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 BodyStructure

The Genomics BodyStructure is currently based on the HL7 international version of the resource as a profile for BodyStructure does not exist in UKCore. Once this profile becomes active in UKCore its suitability for use and need for profiling within Genomics will be assessed.

The base BodyStructure resource is provided below for completeness.

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

Usage

Use of this resource is meant to replace the Genomics extensions for topology and morphology on the Specimen profile

BodyStructure	I		DomainResource	Element id BodyStructure Short description Specific and identified anatomical structure Alternate names anatomical location Definition Record details about an anatomical structure. This resource may be used when a coded concept does not provide the necessary detail needed for the use case. 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: ActSIte openehr: Archetype ID openEHR-EHR-CLUSTER.anatomical_location.v1 Concept name Anatomical Location Concept description Record details about an anatomical location. Keywords location, site, anatomical Copyright © openEHR Foundation Purpose To record details about anatomical location. Misuse Not for specifiying unilateral/bilateral occurrence - this is related to an evaluation which perhaps includes multiple locations. Author Author name: Heather Leslie Organization: Ocean Informatics Email: heather.leslie@oceaninformatics.com Date of Origination: 2008-11-10 Translator Norwegian Bokmål: Lars Bitsch-Larsen, Haukeland University Hospital of Bergen, Norway, MD, DEAA, MBA, spec in anesthesia, spec in tropical medicine. Arabic (Syria): Mona Saleh Other contributors Heather Leslie, Ocean Informatics, Australia (Editor) Ian McNicoll, freshEHR Clinical Informatics, United Kingdom (Editor) Dunmail Hodkinson, Black Pear Software Ltd, UK References Use cases: - 5LICS, midclavicular line - L forearm, 2cm anterior to the cubital fossa - Right iliac fossa - 5 cm below L tibial tuberosity - 2 cm medial to R nipple - 4 cm below R costal margin in midclavicular line - R femur - midline nose - medial aspect of R great toe nail.
id	Σ	0..1	string	There are no (further) constraints on this element Element id BodyStructure.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 BodyStructure.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 BodyStructure.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 BodyStructure.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 BodyStructure.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 BodyStructure.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 BodyStructure.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 BodyStructure.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
identifier	Σ	0..*	Identifier	Element id BodyStructure.identifier Short description Bodystructure identifier Definition Identifier for this instance of the anatomical structure. Data type Identifier Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CX / EI (occasionally, more often EI maps to a resource id or a URL) rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT] servd: Identifier w5: FiveWs.identifier rim: .id openehr: Specific location Cluster Optional (0..1) Cardinality: Mandatory, repeating, unordered (1..*)
active	Σ ?!	0..1	boolean	Element id BodyStructure.active Short description Whether this record is in active use Definition Whether this body site is in active use. Requirements Need to be able to mark a body site entry as not to be used because it was created in error. Comments This element is labeled as a modifier because it may be used to mark that the resource was created in error. Meaning when missing This resource is generally assumed to be active if no value is provided for the active element Data type boolean Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a w5: FiveWs.status rim: statusCode
morphology	Σ	0..1	CodeableConcept	Element id BodyStructure.morphology Short description Kind of Structure Definition The kind of structure being represented by the body structure at `BodyStructure.location`. This can define both normal and abnormal morphologies. Comments The minimum cardinality of 0 supports the use case of specifying a location without defining a morphology. Data type CodeableConcept Binding Codes describing anatomic morphology. SNOMEDCTMorphologicAbnormalities (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 w5: FiveWs.what[x] v2: SPM-4/SPM-5
location	Σ	0..1	CodeableConcept	Element id BodyStructure.location Short description Body site Definition The anatomical location or region of the specimen, lesion, or body structure. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding Codes describing anatomical locations. May include laterality. SNOMEDCTBodyStructures (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 w5: FiveWs.what[x] v2: OBX-20/SPM-8/SPM-10 rim: .targetSiteCode openehr: Name of location
locationQualifier		0..*	CodeableConcept	Element id BodyStructure.locationQualifier Short description Body site modifier Definition Qualifier to refine the anatomical location. These include qualifiers for laterality, relative location, directionality, number, and plane. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding Concepts modifying the anatomic location. BodystructureLocationQualifier (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 w5: FiveWs.what[x] v2: No distinct element defined in V2.x. The IHE Radiology Technical Framework directs the use of OBR-15-specimen source to contain laterality for imaging studies./SPM-9 rim: .targetSiteCode openehr: Combines Side, Numerical identifier, Anatomical plane,and Aspect
description	Σ	0..1	string	Element id BodyStructure.description Short description Text description Definition A summary, characterization or explanation of the body structure. Comments This description could include any visual markings used to orientate the viewer e.g. external reference points, special sutures, ink markings. 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 w5: FiveWs.what[x] v2: NTE rim: .text openehr: Description of anatomical location/Visual markings/orientation
image	I	0..*	Attachment	Element id BodyStructure.image Short description Attached images Definition Image or images used to identify a location. Comments When providing a summary view (for example with Observation.value[x]) Attachment should be represented with a brief display text such as "Signed Procedure Consent". Data type Attachment Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` att-1: If the Attachment has data, it SHALL have a contentType `data.empty() or contentType.exists()` Mappings rim: n/a v2: ED/RP rim: ED w5: FiveWs.what[x] v2: OBX rim: outboundRelationship[typeCode=COMP].target openehr: Image
patient	Σ I	1..1	Reference(Patient)	Element id BodyStructure.patient Short description Who this is about Definition The person to which the body site belongs. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Patient) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) w5: FiveWs.subject[x] v2: PID-3 rim: .scoper or .scoper.playsRole w5: FiveWs.subject

FHIR	MDS	HL7v2
BodyStructure.morphology	Primary Sample - Solid tumour morphology	Additional SPM-4/5 qualifiers
BodyStructure.location	Primary Sample - Solid tumour histological type (topography)	SPM-8