/$validate?system=http://snomed.info/sct&code=X&uri=http://hl7.org/fhir/ValueSet/snomedct?base=Y
Server response:
HTTP/1.1 200 OK
[other headers]
{
"resourceType" : "Parameters",
"parameter" : [
{
"name" : "result",
"valueBoolean" : "false"
},
]
}
It's also possible to validate a set of concepts against their relevant value sets in a single batch operation, to support high-volume process and reduce network latency effects. In this case, the client passes the server the following information:
Code system URIs may be used to refer to the implicit value set that includes all the codes in the code system (as described for the validation operation).
The server returns a series of parameters, one for each submitted item, each of which has a result, a message, and a display (same as for the $validate operation).
This operation could be used, for instance, to validate a set of codes in a CDA document, by converting from the CDA CD data type to CodeableConcepts.
Examples
A request to validate 2 concepts from a CDA document, with OIDs for value set identifiers:
POST [base]/ValueSet/$batch
[other headers]
{
"ResourceType" : "Parameters",
"parameter" : [
{
"name" : "item",
"part" : [
{
"name" : "concept",
"valueCodeableConcept" : {
"system" : "http://loinc.org",
"code" : "2324-4"
},
}
"name" : "uri",
"valueUri" : "urn:oid:1.2.3.4.6"
]
},
{
"name" : "item",
"part" : [
{
"name" : "concept",
"valueCodeableConcept" : {
"system" : "http://snomed.info/sct",
"code" : "22298006"
},
}
"name" : "uri",
"valueUri" : "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" : "Parameters",
"parameter" : [
{
"name" : "item",
"part" : [
{
"name" : "result",
"valueBoolean" : "false"
},
{
"name" : "message",
"valueString" : "'2324-4' is not a valid LOINC code"
}
]
},
{
"name" : "item",
"part" : [
{
"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 v3 code to a 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 V3 Act Status (based on this defined concept map:
GET [base]/ConceptMap/$validate?system=http://hl7.org/fhir/composition-status &code=preliminary&valueSet= http://hl7.org/fhir/vs/composition-status &target=http://hl7.org/fhir/v3/vs/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's also possible to translate a set of concepts in a single batch operation, to support high-volume process and reduce network latency effects. In this case, the client passes the server the following information:
The server returns a series of parameters, one for each submitted item, each of which has a result, a message, and an outcome (same as for the $translate operation).
Examples
A request to translate 2 concepts from a CDA document, with OIDs for value set identifiers:
POST [base]/ConceptMap/$batch
[other headers]
{
"ResourceType" : "Parameters",
"parameter" : [
{
"name" : "item",
"part" : [
{
"name" : "concept",
"valueCodeableConcept" : {
"system" : "http://loinc.org",
"code" : "2324-4"
},
}
"name" : "target",
"valueUri" : "urn:oid:1.2.3.4.6"
]
},
{
"name" : "item",
"part" : [
{
"name" : "concept",
"valueCodeableConcept" : {
"system" : "http://snomed.info/sct",
"code" : "22298006"
},
}
"name" : "target",
"valueUri" : "urn:oid:1.2.3.4.7"
]
}
]
}
The server responds with a series of validation outcomes:
HTTP/1.1 200 OK
[other headers]
{
"resourceType" : "Parameters",
"parameter" : [
{
"name" : "item",
"part" : [
{
"name" : "result",
"valueBoolean" : "false"
},
{
"name" : "message",
"valueString" : "'2324-4' is not a valid LOINC code"
}
]
},
{
"name" : "item",
"part" : [
{
"name" : "result",
"valueBoolean" : "false"
},
{
"name" : "outcome",
"valueCodeableConcept" : {
"coding" : {
"system" : "http://example.com/codesystems/example",
"code" : "xxxx"
}
}
}
]
}]
}
The 4 operations Expand, Lookup, Validate, 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 search.
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 valueset 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 this data 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 with search execution based on the other relationships the criteria is expressed.
On 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 don't 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 $closure operation takes 2 parameters:
The operation returns a concept map which has a list of mappings that represent new entries to make in the closure table.
The closure table can be resynchronized by passing an additional "version" parameter, which is a value taken from the version in one of the delta responses. This is a request to replay all the mapping changes since that delta was sent.
Example
The client sees a new SNOMED CT concept "22298006" in a data element it is tracking as "patient-problems":
POST [base]/$closure
{
"resourceType" : "Parameters",
"parameter" : [
{
"name" : "name",
"valueId : "patient-problems"
},
{
"name" : "concept",
"valueCoding" : {
"system" : "http://snomed.info/sct",
"code" : "22298006",
}
}
]
}
The server responds with a set of new entries to add to the concept map. It provides one important piece of metadata - the version, which the client can use to resynchronize the closure table:
HTTP/1.1 200 OK
[other headers]
{
"resourceType": "ConceptMap",
"identifier": "49088976-d54d-4d19-b868-3d4c18cebabb",
"version": "8",
"status": "active",
"experimental": true,
"date": "2012-06-13",
"element": [
{
"codeSystem": "http://snomed.info/sct",
"code": "22298006",
"map": [
{
"codeSystem": "http://snomed.info/sct",
"code": "128599005",
"equivalence": "narrower"
}
]
},
]
}
Notes:
In order to support terminology operations in FHIR a minimal set of terminology operations would be necessary. These operations are a sub set of the available terminology service operations defined in the [http://www.omg.org/spec/CTS2/1.0/ Common Terminology Services - Release 2 (CTS2) specification] and can be categorized as:
Functional operations within these categories support the access and management of terminology objects such as Code Systems, Concepts, Value Sets and Concept Mappings. The functional operations necessary to support a FHIR terminology service are outlined here.
Concepts
Code System
Value Set
Mapping
Concepts
Value Set
Mapping
© HL7.org 2011+. FHIR DSTU (v0.5.0-5149) generated on Fri, Apr 3, 2015 14:36+1100.
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