{
"description": "This profile defines the Genomics constraints and extensions on the UK Core FHIR resource [Specimen](https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen).",
"_filename": "NHSEngland-Specimen-Genomics.json",
"package_name": "uk.nhsengland.genomics.r4",
"date": "2026-04-16",
"derivation": "constraint",
"publisher": "NHS England",
"fhirVersion": "4.0.1",
"purpose": "Used to capture information on Samples which will undergo or have undergone processing for genomic testing.",
"name": "NHSEngland_Specimen_Genomics",
"abstract": false,
"copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\\\\\"License\\\\\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\\\\\"AS IS\\\\\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.",
"type": "Specimen",
"experimental": null,
"resourceType": "StructureDefinition",
"title": "NHSEngland Specimen Genomics",
"package_version": "0.6.1-pre-release",
"snapshot": {
"element": [ {
"constraint": [ {
"key": "dom-2",
"human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources",
"xpath": "not(parent::f:contained and f:contained)",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource",
"severity": "error",
"expression": "contained.contained.empty()"
}, {
"key": "dom-4",
"human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated",
"xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource",
"severity": "error",
"expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()"
}, {
"key": "dom-3",
"human": "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",
"xpath": "not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource",
"severity": "error",
"expression": "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()"
}, {
"key": "dom-6",
"human": "A resource should have narrative for robust management",
"xpath": "exists(f:text/h:div)",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource",
"severity": "warning",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice",
"valueBoolean": true
}, {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation",
"valueMarkdown": "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time."
} ],
"expression": "text.`div`.exists()"
}, {
"key": "dom-5",
"human": "If a resource is contained in another resource, it SHALL NOT have a security label",
"xpath": "not(exists(f:contained/*/f:meta/f:security))",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource",
"severity": "error",
"expression": "contained.meta.security.empty()"
}, {
"key": "ukcore-spec-001",
"human": "There SHALL be only one reference between collection.collector and the extension collectionCollectorR5",
"source": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen",
"severity": "error",
"expression": "collection.collector.reference.empty() or collection.collector.extension('http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.collector').empty()"
} ],
"path": "Specimen",
"min": 0,
"definition": "A sample to be used for analysis.",
"short": "Sample for analysis",
"mapping": [ {
"map": "Entity. Role, or Act",
"identity": "rim"
}, {
"map": "Role[classCode=SPEC]",
"identity": "rim"
} ],
"max": "*",
"id": "Specimen",
"base": {
"max": "*",
"min": 0,
"path": "Specimen"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.id",
"min": 0,
"definition": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.",
"short": "Logical id of this artifact",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "id",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"max": "1",
"id": "Specimen.id",
"condition": [ "ele-1" ],
"comment": "The only time that a resource does not have an id is when it is being submitted to the server using a create operation.",
"base": {
"max": "1",
"min": 0,
"path": "Resource.id"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.meta",
"min": 0,
"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.",
"short": "Metadata about the resource",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Meta"
} ],
"max": "1",
"id": "Specimen.meta",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Resource.meta"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.implicitRules",
"min": 0,
"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.",
"isModifier": true,
"short": "A set of rules under which this content was created",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "uri"
} ],
"max": "1",
"id": "Specimen.implicitRules",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "1",
"min": 0,
"path": "Resource.implicitRules"
},
"isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation",
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.language",
"min": 0,
"definition": "The base language in which the resource is written.",
"short": "Language of the resource content",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "code"
} ],
"binding": {
"strength": "preferred",
"valueSet": "http://hl7.org/fhir/ValueSet/languages",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet",
"valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages"
}, {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "Language"
} ],
"description": "A human language."
},
"max": "1",
"id": "Specimen.language",
"condition": [ "ele-1" ],
"comment": "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).",
"base": {
"max": "1",
"min": 0,
"path": "Resource.language"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.text",
"min": 0,
"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.",
"short": "Text summary of the resource, for human interpretation",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
}, {
"map": "Act.text?",
"identity": "rim"
} ],
"type": [ {
"code": "Narrative"
} ],
"alias": [ "narrative", "html", "xhtml", "display" ],
"max": "1",
"id": "Specimen.text",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "1",
"min": 0,
"path": "DomainResource.text"
}
}, {
"path": "Specimen.contained",
"min": 0,
"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.",
"short": "Contained, inline Resources",
"mapping": [ {
"map": "Entity. Role, or Act",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Resource"
} ],
"alias": [ "inline resources", "anonymous resources", "contained resources" ],
"max": "*",
"id": "Specimen.contained",
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "DomainResource.contained"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "DomainResource.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.extension",
"min": 0,
"definition": "Allows the categorisation of a sample into either tumour or germline. Required for WGS Cancer Testing, though not currently part of the Order Management MDS. Additional terms may be added upon review though the valueCodeableConcept.text field MAY be used as a free text representation if needed.",
"isModifier": false,
"short": "An extension to record the category of the sample.",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension",
"profile": [ "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory" ]
} ],
"sliceName": "sampleCategory",
"alias": [ "extensions", "user content" ],
"max": "1",
"id": "Specimen.extension:sampleCategory",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "DomainResource.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.modifierExtension",
"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](extensibility.html#modifierExtension).",
"min": 0,
"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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"isModifier": true,
"short": "Extensions that cannot be ignored",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.modifierExtension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "DomainResource.modifierExtension"
},
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them"
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier",
"min": 1,
"definition": "Multiple identifiers MAY be assigned to a sample as it travels between labs. Each lab SHOULD append their local identifier to the identifier array if needed, ensuring either the system or assigner, is able to disambiguate any identifiers from possibly overlapping numbers from other organizations. Assigner is preferred in this case (see identifier example on the UKCore-Patient page for further guidance)\r\nNote: accessionIdentifier is unused by the Genomic Medicine Service to facilitate movement of samples across organizational boundaries.",
"short": "External Identifier",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX / EI (occasionally, more often EI maps to a resource id or a URL)",
"identity": "v2"
}, {
"map": "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]",
"identity": "rim"
}, {
"map": "Identifier",
"identity": "servd"
}, {
"map": "FiveWs.identifier",
"identity": "w5"
}, {
"map": "SPM-2",
"identity": "v2"
}, {
"map": ".id",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"discriminator": [ {
"path": "system",
"type": "pattern"
} ]
},
"type": [ {
"code": "Identifier"
} ],
"max": "*",
"id": "Specimen.identifier",
"condition": [ "ele-1" ],
"base": {
"max": "*",
"min": 0,
"path": "Specimen.identifier"
},
"isSummary": true
}, {
"path": "Specimen.identifier.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.identifier.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.identifier.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.identifier.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.use",
"requirements": "Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.",
"min": 0,
"definition": "The purpose of this identifier.",
"isModifier": true,
"short": "usual | official | temp | secondary | old (If known)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "v2"
}, {
"map": "Role.code or implied by context",
"identity": "rim"
} ],
"type": [ {
"code": "code"
} ],
"binding": {
"strength": "required",
"valueSet": "http://hl7.org/fhir/ValueSet/identifier-use|4.0.1",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierUse"
} ],
"description": "Identifies the purpose for this identifier, if known ."
},
"max": "1",
"id": "Specimen.identifier.use",
"condition": [ "ele-1" ],
"comment": "Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.use"
},
"isModifierReason": "This is labeled as \"Is Modifier\" because applications should not mistake a temporary id for a permanent one.",
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.type",
"requirements": "Allows users to make use of identifiers when the identifier system is not known.",
"min": 0,
"definition": "A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.",
"short": "Description of identifier",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": "CX.5",
"identity": "v2"
}, {
"map": "Role.code or implied by context",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/identifier-type",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierType"
} ],
"description": "A coded type for an identifier that can be used to determine which identifier to use for a specific purpose."
