FHIR Genomics Implementation Guide

Notice

Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.

StructureDefinition OperationOutcome

The Genomics OperationOutcome is the same as provided within FHIR R4. The FHIR R4 OperationOutcome is provided below for completeness.

OperationOutcomes are expected for any create or update operations made on the server resulting in validation messages (or any create or update operations made within a transaction bundle). It is not expected that connecting systems would need to construct OperationOutcome resources or submit these to the server, though key elements within the resource are detailed here for receiving systems.

It is expected that all issue codes raised by the Genomic Medicine Service will fall under existing codes bound in the below resource. If further codes are needed, these will be promoted to UK Core for release in a future ballot/sprint.

Profile url	FHIR Module	Normative Status
http://hl7.org/fhir/StructureDefinition/OperationOutcome	HL7 International	trial-use

OperationOutcome	I		DomainResource	Element id OperationOutcome Short description Information about the success/failure of an action Definition A collection of error, warning, or information messages that result from a system action. Comments Can result from the failure of a REST call or be part of the response message returned from a request message. Data type DomainResource Constraints dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources `contained.contained.empty()` dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated `contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()` dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource `contained.where((('#'+id in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()` dom-6: A resource should have narrative for robust management text.`div`.exists() dom-5: If a resource is contained in another resource, it SHALL NOT have a security label `contained.meta.security.empty()` Mappings rim: Entity. Role, or Act rim: Grouping is handled through multiple repetitions from whatever context references the outcomes (no specific grouper required)
id	Σ	0..1	string	There are no (further) constraints on this element Element id OperationOutcome.id Short description Logical id of this artifact Definition The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. Comments The only time that a resource does not have an id is when it is being submitted to the server using a create operation. Data type string
meta	Σ	0..1	Meta	There are no (further) constraints on this element Element id OperationOutcome.meta Short description Metadata about the resource Definition The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. Data type Meta Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
implicitRules	Σ ?!	0..1	uri	There are no (further) constraints on this element Element id OperationOutcome.implicitRules Short description A set of rules under which this content was created Definition A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. Comments Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc. Data type uri Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a
language		0..1	codeBinding	There are no (further) constraints on this element Element id OperationOutcome.language Short description Language of the resource content Definition The base language in which the resource is written. Comments Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute). Data type code Binding A human language. CommonLanguages (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a
text		0..1	Narrative	There are no (further) constraints on this element Element id OperationOutcome.text Short description Text summary of the resource, for human interpretation Alternate names narrative, html, xhtml, display Definition A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. Comments Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later. Data type Narrative Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A rim: Act.text?
contained		0..*	Resource	There are no (further) constraints on this element Element id OperationOutcome.contained Short description Contained, inline Resources Alternate names inline resources, anonymous resources, contained resources Definition These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. Comments This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels. Data type Resource Mappings rim: Entity. Role, or Act rim: N/A
extension	I	0..*	Extension	There are no (further) constraints on this element Element id OperationOutcome.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	?! I	0..*	Extension	There are no (further) constraints on this element Element id OperationOutcome.modifierExtension Short description Extensions that cannot be ignored Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
issue	Σ	1..*	BackboneElement	Element id OperationOutcome.issue Short description A single issue associated with the action Definition An error, warning, or information message that results from a system action. Data type BackboneElement Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: ERR rim: AcknowledgementDetail or Observation[classCode="ALRT" and moodCode="EVN"]
id		0..1	string	There are no (further) constraints on this element Element id OperationOutcome.issue.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id OperationOutcome.issue.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	Σ ?! I	0..*	Extension	There are no (further) constraints on this element Element id OperationOutcome.issue.modifierExtension Short description Extensions that cannot be ignored even if unrecognized Alternate names extensions, user content, modifiers Definition May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