},
"max": "1",
"id": "Specimen.identifier.type",
"condition": [ "ele-1" ],
"comment": "This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.type"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.system",
"requirements": "There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.",
"min": 0,
"definition": "Establishes the namespace for the value - that is, a URL that describes a set values that are unique.",
"short": "The namespace for the identifier value",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX.4 / EI-2-4",
"identity": "v2"
}, {
"map": "II.root or Role.id.root",
"identity": "rim"
}, {
"map": "./IdentifierType",
"identity": "servd"
} ],
"type": [ {
"code": "uri"
} ],
"max": "1",
"id": "Specimen.identifier.system",
"condition": [ "ele-1" ],
"comment": "Identifier.system is always case sensitive.",
"example": [ {
"label": "General",
"valueUri": "http://www.acme.com/identifiers/patient"
} ],
"base": {
"max": "1",
"min": 0,
"path": "Identifier.system"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.value",
"min": 0,
"definition": "The portion of the identifier typically relevant to the user and which is unique within the context of the system.",
"short": "The value that is unique",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX.1 / EI.1",
"identity": "v2"
}, {
"map": "II.extension or II.root if system indicates OID or GUID (Or Role.id.extension or root)",
"identity": "rim"
}, {
"map": "./Value",
"identity": "servd"
} ],
"type": [ {
"code": "string"
} ],
"max": "1",
"id": "Specimen.identifier.value",
"condition": [ "ele-1" ],
"comment": "If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the [Rendered Value extension](extension-rendered-value.html). Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.",
"example": [ {
"label": "General",
"valueString": "123456"
} ],
"base": {
"max": "1",
"min": 0,
"path": "Identifier.value"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "per-1",
"human": "If present, start SHALL have a lower value than end",
"xpath": "not(exists(f:start/@value)) or not(exists(f:end/@value)) or (xs:dateTime(f:start/@value) <= xs:dateTime(f:end/@value))",
"source": "http://hl7.org/fhir/StructureDefinition/Period",
"severity": "error",
"expression": "start.hasValue().not() or end.hasValue().not() or (start <= end)"
} ],
"path": "Specimen.identifier.period",
"min": 0,
"definition": "Time period during which identifier is/was valid for use.",
"short": "Time period when id is/was valid for use",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "DR",
"identity": "v2"
}, {
"map": "IVL[lowClosed=\"true\" and highClosed=\"true\"] or URG[lowClosed=\"true\" and highClosed=\"true\"]",
"identity": "rim"
}, {
"map": "CX.7 + CX.8",
"identity": "v2"
}, {
"map": "Role.effectiveTime or implied by context",
"identity": "rim"
}, {
"map": "./StartDate and ./EndDate",
"identity": "servd"
} ],
"type": [ {
"code": "Period"
} ],
"max": "1",
"id": "Specimen.identifier.period",
"condition": [ "ele-1" ],
"comment": "A Period specifies a range of time; the context of use will specify whether the entire range applies (e.g. \"the patient was an inpatient of the hospital for this time range\") or one value from the range applies (e.g. \"give to the patient between these two times\").\n\nPeriod is not used for a duration (a measure of elapsed time). See [Duration](datatypes.html#Duration).",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.period"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ref-1",
"human": "SHALL have a contained resource if a local reference is provided",
"xpath": "not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])",
"source": "http://hl7.org/fhir/StructureDefinition/Reference",
"severity": "error",
"expression": "reference.exists() implies (reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids')) or (reference='#' and %rootResource!=%resource))"
} ],
"path": "Specimen.identifier.assigner",
"min": 0,
"definition": "Organization that issued/manages the identifier.",
"short": "Organization that issued id (may be just text)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "The target of a resource reference is a RIM entry point (Act, Role, or Entity)",
"identity": "rim"
}, {
"map": "CX.4 / (CX.4,CX.9,CX.10)",
"identity": "v2"
}, {
"map": "II.assigningAuthorityName but note that this is an improper use by the definition of the field. Also Role.scoper",
"identity": "rim"
}, {
"map": "./IdentifierIssuingAuthority",
"identity": "servd"
} ],
"type": [ {
"code": "Reference",
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Organization-Genomics" ]
} ],
"max": "1",
"id": "Specimen.identifier.assigner",
"condition": [ "ele-1" ],
"comment": "The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.assigner"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier",
"min": 0,
"definition": "Id for specimen.",
"short": "External Identifier",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX / EI (occasionally, more often EI maps to a resource id or a URL)",
"identity": "v2"
}, {
"map": "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]",
"identity": "rim"
}, {
"map": "Identifier",
"identity": "servd"
}, {
"map": "FiveWs.identifier",
"identity": "w5"
}, {
"map": "SPM-2",
"identity": "v2"
}, {
"map": ".id",
"identity": "rim"
} ],
"type": [ {
"code": "Identifier"
} ],
"sliceName": "identifierGMSSpecimen",
"max": "1",
"id": "Specimen.identifier:identifierGMSSpecimen",
"condition": [ "ele-1" ],
"base": {
"max": "*",
"min": 0,
"path": "Specimen.identifier"
},
"isSummary": true
}, {
"path": "Specimen.identifier.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.identifier:identifierGMSSpecimen.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.identifier.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.identifier:identifierGMSSpecimen.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.use",
"requirements": "Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.",
"min": 0,
"definition": "The purpose of this identifier.",
"isModifier": true,
"short": "usual | official | temp | secondary | old (If known)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "v2"
}, {
"map": "Role.code or implied by context",
"identity": "rim"
} ],
"type": [ {
"code": "code"
} ],
"binding": {
"strength": "required",
"valueSet": "http://hl7.org/fhir/ValueSet/identifier-use|4.0.1",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierUse"
} ],
"description": "Identifies the purpose for this identifier, if known ."
},
"max": "0",
"id": "Specimen.identifier:identifierGMSSpecimen.use",
"condition": [ "ele-1" ],
"comment": "Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.use"
},
"isModifierReason": "This is labeled as \"Is Modifier\" because applications should not mistake a temporary id for a permanent one.",
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.type",
"requirements": "Allows users to make use of identifiers when the identifier system is not known.",
"min": 0,
"definition": "A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.",
"short": "Description of identifier",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": "CX.5",
"identity": "v2"
}, {
"map": "Role.code or implied by context",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/identifier-type",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierType"
} ],
"description": "A coded type for an identifier that can be used to determine which identifier to use for a specific purpose."
},
"max": "0",
"id": "Specimen.identifier:identifierGMSSpecimen.type",
"condition": [ "ele-1" ],
"comment": "This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.type"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.system",
"requirements": "There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.",
"min": 1,
"definition": "Establishes the namespace for the value - that is, a URL that describes a set values that are unique.",
"short": "The namespace for the identifier value",
"fixedUri": "https://fhir.nhs.uk/Id/GMSSpecimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX.4 / EI-2-4",
"identity": "v2"
}, {
"map": "II.root or Role.id.root",
"identity": "rim"
}, {
"map": "./IdentifierType",
"identity": "servd"
} ],
"type": [ {
"code": "uri"
} ],
"max": "1",
"id": "Specimen.identifier:identifierGMSSpecimen.system",
"condition": [ "ele-1" ],
"comment": "Identifier.system is always case sensitive.",
"example": [ {
"label": "General",
"valueUri": "http://www.acme.com/identifiers/patient"
} ],
"base": {
"max": "1",
"min": 0,
"path": "Identifier.system"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.value",
"min": 1,
"definition": "The portion of the identifier typically relevant to the user and which is unique within the context of the system.",
"short": "The value that is unique",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX.1 / EI.1",
"identity": "v2"
}, {
"map": "II.extension or II.root if system indicates OID or GUID (Or Role.id.extension or root)",
"identity": "rim"
}, {
"map": "./Value",
"identity": "servd"
} ],
"type": [ {
"code": "string"
} ],
"max": "1",
"id": "Specimen.identifier:identifierGMSSpecimen.value",
"condition": [ "ele-1" ],
"comment": "If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the [Rendered Value extension](extension-rendered-value.html). Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.",
"example": [ {
"label": "General",
"valueString": "123456"
} ],
"base": {
"max": "1",
"min": 0,
"path": "Identifier.value"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "per-1",
"human": "If present, start SHALL have a lower value than end",
"xpath": "not(exists(f:start/@value)) or not(exists(f:end/@value)) or (xs:dateTime(f:start/@value) <= xs:dateTime(f:end/@value))",
"source": "http://hl7.org/fhir/StructureDefinition/Period",
"severity": "error",
"expression": "start.hasValue().not() or end.hasValue().not() or (start <= end)"
} ],
"path": "Specimen.identifier.period",
"min": 0,
"definition": "Time period during which identifier is/was valid for use.",
"short": "Time period when id is/was valid for use",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "DR",
"identity": "v2"
}, {
"map": "IVL[lowClosed=\"true\" and highClosed=\"true\"] or URG[lowClosed=\"true\" and highClosed=\"true\"]",
"identity": "rim"
}, {
"map": "CX.7 + CX.8",
"identity": "v2"
}, {
"map": "Role.effectiveTime or implied by context",
"identity": "rim"
}, {
"map": "./StartDate and ./EndDate",
"identity": "servd"
} ],
"type": [ {
"code": "Period"
} ],
"max": "0",
"id": "Specimen.identifier:identifierGMSSpecimen.period",
"condition": [ "ele-1" ],
"comment": "A Period specifies a range of time; the context of use will specify whether the entire range applies (e.g. \"the patient was an inpatient of the hospital for this time range\") or one value from the range applies (e.g. \"give to the patient between these two times\").\n\nPeriod is not used for a duration (a measure of elapsed time). See [Duration](datatypes.html#Duration).",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.period"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ref-1",
"human": "SHALL have a contained resource if a local reference is provided",
"xpath": "not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])",
"source": "http://hl7.org/fhir/StructureDefinition/Reference",
"severity": "error",
"expression": "reference.exists() implies (reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids')) or (reference='#' and %rootResource!=%resource))"
} ],
"path": "Specimen.identifier.assigner",
"min": 0,
"definition": "Organization that issued/manages the identifier.",
"short": "Organization that issued id (may be just text)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "The target of a resource reference is a RIM entry point (Act, Role, or Entity)",
"identity": "rim"
}, {
"map": "CX.4 / (CX.4,CX.9,CX.10)",
"identity": "v2"
}, {
"map": "II.assigningAuthorityName but note that this is an improper use by the definition of the field. Also Role.scoper",
"identity": "rim"
}, {
"map": "./IdentifierIssuingAuthority",
"identity": "servd"
} ],
"type": [ {
"code": "Reference",
"targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Organization" ]
} ],
"max": "0",
"id": "Specimen.identifier:identifierGMSSpecimen.assigner",
"condition": [ "ele-1" ],
"comment": "The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.assigner"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier",
"min": 0,
"definition": "Id for specimen.",
"short": "External Identifier",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX / EI (occasionally, more often EI maps to a resource id or a URL)",
"identity": "v2"
}, {
"map": "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]",
"identity": "rim"
}, {
"map": "Identifier",
"identity": "servd"
}, {
"map": "FiveWs.identifier",
"identity": "w5"
}, {
"map": "SPM-2",
"identity": "v2"
}, {
"map": ".id",
"identity": "rim"
} ],
"type": [ {
"code": "Identifier"
} ],
"sliceName": "localIdentifier",
"max": "*",
"id": "Specimen.identifier:localIdentifier",
"condition": [ "ele-1" ],
"base": {
"max": "*",
"min": 0,
"path": "Specimen.identifier"
},
"isSummary": true
}, {
"path": "Specimen.identifier.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.identifier:localIdentifier.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.identifier.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.identifier:localIdentifier.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.use",
"requirements": "Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.",
"min": 0,
"definition": "The purpose of this identifier.",
"isModifier": true,
"short": "usual | official | temp | secondary | old (If known)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "v2"
}, {
"map": "Role.code or implied by context",
"identity": "rim"
} ],
"type": [ {
"code": "code"
} ],
"binding": {
"strength": "required",
"valueSet": "http://hl7.org/fhir/ValueSet/identifier-use|4.0.1",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierUse"
} ],
"description": "Identifies the purpose for this identifier, if known ."
},
"max": "1",
"id": "Specimen.identifier:localIdentifier.use",
"condition": [ "ele-1" ],
"comment": "Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.use"
},
"isModifierReason": "This is labeled as \"Is Modifier\" because applications should not mistake a temporary id for a permanent one.",
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.type",
"requirements": "Allows users to make use of identifiers when the identifier system is not known.",
"min": 0,
"definition": "A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.",
"short": "Description of identifier",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": "CX.5",
"identity": "v2"
}, {
"map": "Role.code or implied by context",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/identifier-type",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierType"
} ],
"description": "A coded type for an identifier that can be used to determine which identifier to use for a specific purpose."
},
"max": "1",
"id": "Specimen.identifier:localIdentifier.type",
"condition": [ "ele-1" ],
"comment": "This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.type"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.system",
"requirements": "There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.",
"min": 1,
"definition": "Establishes the namespace for the value - that is, a URL that describes a set values that are unique.",
"short": "The namespace for the identifier value",
"fixedUri": "https://fhir.nhs.uk/local-identifier/specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX.4 / EI-2-4",
"identity": "v2"
}, {
"map": "II.root or Role.id.root",
"identity": "rim"
}, {
"map": "./IdentifierType",
"identity": "servd"
} ],
"type": [ {
"code": "uri"
} ],
"max": "1",
"id": "Specimen.identifier:localIdentifier.system",
"condition": [ "ele-1" ],
"comment": "Identifier.system is always case sensitive.",
"example": [ {
"label": "General",
"valueUri": "http://www.acme.com/identifiers/patient"
} ],
"base": {
"max": "1",
"min": 0,
"path": "Identifier.system"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.value",
"min": 1,
"definition": "The portion of the identifier typically relevant to the user and which is unique within the context of the system.",
"short": "The value that is unique",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX.1 / EI.1",
"identity": "v2"
}, {
"map": "II.extension or II.root if system indicates OID or GUID (Or Role.id.extension or root)",
"identity": "rim"
}, {
"map": "./Value",
"identity": "servd"
} ],
"type": [ {
"code": "string"
} ],
"max": "1",
"id": "Specimen.identifier:localIdentifier.value",
"condition": [ "ele-1" ],
"comment": "If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the [Rendered Value extension](extension-rendered-value.html). Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.",
"example": [ {
"label": "General",
"valueString": "123456"
} ],
"base": {
"max": "1",
"min": 0,
"path": "Identifier.value"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "per-1",
"human": "If present, start SHALL have a lower value than end",
"xpath": "not(exists(f:start/@value)) or not(exists(f:end/@value)) or (xs:dateTime(f:start/@value) <= xs:dateTime(f:end/@value))",
"source": "http://hl7.org/fhir/StructureDefinition/Period",
"severity": "error",
"expression": "start.hasValue().not() or end.hasValue().not() or (start <= end)"
} ],
"path": "Specimen.identifier.period",
"min": 0,
"definition": "Time period during which identifier is/was valid for use.",
"short": "Time period when id is/was valid for use",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "DR",
"identity": "v2"
}, {
"map": "IVL[lowClosed=\"true\" and highClosed=\"true\"] or URG[lowClosed=\"true\" and highClosed=\"true\"]",
"identity": "rim"
}, {
"map": "CX.7 + CX.8",
"identity": "v2"
}, {
"map": "Role.effectiveTime or implied by context",
"identity": "rim"
}, {
"map": "./StartDate and ./EndDate",
"identity": "servd"
} ],
"type": [ {
"code": "Period"
} ],
"max": "1",
"id": "Specimen.identifier:localIdentifier.period",
"condition": [ "ele-1" ],
"comment": "A Period specifies a range of time; the context of use will specify whether the entire range applies (e.g. \"the patient was an inpatient of the hospital for this time range\") or one value from the range applies (e.g. \"give to the patient between these two times\").\n\nPeriod is not used for a duration (a measure of elapsed time). See [Duration](datatypes.html#Duration).",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.period"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ref-1",
"human": "SHALL have a contained resource if a local reference is provided",
"xpath": "not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])",
"source": "http://hl7.org/fhir/StructureDefinition/Reference",
"severity": "error",
"expression": "reference.exists() implies (reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids')) or (reference='#' and %rootResource!=%resource))"
} ],
"path": "Specimen.identifier.assigner",
"min": 1,
"definition": "Organization that issued/manages the identifier.",
"short": "Organization that issued id (may be just text)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "The target of a resource reference is a RIM entry point (Act, Role, or Entity)",
"identity": "rim"
}, {
"map": "CX.4 / (CX.4,CX.9,CX.10)",
"identity": "v2"
}, {
"map": "II.assigningAuthorityName but note that this is an improper use by the definition of the field. Also Role.scoper",
"identity": "rim"
}, {
"map": "./IdentifierIssuingAuthority",
"identity": "servd"
} ],
"type": [ {
"code": "Reference",
"targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Organization" ]
} ],
"max": "1",
"id": "Specimen.identifier:localIdentifier.assigner",
"condition": [ "ele-1" ],
"comment": "The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.",
"base": {
"max": "1",
"min": 0,
"path": "Identifier.assigner"
},
"isSummary": true
}, {
"path": "Specimen.identifier.assigner.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.identifier:localIdentifier.assigner.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.identifier.assigner.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.identifier:localIdentifier.assigner.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.assigner.reference",
"min": 0,
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"short": "Literal reference, Relative, internal or absolute URL",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "string"
} ],
"max": "0",
"id": "Specimen.identifier:localIdentifier.assigner.reference",
"condition": [ "ele-1", "ref-1" ],
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"base": {
"max": "1",
"min": 0,
"path": "Reference.reference"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.assigner.type",
"min": 0,
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"short": "Type the reference refers to (e.g. \"Patient\")",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "uri"
} ],
"binding": {
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
} ],
"description": "Aa resource (or, for logical models, the URI of the logical model)."
},
"max": "1",
"id": "Specimen.identifier:localIdentifier.assigner.type",
"condition": [ "ele-1" ],
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"base": {
"max": "1",
"min": 0,
"path": "Reference.type"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.assigner.identifier",
"min": 1,
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"short": "Logical reference, when literal reference is not known",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX / EI (occasionally, more often EI maps to a resource id or a URL)",
"identity": "v2"
}, {
"map": "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]",
"identity": "rim"
}, {
"map": "Identifier",
"identity": "servd"
}, {
"map": ".identifier",
"identity": "rim"
} ],
"fixedIdentifier": {
"system": "https://fhir.nhs.uk/Id/ods-organization-code"
},
"type": [ {
"code": "Identifier"
} ],
"max": "1",
"id": "Specimen.identifier:localIdentifier.assigner.identifier",
"condition": [ "ele-1" ],
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"base": {
"max": "1",
"min": 0,
"path": "Reference.identifier"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.identifier.assigner.display",
"min": 0,
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"short": "Text alternative for the resource",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "string"
} ],
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
} ],
"max": "1",
"id": "Specimen.identifier:localIdentifier.assigner.display",
"condition": [ "ele-1" ],
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"base": {
"max": "1",
"min": 0,
"path": "Reference.display"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.accessionIdentifier",
"min": 0,
"definition": "The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab procedures.",
"short": "Identifier assigned by the lab",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX / EI (occasionally, more often EI maps to a resource id or a URL)",
"identity": "v2"
}, {
"map": "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]",
"identity": "rim"
}, {
"map": "Identifier",
"identity": "servd"
}, {
"map": "FiveWs.identifier",
"identity": "w5"
}, {
"map": "SPM-30 (v2.7+)",
"identity": "v2"
}, {
"map": ".participation[typeCode=SBJ].act[classCode=ACSN, moodCode=EVN].id",
"identity": "rim"
} ],
"type": [ {
"code": "Identifier"
} ],
"max": "0",
"id": "Specimen.accessionIdentifier",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Specimen.accessionIdentifier"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.status",
"min": 1,
"definition": "If a Specimen has not been collected, the status SHOULD be marked as 'unavailable'. If the quality of the Specimen is such that it cannot be processed, the status SHOULD be 'unsatisfactory' (this is equivalent to a QC status of Failed). If the Specimen passes quality control, the status SHOULD be set as 'available'",
"isModifier": true,
"short": "available | unavailable | unsatisfactory | entered-in-error",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "FiveWs.status",
"identity": "w5"
}, {
"map": "SPM-20",
"identity": "v2"
}, {
"map": "status",
"identity": "rim"
} ],
"type": [ {
"code": "code"
} ],
"mustSupport": true,
"binding": {
"strength": "required",
"valueSet": "http://hl7.org/fhir/ValueSet/specimen-status|4.0.1",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SpecimenStatus"
} ],
"description": "Codes providing the status/availability of a specimen."