severity	Σ	1..1	codeBinding	Element id OperationOutcome.issue.severity Short description fatal \| error \| warning \| information Definition Indicates whether the issue indicates a variation from successful processing. Requirements Indicates how relevant the issue is to the overall success of the action. Comments This is labeled as "Is Modifier" because applications should not confuse hints and warnings with errors. Data type code Binding How the issue affects the success of the action. IssueSeverity (required) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: ERR-4 rim: ./typeCode[parent::AcknowledgmentDetail] or unique(./inboundRelationship[parent::Observation and typeCode='SUBJ' and isNormalActRelationship()]/source[classCode="OBS" and moodCode="EVN" and implies(code, ActCode#SEV and isNormalAct())/value[xsi:type="CD"]
code	Σ	1..1	codeBinding	Element id OperationOutcome.issue.code Short description Error or warning code Definition Describes the type of the issue. The system that creates an OperationOutcome SHALL choose the most applicable code from the IssueType value set, and may additional provide its own code for the error in the details element. Requirements Expresses the issue in a human and computer-friendly way, allowing the requesting system to behave differently based on the type of issue. The required element provides a base level of computable interoperability across all systems for processing an outcome, allowing systems to respond appropriately regardless of the internal system error codes returned. Comments Note that FHIR strings SHALL NOT exceed 1MB in size Data type code Binding A code that describes the type of issue. IssueType (required) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: ERR-3 rim: ./code
details	Σ	0..1	CodeableConcept	Element id OperationOutcome.issue.details Short description Additional details about the error Definition Additional details about the error. This may be a text description of the error or a system code that identifies the error. Comments A human readable description of the error issue SHOULD be placed in details.text. Data type CodeableConcept Binding A code that provides details as the exact issue. OperationOutcomeCodes (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD v2: ERR-5 rim: ./code
diagnostics	Σ	0..1	string	Element id OperationOutcome.issue.diagnostics Short description Additional diagnostic information about the issue Definition Additional diagnostic information about the issue. Comments This may be a description of how a value is erroneous, a stack dump to help trace the issue or other troubleshooting information. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: ERR-8 rim: ./text[parent::AcknowledgmentDetail]
location	Σ	0..*	string	Element id OperationOutcome.issue.location Short description Deprecated: Path of element(s) related to issue Definition This element is deprecated because it is XML specific. It is replaced by issue.expression, which is format independent, and simpler to parse. For resource issues, this will be a simple XPath limited to element names, repetition indicators and the default child accessor that identifies one of the elements in the resource that caused this issue to be raised. For HTTP errors, will be "http." + the parameter name. Requirements Allows systems to highlight or otherwise guide users to elements implicated in issues to allow them to be fixed more easily. Comments The root of the XPath is the resource or bundle that generated OperationOutcome. Each XPath SHALL resolve to a single node. This element is deprecated, and is being replaced by expression. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: ERR-2 rim: ./location[parent::AcknowledgmentDetail]
expression	Σ	0..*	string	Element id OperationOutcome.issue.expression Short description FHIRPath of element(s) related to issue Definition A simple subset of FHIRPath limited to element names, repetition indicators and the default child accessor that identifies one of the elements in the resource that caused this issue to be raised. Requirements Allows systems to highlight or otherwise guide users to elements implicated in issues to allow them to be fixed more easily. Comments The root of the FHIRPath is the resource or bundle that generated OperationOutcome. Each FHIRPath SHALL resolve to a single node. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: ERR-2 rim: ./location[parent::AcknowledgmentDetail]

OperationOutcome-SuccessfulValidation-Example

Additional Guidance

issue

issue

An issue element will be included within the OperationOutcome for each issue that needs to be communicated to the requesting system, e.g. errors, warnings or informational messages. Appropriate 'severity' and 'code' codes will be assigned to help categorization of an messages returned, using the standard HL7 bound ValueSets.

The diagnostics field will be used to present a human readable version of the message and location will be used to detail the location within the request payload that resulted in the associated issue/message.

If an error or warning is returned, the 'details' element will be populated with any validation specific messages. Details of the systems and codes used for these messages will be determined by the validation package used by the central order management broker (this is still to be determined at the time of publication).

"issue":[
            {
              "severity":"error",
              "code":"processing",
              "details":{
                "coding":[
                  {
                    "system": "http://terminology.hl7.org/CodeSystem/operation-outcome",
                    "code": "MSG_LOCAL_FAIL",
                    "display": "Unable to resolve local reference to resource Patient/Patient-MeirLieberman-Example"
                  }
                ]
              },
              "diagnostics": "Validation errors occurred during processing",
              "location": [
                  "Bundle.entry[1].resource.ofType(ServiceRequest)"
              ]
            }
          ]