},
"max": "1",
"id": "Specimen.status",
"condition": [ "ele-1" ],
"comment": "This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.status"
},
"isModifierReason": "This element is labelled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid",
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.type",
"min": 1,
"definition": "The sample type, SNOMED CT preferred. Used to differentiate between raw and extracted (DNA) samples.\r\nConceptMaps for the allowed values for primary (raw) and final (extracted DNA) samples upon release of MDSv1.04, to aid identification of whether a sample is primary vs. final",
"short": "Kind of material that forms the specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": "FiveWs.what[x]",
"identity": "w5"
}, {
"map": "SPM-4 and possibly SPM-5",
"identity": "v2"
}, {
"map": ".code",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"mustSupport": true,
"binding": {
"strength": "preferred",
"valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-SpecimenType",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SpecimenType"
} ],
"description": "A code from the SNOMED CT UK Clinical Terminology coding system"
},
"max": "1",
"id": "Specimen.type",
"condition": [ "ele-1" ],
"comment": "The type can change the way that a specimen is handled and drives what kind of analyses can properly be performed on the specimen. It is frequently used in diagnostic work flow decision making systems.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.type"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ref-1",
"human": "SHALL have a contained resource if a local reference is provided",
"xpath": "not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])",
"source": "http://hl7.org/fhir/StructureDefinition/Reference",
"severity": "error",
"expression": "reference.exists() implies (reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids')) or (reference='#' and %rootResource!=%resource))"
} ],
"path": "Specimen.subject",
"requirements": "Must know the subject context.",
"min": 1,
"definition": "SHALL be provided. This SHOULD be a reference to the Patient resource or the identifier, NHS number, for the patient.\r\nSamples collected from a Fetus SHOULD reference a Patient resource for the Fetus. This should then be linked to relevant maternal/paternal resources through the RelatedPerson resource. Further information can be found on the Fetus Management clinical scenario. It is not envisaged that samples would need to be linked to more than one person e.g. both fetus and mother, though this assumption will be tested within the Alpha phase of the Genomic Medicine Service.",
"short": "Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "The target of a resource reference is a RIM entry point (Act, Role, or Entity)",
"identity": "rim"
}, {
"map": "FiveWs.subject[x]",
"identity": "w5"
}, {
"map": ".scoper or .scoper.playsRole",
"identity": "rim"
}, {
"map": "FiveWs.subject",
"identity": "w5"
} ],
"type": [ {
"code": "Reference",
"aggregation": [ "referenced", "bundled" ],
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics" ]
} ],
"mustSupport": true,
"max": "1",
"id": "Specimen.subject",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.subject"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.receivedTime",
"min": 0,
"definition": "SHOULD be updated upon receipt at a destination lab",
"short": "The time when specimen was received for processing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "FiveWs.done[x]",
"identity": "w5"
}, {
"map": "SPM-18",
"identity": "v2"
}, {
"map": ".participation[typeCode=SBJ].act[code=SPCREC, moodCode=EVN].effectiveTime",
"identity": "rim"
} ],
"type": [ {
"code": "dateTime"
} ],
"mustSupport": true,
"max": "1",
"id": "Specimen.receivedTime",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Specimen.receivedTime"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ref-1",
"human": "SHALL have a contained resource if a local reference is provided",
"xpath": "not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])",
"source": "http://hl7.org/fhir/StructureDefinition/Reference",
"severity": "error",
"expression": "reference.exists() implies (reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids')) or (reference='#' and %rootResource!=%resource))"
} ],
"path": "Specimen.parent",
"min": 0,
"definition": "If a sample has been split into multiple parts, such as DNA being extracted from a primary sample, each SHOULD be represented using an additional Specimen resource, referencing the parent sample through the parent element.\r\nThe central Order Management broker will only create Tasks for Specimen resources which do not have a parent element, i.e. primary samples. If required, clients can create Tasks for processing of derivative samples manually.\r\n\r\nMAY also be used to record the Block identifier for FFPE/Tissue samples, using the reference.identifier element, where a reference to a Specimen resource is not required.",
"short": "Specimen from which this specimen originated",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "The target of a resource reference is a RIM entry point (Act, Role, or Entity)",
"identity": "rim"
}, {
"map": ".scoper (if parent) .player.scopesRole[classCode=SPEC].player (if child)",
"identity": "rim"
} ],
"type": [ {
"code": "Reference",
"aggregation": [ "referenced", "bundled" ],
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Specimen-Genomics" ]
} ],
"max": "1",
"id": "Specimen.parent",
"condition": [ "ele-1" ],
"comment": "The parent specimen could be the source from which the current specimen is derived by some processing step (e.g. an aliquot or isolate or extracted nucleic acids from clinical samples) or one of many specimens that were combined to create a pooled sample.",
"base": {
"max": "*",
"min": 0,
"path": "Specimen.parent"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ref-1",
"human": "SHALL have a contained resource if a local reference is provided",
"xpath": "not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])",
"source": "http://hl7.org/fhir/StructureDefinition/Reference",
"severity": "error",
"expression": "reference.exists() implies (reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids')) or (reference='#' and %rootResource!=%resource))"
} ],
"path": "Specimen.request",
"min": 1,
"definition": "SHALL be provided. This SHOULD be a reference to the request which initiated collection of the sample. SHALL NOT be updated if the sample is used for another test e.g. for re-analysis. In the case that a Specimen needs to be processed as part of a new request, e.g. using a sample in storage, the ServiceRequest SHALL reference the pre-existing sample via ServiceRequest.specimen.",
"short": "Why the specimen was collected",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "The target of a resource reference is a RIM entry point (Act, Role, or Entity)",
"identity": "rim"
}, {
"map": "FiveWs.why[x]",
"identity": "w5"
}, {
"map": "ORC? OBR-2/3?",
"identity": "v2"
}, {
"map": "outboundRelationship[typeCode=FLFS].target",
"identity": "rim"
} ],
"type": [ {
"code": "Reference",
"aggregation": [ "referenced", "bundled" ],
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics" ]
} ],
"max": "1",
"id": "Specimen.request",
"condition": [ "ele-1" ],
"comment": "The request may be explicit or implied such with a ServiceRequest that requires a blood draw.",
"base": {
"max": "*",
"min": 0,
"path": "Specimen.request"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection",
"min": 0,
"definition": "Additional information which can be collected about the circumstances under which as sample was collected, if relevant. This include extensions for specialHandling of the sample, e.g. due to high risk of infection, as well as an extension to bodySite to extend the coding to a BodyStructure reference, for more detailed collection of structural information e.g. where tumour morphology and topography need to be collected (only required where morphology and topography are required.\r\nWhere the collector is an Organization, or where the individual is not known, ODS codes MAY be used as identifiers in place of SDS-User-IDs. However, if referencing a resource, the PractitionerRole resource SHOULD still be referenced. In this case the PractitionerRole.identifier and PractitionerRole.practitioner reference would not be filled, leaving only the reference to an Organization from PractitionerRole.organization.",
"short": "Collection details",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "SPM-14",
"identity": "v2"
}, {
"map": ".participation[typeCode=SBJ].act[classCode=SPECCOLLECT, moodCode=EVN]",
"identity": "rim"
} ],
"type": [ {
"code": "BackboneElement"
} ],
"max": "1",
"id": "Specimen.collection",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Specimen.collection"
}
}, {
"path": "Specimen.collection.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.collection.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.collection.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.extension",
"min": 0,
"definition": "Special handling during the collection, transport, or storage of the specimen.",
"short": "Special handling of the specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension",
"profile": [ "http://hl7.org/fhir/StructureDefinition/specimen-specialHandling" ]
} ],
"sliceName": "specialHandling",
"binding": {
"strength": "preferred",
"valueSet": "https://fhir.nhs.uk/ValueSet/genomics-specimen-collection-specialhandling"
},
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.collection.extension:specialHandling",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.modifierExtension",
"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](extensibility.html#modifierExtension).",
"min": 0,
"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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"isModifier": true,
"short": "Extensions that cannot be ignored even if unrecognized",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content", "modifiers" ],
"max": "*",
"id": "Specimen.collection.modifierExtension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "BackboneElement.modifierExtension"
},
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ref-1",
"human": "SHALL have a contained resource if a local reference is provided",
"xpath": "not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])",
"source": "http://hl7.org/fhir/StructureDefinition/Reference",
"severity": "error",
"expression": "reference.exists() implies (reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids')) or (reference='#' and %rootResource!=%resource))"
} ],
"path": "Specimen.collection.collector",
"min": 0,
"definition": "Person who collected the specimen.",
"short": "Who collected the specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "The target of a resource reference is a RIM entry point (Act, Role, or Entity)",
"identity": "rim"
}, {
"map": "FiveWs.actor",
"identity": "w5"
}, {
"map": "PRT",
"identity": "v2"
}, {
"map": ".participation[typeCode=PFM].role",
"identity": "rim"
} ],
"type": [ {
"code": "Reference",
"aggregation": [ "referenced", "bundled" ],
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics" ]
} ],
"max": "1",
"id": "Specimen.collection.collector",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.collection.collector"
},
"isSummary": true
}, {
"path": "Specimen.collection.collector.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.collection.collector.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.collector.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.collection.collector.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.collector.extension",
"min": 0,
"definition": "Person who collected the specimen. This is an R5 backport",
"isModifier": false,
"short": "Person who collected the specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension",
"profile": [ "http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.collector" ]
} ],
"sliceName": "collectionCollectorR5",
"alias": [ "extensions", "user content" ],
"max": "1",
"id": "Specimen.collection.collector.extension:collectionCollectorR5",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"path": "Specimen.collection.collector.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.collection.collector.extension:collectionCollectorR5.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.collector.extension.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.collection.collector.extension:collectionCollectorR5.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"path": "Specimen.collection.collector.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"short": "identifies the meaning of the extension",
"fixedUri": "http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.collector",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.collection.collector.extension:collectionCollectorR5.url",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.collector.extension.value[x]",
"min": 1,
"definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](extensibility.html) for a list).",
"short": "Person who collected the specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Reference",
"targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Patient", "http://hl7.org/fhir/StructureDefinition/RelatedPerson" ]
} ],
"max": "1",
"id": "Specimen.collection.collector.extension:collectionCollectorR5.value[x]",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.collector.reference",
"min": 0,
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"short": "Literal reference, Relative, internal or absolute URL",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "string"
} ],
"max": "1",
"id": "Specimen.collection.collector.reference",
"condition": [ "ele-1", "ref-1" ],
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"base": {
"max": "1",
"min": 0,
"path": "Reference.reference"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.collector.type",
"min": 0,
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"short": "Type the reference refers to (e.g. \"Patient\")",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "uri"
} ],
"binding": {
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
} ],
"description": "Aa resource (or, for logical models, the URI of the logical model)."
},
"max": "1",
"id": "Specimen.collection.collector.type",
"condition": [ "ele-1" ],
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"base": {
"max": "1",
"min": 0,
"path": "Reference.type"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.collector.identifier",
"min": 0,
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"short": "Logical reference, when literal reference is not known",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX / EI (occasionally, more often EI maps to a resource id or a URL)",
"identity": "v2"
}, {
"map": "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]",
"identity": "rim"
}, {
"map": "Identifier",
"identity": "servd"
}, {
"map": ".identifier",
"identity": "rim"
} ],
"type": [ {
"code": "Identifier"
} ],
"max": "1",
"id": "Specimen.collection.collector.identifier",
"condition": [ "ele-1" ],
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"base": {
"max": "1",
"min": 0,
"path": "Reference.identifier"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.collector.display",
"min": 0,
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"short": "Text alternative for the resource",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "string"
} ],
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
} ],
"max": "1",
"id": "Specimen.collection.collector.display",
"condition": [ "ele-1" ],
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"base": {
"max": "1",
"min": 0,
"path": "Reference.display"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.collected[x]",
"min": 1,
"definition": "Time when specimen was collected from subject - the physiologically relevant time.",
"short": "Collection time",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "FiveWs.init",
"identity": "w5"
}, {
"map": "SPM-17",
"identity": "v2"
}, {
"map": ".effectiveTime",
"identity": "rim"
} ],
"type": [ {
"code": "dateTime"
}, {
"code": "Period"
} ],
"max": "1",
"id": "Specimen.collection.collected[x]",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Specimen.collection.collected[x]"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "qty-3",
"human": "If a code for the unit is present, the system SHALL also be present",
"xpath": "not(exists(f:code)) or exists(f:system)",
"source": "http://hl7.org/fhir/StructureDefinition/Quantity",
"severity": "error",
"expression": "code.empty() or system.exists()"
}, {
"key": "drt-1",
"human": "There SHALL be a code if there is a value and it SHALL be an expression of time. If system is present, it SHALL be UCUM.",
"xpath": "(f:code or not(f:value)) and (not(exists(f:system)) or f:system/@value='http://unitsofmeasure.org')",
"source": "http://hl7.org/fhir/StructureDefinition/Duration",
"severity": "error",
"expression": "code.exists() implies ((system = %ucum) and value.exists())"
} ],
"path": "Specimen.collection.duration",
"min": 0,
"definition": "The span of time over which the collection of a specimen occurred.",
"short": "How long it took to collect specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "SN (see also Range) or CQ",
"identity": "v2"
}, {
"map": "PQ, IVL, MO, CO, depending on the values",
"identity": "rim"
}, {
"map": "PQ, IVL depending on the values",
"identity": "rim"
}, {
"map": "FiveWs.init",
"identity": "w5"
} ],
"type": [ {
"code": "Duration"
} ],
"max": "1",
"id": "Specimen.collection.duration",
"condition": [ "ele-1" ],
"comment": "The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.collection.duration"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "qty-3",
"human": "If a code for the unit is present, the system SHALL also be present",
"xpath": "not(exists(f:code)) or exists(f:system)",
"source": "http://hl7.org/fhir/StructureDefinition/Quantity",
"severity": "error",
"expression": "code.empty() or system.exists()"
}, {
"key": "sqty-1",
"human": "The comparator is not used on a SimpleQuantity",
"xpath": "not(exists(f:comparator))",
"source": "http://hl7.org/fhir/StructureDefinition/SimpleQuantity",
"severity": "error",
"expression": "comparator.empty()"
} ],
"path": "Specimen.collection.quantity",
"min": 0,
"definition": "The Specimen.collection.quantity is the amount of the sample collected at collection time. This quantity does not change as the sample is processed.\r\n\r\nThe Specimen.container.specimenQuantity is the amount of sample remaining in a container, this is equivalent to GEL 1001 banked volume. This value should be updated as the specimen is used.\r\n\r\nIf a specimen is split, additional specimen resources SHOULD be created (referencing the parent specimen), with individual container.specimenQuantity values.",
"isModifier": false,
"short": "The quantity of specimen collected",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "SN (see also Range) or CQ",
"identity": "v2"
}, {
"map": "PQ, IVL, MO, CO, depending on the values",
"identity": "rim"
}, {
"map": "SPM-12",
"identity": "v2"
}, {
"map": ".participation[typeCode=SBJ].role[classCode=SPEC].player.quantity",
"identity": "rim"
} ],
"type": [ {
"code": "Quantity",
"profile": [ "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" ]
} ],
"max": "1",
"id": "Specimen.collection.quantity",
"condition": [ "ele-1" ],
"comment": "The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.collection.quantity"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.method",
"min": 0,
"definition": "A coded value specifying the technique that is used to perform the procedure.",
"short": "Technique used to perform collection",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": "SPM-7",
"identity": "v2"
}, {
"map": ".methodCode",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "example",
"valueSet": "http://hl7.org/fhir/ValueSet/specimen-collection-method",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SpecimenCollectionMethod"
} ],
"description": "The technique that is used to perform the procedure."
},
"max": "1",
"id": "Specimen.collection.method",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.collection.method"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.bodySite",
"min": 0,
"definition": "Anatomical location from which the specimen was collected (if subject is a patient). This is the target site. This element is not used for environmental specimens.",
"short": "Anatomical collection site",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": "SPM-8 and SPM-9",
"identity": "v2"
}, {
"map": ".targetSiteCode",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "preferred",
"valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-SpecimenBodySite",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "BodySite"
} ],
"description": "Codes describing anatomical locations. May include laterality."
},
"max": "1",
"id": "Specimen.collection.bodySite",
"condition": [ "ele-1" ],
"comment": "If the use case requires BodySite to be handled as a separate resource instead of an inline coded element (e.g. to identify and track separately) then use the standard extension [bodySite](extension-bodysite.html).",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.collection.bodySite"
}
}, {
"path": "Specimen.collection.bodySite.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.collection.bodySite.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.bodySite.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.collection.bodySite.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.bodySite.extension",
"min": 0,
"definition": "An extension to replicate the changes within R5 altering the data type of Specimen.collection.bodySite from CodeableConcept to CodeableReference (bodyStructure).",
"isModifier": false,
"short": "An extension to allow referencing to a BodyStructure",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension",
"profile": [ "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BodySiteReference" ]
} ],
"sliceName": "bodySiteReference",
"alias": [ "extensions", "user content" ],
"max": "1",
"id": "Specimen.collection.bodySite.extension:bodySiteReference",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"path": "Specimen.collection.bodySite.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.collection.bodySite.extension:bodySiteReference.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.bodySite.extension.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.collection.bodySite.extension:bodySiteReference.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"path": "Specimen.collection.bodySite.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"short": "identifies the meaning of the extension",
"fixedUri": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BodySiteReference",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.collection.bodySite.extension:bodySiteReference.url",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.bodySite.extension.value[x]",
"min": 1,
"definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](extensibility.html) for a list).",
"short": "A reference to a BodyStructure",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Reference",
"targetProfile": [ "http://hl7.org/fhir/StructureDefinition/BodyStructure" ]
} ],
"max": "1",
"id": "Specimen.collection.bodySite.extension:bodySiteReference.value[x]",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.collection.bodySite.extension",
"min": 0,
"definition": "Record details about the anatomical location of a specimen or body part. This resource may be used when a coded concept does not provide the necessary detail needed for the use case.",
"isModifier": false,
"short": "Target anatomic location or structure",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension",
"profile": [ "http://hl7.org/fhir/StructureDefinition/bodySite" ]
} ],
"sliceName": "bodyStructureReference",
"alias": [ "extensions", "user content" ],
"max": "1",
"id": "Specimen.collection.bodySite.extension:bodyStructureReference",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.bodySite.coding",
"requirements": "Allows for alternative encodings within a code system, and translations to other code systems.",
"min": 0,
"definition": "A reference to a code defined by a terminology system.",
"short": "Code defined by a terminology system",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE subset one of the sets of component 1-3 or 4-6",
"identity": "v2"
}, {
"map": "CV",
"identity": "rim"
}, {
"map": "fhir:Coding rdfs:subClassOf dt:CDCoding",
"identity": "orim"
}, {
"map": "C*E.1-8, C*E.10-22",
"identity": "v2"
}, {
"map": "union(., ./translation)",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding",
"identity": "orim"
} ],
"type": [ {
"code": "Coding"
} ],
"max": "*",
"id": "Specimen.collection.bodySite.coding",
"condition": [ "ele-1" ],
"comment": "Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.",
"base": {
"max": "*",
"min": 0,
"path": "CodeableConcept.coding"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.bodySite.text",
"requirements": "The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.",
"min": 0,
"definition": "A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.",
"short": "Plain text representation of the concept",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "C*E.9. But note many systems use C*E.2 for this",
"identity": "v2"
}, {
"map": "./originalText[mediaType/code=\"text/plain\"]/data",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText",
"identity": "orim"
} ],
"type": [ {
"code": "string"
} ],
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
} ],
"max": "1",
"id": "Specimen.collection.bodySite.text",
"condition": [ "ele-1" ],
"comment": "Very often the text is the same as a displayName of one of the codings.",
"base": {
"max": "1",
"min": 0,
"path": "CodeableConcept.text"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.collection.fastingStatus[x]",
"requirements": "Many diagnostic tests require fasting to facilitate accurate interpretation.",
"min": 0,
"definition": "Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection.",
"short": "Whether or how long patient abstained from food and/or drink",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "OBR-",
"identity": "v2"
} ],
"type": [ {
"code": "CodeableConcept"
}, {
"code": "Duration"
} ],
"binding": {
"strength": "extensible",
"valueSet": "http://terminology.hl7.org/ValueSet/v2-0916",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FastingStatus"
} ],
"description": "Codes describing the fasting status of the patient."
},
"max": "1",
"id": "Specimen.collection.fastingStatus[x]",
"condition": [ "ele-1" ],
"comment": "Representing fasting status using this element is preferred to representing it with an observation using a 'pre-coordinated code' such as LOINC 2005-7 (Calcium [Moles/time] in 2 hour Urine --12 hours fasting), or using a component observation ` such as `Observation.component code` = LOINC 49541-6 (Fasting status - Reported).",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.collection.fastingStatus[x]"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing",
"min": 0,
"definition": "SHOULD be updated if processing occurs on the sample which affects later use, e.g. additives added",
"short": "Processing and processing step details",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": ".participation[typeCode=SBJ].act[code=SPCTRT, moodCode=EVN]",
"identity": "rim"
} ],
"type": [ {
"code": "BackboneElement"
} ],
"max": "*",
"id": "Specimen.processing",
"condition": [ "ele-1" ],
"base": {
"max": "*",
"min": 0,
"path": "Specimen.processing"
}
}, {
"path": "Specimen.processing.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.processing.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.processing.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.processing.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.processing.modifierExtension",
"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](extensibility.html#modifierExtension).",
"min": 0,
"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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"isModifier": true,
"short": "Extensions that cannot be ignored even if unrecognized",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content", "modifiers" ],
"max": "*",
"id": "Specimen.processing.modifierExtension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "BackboneElement.modifierExtension"
},
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.description",
"min": 0,
"definition": "Textual description of procedure.",
"short": "Textual description of procedure",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": ".text",
"identity": "rim"
} ],
"type": [ {
"code": "string"
} ],
"max": "1",
"id": "Specimen.processing.description",
"condition": [ "ele-1" ],
"comment": "Note that FHIR strings SHALL NOT exceed 1MB in size",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.processing.description"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure",
"min": 0,
"definition": "A coded value specifying the procedure used to process the specimen.",
"short": "Indicates the treatment step applied to the specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": ".code",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "example",
"valueSet": "http://hl7.org/fhir/ValueSet/specimen-processing-procedure",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SpecimenProcessingProcedure"
} ],
"description": "Type indicating the technique used to process the specimen."
},
"max": "1",
"id": "Specimen.processing.procedure",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.processing.procedure"
}
}, {
"path": "Specimen.processing.procedure.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.processing.procedure.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.processing.procedure.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.processing.procedure.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure.coding",
"requirements": "Allows for alternative encodings within a code system, and translations to other code systems.",
"min": 0,
"definition": "A reference to a code defined by a terminology system.",
"short": "Code defined by a terminology system",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE subset one of the sets of component 1-3 or 4-6",
"identity": "v2"
}, {
"map": "CV",
"identity": "rim"
}, {
"map": "fhir:Coding rdfs:subClassOf dt:CDCoding",
"identity": "orim"
}, {
"map": "C*E.1-8, C*E.10-22",
"identity": "v2"
}, {
"map": "union(., ./translation)",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding",
"identity": "orim"
} ],
"slicing": {
"rules": "open",
"discriminator": [ {
"path": "system",
"type": "pattern"
} ]
},
"type": [ {
"code": "Coding"
} ],
"max": "*",
"id": "Specimen.processing.procedure.coding",
"condition": [ "ele-1" ],
"comment": "Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.",
"base": {
"max": "*",
"min": 0,
"path": "CodeableConcept.coding"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure.coding",
"requirements": "Allows for alternative encodings within a code system, and translations to other code systems.",
"min": 0,
"definition": "codes from https://fhir.nhs.uk/ConceptMap/genomics-samplepreparation",
"short": "Code defined by a terminology system",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE subset one of the sets of component 1-3 or 4-6",
"identity": "v2"
}, {
"map": "CV",
"identity": "rim"
}, {
"map": "fhir:Coding rdfs:subClassOf dt:CDCoding",
"identity": "orim"
}, {
"map": "C*E.1-8, C*E.10-22",
"identity": "v2"
}, {
"map": "union(., ./translation)",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding",
"identity": "orim"
} ],
"type": [ {
"code": "Coding"
} ],
"sliceName": "codingSnomedCT",
"max": "*",
"id": "Specimen.processing.procedure.coding:codingSnomedCT",
"condition": [ "ele-1" ],
"comment": "Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.",
"base": {
"max": "*",
"min": 0,
"path": "CodeableConcept.coding"
},
"isSummary": true
}, {
"path": "Specimen.processing.procedure.coding.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.processing.procedure.coding:codingSnomedCT.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.processing.procedure.coding.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.processing.procedure.coding:codingSnomedCT.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure.coding.system",
"requirements": "Need to be unambiguous about the source of the definition of the symbol.",
"min": 0,
"definition": "The identification of the code system that defines the meaning of the symbol in the code.",
"short": "Identity of the terminology system",
"fixedUri": "http://snomed.info/sct",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "C*E.3",
"identity": "v2"
}, {
"map": "./codeSystem",
"identity": "rim"
}, {
"map": "fhir:Coding.system rdfs:subPropertyOf dt:CDCoding.codeSystem",
"identity": "orim"
} ],
"type": [ {
"code": "uri"
} ],
"max": "1",
"id": "Specimen.processing.procedure.coding:codingSnomedCT.system",
"condition": [ "ele-1" ],
"comment": "The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously.",
"base": {
"max": "1",
"min": 0,
"path": "Coding.system"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure.coding.version",
"min": 0,
"definition": "The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.",
"short": "Version of the system - if relevant",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "C*E.7",
"identity": "v2"
}, {
"map": "./codeSystemVersion",
"identity": "rim"
}, {
"map": "fhir:Coding.version rdfs:subPropertyOf dt:CDCoding.codeSystemVersion",
"identity": "orim"
} ],
"type": [ {
"code": "string"
} ],
"max": "1",
"id": "Specimen.processing.procedure.coding:codingSnomedCT.version",
"condition": [ "ele-1" ],
"comment": "Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date.",
"base": {
"max": "1",
"min": 0,
"path": "Coding.version"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure.coding.code",
"requirements": "Need to refer to a particular code in the system.",
"min": 0,
"definition": "A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).",
"short": "Symbol in syntax defined by the system",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "C*E.1",
"identity": "v2"
}, {
"map": "./code",
"identity": "rim"
}, {
"map": "fhir:Coding.code rdfs:subPropertyOf dt:CDCoding.code",
"identity": "orim"
} ],
"type": [ {
"code": "code"
} ],
"max": "1",
"id": "Specimen.processing.procedure.coding:codingSnomedCT.code",
"condition": [ "ele-1" ],
"comment": "Note that FHIR strings SHALL NOT exceed 1MB in size",
"base": {
"max": "1",
"min": 0,
"path": "Coding.code"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure.coding.display",
"requirements": "Need to be able to carry a human-readable meaning of the code for readers that do not know the system.",
"min": 0,
"definition": "A representation of the meaning of the code in the system, following the rules of the system.",
"short": "Representation defined by the system",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "C*E.2 - but note this is not well followed",
"identity": "v2"
}, {
"map": "CV.displayName",
"identity": "rim"
}, {
"map": "fhir:Coding.display rdfs:subPropertyOf dt:CDCoding.displayName",
"identity": "orim"
} ],
"type": [ {
"code": "string"
} ],
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
} ],
"max": "1",
"id": "Specimen.processing.procedure.coding:codingSnomedCT.display",
"condition": [ "ele-1" ],
"comment": "Note that FHIR strings SHALL NOT exceed 1MB in size",
"base": {
"max": "1",
"min": 0,
"path": "Coding.display"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure.coding.userSelected",
"requirements": "This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.",
"min": 0,
"definition": "Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).",
"short": "If this coding was chosen directly by the user",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "Sometimes implied by being first",
"identity": "v2"
}, {
"map": "CD.codingRationale",
"identity": "rim"
}, {
"map": "fhir:Coding.userSelected fhir:mapsTo dt:CDCoding.codingRationale. fhir:Coding.userSelected fhir:hasMap fhir:Coding.userSelected.map. fhir:Coding.userSelected.map a fhir:Map; fhir:target dt:CDCoding.codingRationale. fhir:Coding.userSelected\\#true a [ fhir:source \"true\"; fhir:target dt:CDCoding.codingRationale\\#O ]",
"identity": "orim"
} ],
"type": [ {
"code": "boolean"
} ],
"max": "1",
"id": "Specimen.processing.procedure.coding:codingSnomedCT.userSelected",
"condition": [ "ele-1" ],
"comment": "Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely.",
"base": {
"max": "1",
"min": 0,
"path": "Coding.userSelected"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.procedure.text",
"requirements": "The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.",
"min": 0,
"definition": "A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.",
"short": "Plain text representation of the concept",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "C*E.9. But note many systems use C*E.2 for this",
"identity": "v2"
}, {
"map": "./originalText[mediaType/code=\"text/plain\"]/data",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText",
"identity": "orim"
} ],
"type": [ {
"code": "string"
} ],
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
} ],
"max": "1",
"id": "Specimen.processing.procedure.text",
"condition": [ "ele-1" ],
"comment": "Very often the text is the same as a displayName of one of the codings.",
"base": {
"max": "1",
"min": 0,
"path": "CodeableConcept.text"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ref-1",
"human": "SHALL have a contained resource if a local reference is provided",
"xpath": "not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])",
"source": "http://hl7.org/fhir/StructureDefinition/Reference",
"severity": "error",
"expression": "reference.exists() implies (reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids')) or (reference='#' and %rootResource!=%resource))"
} ],
"path": "Specimen.processing.additive",
"min": 0,
"definition": "Material used in the processing step.",
"short": "Material used in the processing step",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "The target of a resource reference is a RIM entry point (Act, Role, or Entity)",
"identity": "rim"
}, {
"map": "SPM-6",
"identity": "v2"
}, {
"map": ".participation[typeCode=CSM].role[classCode=ADTV].code",
"identity": "rim"
} ],
"type": [ {
"code": "Reference",
"targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Substance" ]
} ],
"max": "*",
"id": "Specimen.processing.additive",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Specimen.processing.additive"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.processing.time[x]",
"min": 0,
"definition": "A record of the time or period when the specimen processing occurred. For example the time of sample fixation or the period of time the sample was in formalin.",
"short": "Date and time of specimen processing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": ".effectiveTime",
"identity": "rim"
} ],
"type": [ {
"code": "dateTime"
}, {
"code": "Period"
} ],
"max": "1",
"id": "Specimen.processing.time[x]",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Specimen.processing.time[x]"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.container",
"min": 0,
"definition": "The UK Core STU3 version of Specimen backports the R5 changes to the container BackboneElement to support capturing of storage location for a sample (through `container.location`) and recursive capture of device identifiers (e.g. tube, well, rack, freezer through `container.device`).\r\nThe container.identifier should match the identifier associated with the barcode for the tube/collection device. This can be searched using the container-id SearchParameter.\r\n\r\nAdditional examples/guidance will be provided within this IG once use of the fields has been appropriately tested.\r\n\r\nSample tracking information SHOULD be added to Tasks acting on Specimen resources, e.g. Tasks marked SamplePreparation or SampleProcessing, on either the output or input elements. This information MAY include consignment number, destination, date sent etc.\r\n\r\nIf known, the container type SHOULD be populated, using the example bound ValueSet, in SNOMED CT. If an appropraite code cannot be found, the specimen container type should be populated using free text, in Specimen.container.type.text. Additional container elements, such as capacity or specimenQuantity MAY be populated if known.",
"short": "Direct container of specimen (tube/slide, etc.)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": ".player.scopingRole[classCode=CONT].scoper",
"identity": "rim"
} ],
"type": [ {
"code": "BackboneElement"
} ],
"max": "1",
"id": "Specimen.container",
"condition": [ "ele-1" ],
"base": {
"max": "*",
"min": 0,
"path": "Specimen.container"
}
}, {
"path": "Specimen.container.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Specimen.container.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.container.extension",
"min": 0,
"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.",
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Specimen.container.extension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.container.extension",
"min": 0,
"definition": "R5: `Specimen.container.location` (new:Reference(Location))",
"isModifier": false,
"short": "R5: Where the container is (new)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension",
"profile": [ "http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.location" ]
} ],
"sliceName": "specimenContainerLocationR5",
"alias": [ "extensions", "user content" ],
"max": "1",
"id": "Specimen.container.extension:specimenContainerLocationR5",
"condition": [ "ele-1" ],
"comment": "Element `Specimen.container.location` has a context of Specimen.container based on following the parent source element upwards and mapping to `Specimen`.\nElement `Specimen.container.location` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Specimen.container.modifierExtension",
"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](extensibility.html#modifierExtension).",
"min": 0,
"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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"isModifier": true,
"short": "Extensions that cannot be ignored even if unrecognized",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content", "modifiers" ],
"max": "*",
"id": "Specimen.container.modifierExtension",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "*",
"min": 0,
"path": "BackboneElement.modifierExtension"
},
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.container.identifier",
"min": 0,
"definition": "Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The container ID may differ from the specimen id in some circumstances.",
"short": "Id for the container",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CX / EI (occasionally, more often EI maps to a resource id or a URL)",
"identity": "v2"
}, {
"map": "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]",
"identity": "rim"
}, {
"map": "Identifier",
"identity": "servd"
}, {
"map": "SAC-3",
"identity": "v2"
}, {
"map": ".id",
"identity": "rim"
} ],
"type": [ {
"code": "Identifier"
} ],
"max": "*",
"id": "Specimen.container.identifier",
"condition": [ "ele-1" ],
"base": {
"max": "*",
"min": 0,
"path": "Specimen.container.identifier"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.container.description",
"min": 0,
"definition": "Textual description of the container.",
"short": "Textual description of the container",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": ".desc",
"identity": "rim"
} ],
"type": [ {
"code": "string"
} ],
"max": "1",
"id": "Specimen.container.description",
"condition": [ "ele-1" ],
"comment": "Note that FHIR strings SHALL NOT exceed 1MB in size",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.container.description"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.container.type",
"min": 0,
"definition": "The type of container associated with the specimen (e.g. slide, aliquot, etc.).",
"short": "Kind of container directly associated with specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": "SPM-27",
"identity": "v2"
}, {
"map": ".code",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "preferred",
"valueSet": "http://hl7.org/fhir/ValueSet/specimen-container-type",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SpecimenContainerType"
} ],
"description": "Type of specimen container."
},
"max": "1",
"id": "Specimen.container.type",
"condition": [ "ele-1" ],
"comment": "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.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.container.type"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "qty-3",
"human": "If a code for the unit is present, the system SHALL also be present",
"xpath": "not(exists(f:code)) or exists(f:system)",
"source": "http://hl7.org/fhir/StructureDefinition/Quantity",
"severity": "error",
"expression": "code.empty() or system.exists()"
}, {
"key": "sqty-1",
"human": "The comparator is not used on a SimpleQuantity",
"xpath": "not(exists(f:comparator))",
"source": "http://hl7.org/fhir/StructureDefinition/SimpleQuantity",
"severity": "error",
"expression": "comparator.empty()"
} ],
"path": "Specimen.container.capacity",
"min": 0,
"definition": "The capacity (volume or other measure) the container may contain.",
"isModifier": false,
"short": "Container volume or size",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "SN (see also Range) or CQ",
"identity": "v2"
}, {
"map": "PQ, IVL, MO, CO, depending on the values",
"identity": "rim"
}, {
"map": "one of: SAC 16, SAC17 and SAC 20, or SAC 21 and SAC 20",
"identity": "v2"
}, {
"map": ".quantity",
"identity": "rim"
} ],
"type": [ {
"code": "Quantity",
"profile": [ "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" ]
} ],
"max": "1",
"id": "Specimen.container.capacity",
"condition": [ "ele-1" ],
"comment": "The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.container.capacity"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "qty-3",
"human": "If a code for the unit is present, the system SHALL also be present",
"xpath": "not(exists(f:code)) or exists(f:system)",
"source": "http://hl7.org/fhir/StructureDefinition/Quantity",
"severity": "error",
"expression": "code.empty() or system.exists()"
}, {
"key": "sqty-1",
"human": "The comparator is not used on a SimpleQuantity",
"xpath": "not(exists(f:comparator))",
"source": "http://hl7.org/fhir/StructureDefinition/SimpleQuantity",
"severity": "error",
"expression": "comparator.empty()"
} ],
"path": "Specimen.container.specimenQuantity",
"min": 0,
"definition": "The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type.",
"isModifier": false,
"short": "Quantity of specimen within container",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "SN (see also Range) or CQ",
"identity": "v2"
}, {
"map": "PQ, IVL, MO, CO, depending on the values",
"identity": "rim"
}, {
"map": "SAC-23 (value) SAC-24 (units",
"identity": "v2"
}, {
"map": ".playedRole[classCode=CONT].quantity",
"identity": "rim"
} ],
"type": [ {
"code": "Quantity",
"profile": [ "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" ]
} ],
"max": "1",
"id": "Specimen.container.specimenQuantity",
"condition": [ "ele-1" ],
"comment": "The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.",
"base": {
"max": "1",
"min": 0,
"path": "Specimen.container.specimenQuantity"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.container.additive[x]",
"min": 0,
"definition": "Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA.",
"short": "Additive associated with container",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "SAC-27",
"identity": "v2"
}, {
"map": ".scopesRole[classCode=ADTV].player",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
}, {
"code": "Reference",
"targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Substance" ]
} ],
"binding": {
"strength": "example",
"valueSet": "http://terminology.hl7.org/ValueSet/v2-0371",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SpecimenContainerAdditive"
} ],
"description": "Substance added to specimen container."
},
"max": "1",
"id": "Specimen.container.additive[x]",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Specimen.container.additive[x]"
}
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.condition",
"requirements": "The specimen condition can be used to assess its quality or appropriateness for a specific test.",
"min": 0,
"definition": "Used to record the condition of a specimen. Within Genomics, SHOULD be used to record the fixed/frozen state, using the UK Core bound ValueSet.",
"short": "State of the specimen",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "CE/CNE/CWE",
"identity": "v2"
}, {
"map": "CD",
"identity": "rim"
}, {
"map": "fhir:CodeableConcept rdfs:subClassOf dt:CD",
"identity": "orim"
}, {
"map": "SPM-24",
"identity": "v2"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "extensible",
"valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-BiopsyState",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SpecimenCondition"
} ],
"description": "Codes describing the state of the specimen."
},
"max": "1",
"id": "Specimen.condition",
"condition": [ "ele-1" ],
"comment": "Specimen condition is an observation made about the specimen. It's a point-in-time assessment. It can be used to assess its quality or appropriateness for a specific test.",
"base": {
"max": "*",
"min": 0,
"path": "Specimen.condition"
},
"isSummary": true
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Specimen.note",
"min": 0,
"definition": "To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).",
"short": "Comments",
"mapping": [ {
"map": "n/a",
"identity": "rim"
}, {
"map": "N/A",
"identity": "v2"
}, {
"map": "Act",
"identity": "rim"
}, {
"map": "OBX",
"identity": "v2"
}, {
"map": ".inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code=\"annotation\"].value",
"identity": "rim"
} ],
"type": [ {
"code": "Annotation"
} ],
"max": "*",
"id": "Specimen.note",
"condition": [ "ele-1" ],
"comment": "For systems that do not have structured annotations, they can simply communicate a single annotation with no author or time. This element may need to be included in narrative because of the potential for modifying information. *Annotations SHOULD NOT* be used to communicate \"modifying\" information that could be computable. (This is a SHOULD because enforcing user behavior is nearly impossible).",
"base": {
"max": "*",
"min": 0,
"path": "Specimen.note"
}
} ]
},
"status": "active",
"id": "b04489fe-8db5-4f7b-8506-0b6c7337de09",
"kind": "resource",
"url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Specimen-Genomics",
"version": "0.3.0",
"differential": {
"element": [ {
"id": "Specimen.extension:sampleCategory",
"path": "Specimen.extension",
"sliceName": "sampleCategory",
"definition": "Allows the categorisation of a sample into either tumour or germline. Required for WGS Cancer Testing, though not currently part of the Order Management MDS. Additional terms may be added upon review though the valueCodeableConcept.text field MAY be used as a free text representation if needed."
}, {
"id": "Specimen.identifier",
"min": 1,
"path": "Specimen.identifier",
"slicing": {
"rules": "open",
"discriminator": [ {
"path": "system",
"type": "pattern"
} ]
},
"definition": "Multiple identifiers MAY be assigned to a sample as it travels between labs. Each lab SHOULD append their local identifier to the identifier array if needed, ensuring either the system or assigner, is able to disambiguate any identifiers from possibly overlapping numbers from other organizations. Assigner is preferred in this case (see identifier example on the UKCore-Patient page for further guidance)\r\nNote: accessionIdentifier is unused by the Genomic Medicine Service to facilitate movement of samples across organizational boundaries."
}, {
"id": "Specimen.identifier.assigner",
"path": "Specimen.identifier.assigner",
"type": [ {
"code": "Reference",
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Organization-Genomics" ]
} ]
}, {
"id": "Specimen.identifier:identifierGMSSpecimen",
"max": "1",
"path": "Specimen.identifier",
"sliceName": "identifierGMSSpecimen"
}, {
"id": "Specimen.identifier:identifierGMSSpecimen.use",
"max": "0",
"path": "Specimen.identifier.use"
}, {
"id": "Specimen.identifier:identifierGMSSpecimen.type",
"max": "0",
"path": "Specimen.identifier.type"
}, {
"id": "Specimen.identifier:identifierGMSSpecimen.system",
"min": 1,
"path": "Specimen.identifier.system",
"fixedUri": "https://fhir.nhs.uk/Id/GMSSpecimen"
}, {
"id": "Specimen.identifier:identifierGMSSpecimen.value",
"min": 1,
"path": "Specimen.identifier.value"
}, {
"id": "Specimen.identifier:identifierGMSSpecimen.period",
"max": "0",
"path": "Specimen.identifier.period"
}, {
"id": "Specimen.identifier:identifierGMSSpecimen.assigner",
"max": "0",
"path": "Specimen.identifier.assigner"
}, {
"id": "Specimen.identifier:localIdentifier",
"path": "Specimen.identifier",
"sliceName": "localIdentifier"
}, {
"id": "Specimen.identifier:localIdentifier.system",
"min": 1,
"path": "Specimen.identifier.system",
"fixedUri": "https://fhir.nhs.uk/local-identifier/specimen"
}, {
"id": "Specimen.identifier:localIdentifier.value",
"min": 1,
"path": "Specimen.identifier.value"
}, {
"id": "Specimen.identifier:localIdentifier.assigner",
"min": 1,
"path": "Specimen.identifier.assigner"
}, {
"id": "Specimen.identifier:localIdentifier.assigner.reference",
"max": "0",
"path": "Specimen.identifier.assigner.reference"
}, {
"id": "Specimen.identifier:localIdentifier.assigner.identifier",
"min": 1,
"path": "Specimen.identifier.assigner.identifier",
"fixedIdentifier": {
"system": "https://fhir.nhs.uk/Id/ods-organization-code"
}
}, {
"id": "Specimen.accessionIdentifier",
"max": "0",
"path": "Specimen.accessionIdentifier"
}, {
"id": "Specimen.status",
"min": 1,
"path": "Specimen.status",
"definition": "If a Specimen has not been collected, the status SHOULD be marked as 'unavailable'. If the quality of the Specimen is such that it cannot be processed, the status SHOULD be 'unsatisfactory' (this is equivalent to a QC status of Failed). If the Specimen passes quality control, the status SHOULD be set as 'available'"
}, {
"id": "Specimen.type",
"min": 1,
"path": "Specimen.type",
"definition": "The sample type, SNOMED CT preferred. Used to differentiate between raw and extracted (DNA) samples.\r\nConceptMaps for the allowed values for primary (raw) and final (extracted DNA) samples upon release of MDSv1.04, to aid identification of whether a sample is primary vs. final"
}, {
"id": "Specimen.subject",
"min": 1,
"path": "Specimen.subject",
"type": [ {
"code": "Reference",
"aggregation": [ "referenced", "bundled" ],
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics" ]
} ],
"definition": "SHALL be provided. This SHOULD be a reference to the Patient resource or the identifier, NHS number, for the patient.\r\nSamples collected from a Fetus SHOULD reference a Patient resource for the Fetus. This should then be linked to relevant maternal/paternal resources through the RelatedPerson resource. Further information can be found on the Fetus Management clinical scenario. It is not envisaged that samples would need to be linked to more than one person e.g. both fetus and mother, though this assumption will be tested within the Alpha phase of the Genomic Medicine Service."
}, {
"id": "Specimen.receivedTime",
"path": "Specimen.receivedTime",
"definition": "SHOULD be updated upon receipt at a destination lab"
}, {
"id": "Specimen.parent",
"max": "1",
"path": "Specimen.parent",
"type": [ {
"code": "Reference",
"aggregation": [ "referenced", "bundled" ],
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Specimen-Genomics" ]
} ],
"definition": "If a sample has been split into multiple parts, such as DNA being extracted from a primary sample, each SHOULD be represented using an additional Specimen resource, referencing the parent sample through the parent element.\r\nThe central Order Management broker will only create Tasks for Specimen resources which do not have a parent element, i.e. primary samples. If required, clients can create Tasks for processing of derivative samples manually.\r\n\r\nMAY also be used to record the Block identifier for FFPE/Tissue samples, using the reference.identifier element, where a reference to a Specimen resource is not required."
}, {
"id": "Specimen.request",
"max": "1",
"min": 1,
"path": "Specimen.request",
"type": [ {
"code": "Reference",
"aggregation": [ "referenced", "bundled" ],
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics" ]
} ],
"definition": "SHALL be provided. This SHOULD be a reference to the request which initiated collection of the sample. SHALL NOT be updated if the sample is used for another test e.g. for re-analysis. In the case that a Specimen needs to be processed as part of a new request, e.g. using a sample in storage, the ServiceRequest SHALL reference the pre-existing sample via ServiceRequest.specimen."
}, {
"id": "Specimen.collection",
"path": "Specimen.collection",
"definition": "Additional information which can be collected about the circumstances under which as sample was collected, if relevant. This include extensions for specialHandling of the sample, e.g. due to high risk of infection, as well as an extension to bodySite to extend the coding to a BodyStructure reference, for more detailed collection of structural information e.g. where tumour morphology and topography need to be collected (only required where morphology and topography are required.\r\nWhere the collector is an Organization, or where the individual is not known, ODS codes MAY be used as identifiers in place of SDS-User-IDs. However, if referencing a resource, the PractitionerRole resource SHOULD still be referenced. In this case the PractitionerRole.identifier and PractitionerRole.practitioner reference would not be filled, leaving only the reference to an Organization from PractitionerRole.organization."
}, {
"id": "Specimen.collection.extension:specialHandling",
"path": "Specimen.collection.extension",
"binding": {
"strength": "preferred",
"valueSet": "https://fhir.nhs.uk/ValueSet/genomics-specimen-collection-specialhandling"
},
"sliceName": "specialHandling"
}, {
"id": "Specimen.collection.collector",
"path": "Specimen.collection.collector",
"type": [ {
"code": "Reference",
"aggregation": [ "referenced", "bundled" ],
"targetProfile": [ "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics" ]
} ]
}, {
"id": "Specimen.collection.collected[x]",
"min": 1,
"path": "Specimen.collection.collected[x]"
}, {
"id": "Specimen.collection.quantity",
"path": "Specimen.collection.quantity",
"definition": "The Specimen.collection.quantity is the amount of the sample collected at collection time. This quantity does not change as the sample is processed.\r\n\r\nThe Specimen.container.specimenQuantity is the amount of sample remaining in a container, this is equivalent to GEL 1001 banked volume. This value should be updated as the specimen is used.\r\n\r\nIf a specimen is split, additional specimen resources SHOULD be created (referencing the parent specimen), with individual container.specimenQuantity values."
}, {
"id": "Specimen.collection.bodySite.extension:bodyStructureReference",
"path": "Specimen.collection.bodySite.extension",
"type": [ {
"code": "Extension",
"profile": [ "http://hl7.org/fhir/StructureDefinition/bodySite" ]
} ],
"sliceName": "bodyStructureReference",
"isModifier": false
}, {
"id": "Specimen.processing",
"path": "Specimen.processing",
"definition": "SHOULD be updated if processing occurs on the sample which affects later use, e.g. additives added"
}, {
"id": "Specimen.processing.procedure.coding",
"path": "Specimen.processing.procedure.coding",
"slicing": {
"rules": "open",
"discriminator": [ {
"path": "system",
"type": "pattern"
} ]
}
}, {
"id": "Specimen.processing.procedure.coding:codingSnomedCT",
"path": "Specimen.processing.procedure.coding",
"sliceName": "codingSnomedCT",
"definition": "codes from https://fhir.nhs.uk/ConceptMap/genomics-samplepreparation"
}, {
"id": "Specimen.processing.procedure.coding:codingSnomedCT.system",
"path": "Specimen.processing.procedure.coding.system",
"fixedUri": "http://snomed.info/sct"
}, {
"id": "Specimen.container",
"max": "1",
"path": "Specimen.container",
"definition": "The UK Core STU3 version of Specimen backports the R5 changes to the container BackboneElement to support capturing of storage location for a sample (through `container.location`) and recursive capture of device identifiers (e.g. tube, well, rack, freezer through `container.device`).\r\nThe container.identifier should match the identifier associated with the barcode for the tube/collection device. This can be searched using the container-id SearchParameter.\r\n\r\nAdditional examples/guidance will be provided within this IG once use of the fields has been appropriately tested.\r\n\r\nSample tracking information SHOULD be added to Tasks acting on Specimen resources, e.g. Tasks marked SamplePreparation or SampleProcessing, on either the output or input elements. This information MAY include consignment number, destination, date sent etc.\r\n\r\nIf known, the container type SHOULD be populated, using the example bound ValueSet, in SNOMED CT. If an appropraite code cannot be found, the specimen container type should be populated using free text, in Specimen.container.type.text. Additional container elements, such as capacity or specimenQuantity MAY be populated if known."
}, {
"id": "Specimen.container.extension:specimenContainerLocationR5",
"path": "Specimen.container.extension",
"type": [ {
"code": "Extension",
"profile": [ "http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.location" ]
} ],
"sliceName": "specimenContainerLocationR5"
}, {
"id": "Specimen.condition",
"max": "1",
"path": "Specimen.condition",
"definition": "Used to record the condition of a specimen. Within Genomics, SHOULD be used to record the fixed/frozen state, using the UK Core bound ValueSet."
} ]
},
"contact": [ {
"name": "NHS England",
"telecom": [ {
"use": "work",
"rank": 1,
"value": "interoperabilityteam@nhs.net",
"system": "email"
} ]
} ],
"baseDefinition": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen"
}