UK Core Implementation Guide STU3 Sequence

Please note:

This version of the UK Core is a development copy.
This contains BREAKING CHANGES as a result of the C&TA Sprint 7 Review, and STU2 Sequence ballot reconciliation.
This version is not yet reviewed for implementation. Other versions are available on the UK Core Version History Guide
Please follow the guidance on the Contact Us page if you need any assistance.
A summary of changes is available on the STU3 Sequence Change Log

StructureDefinition Extension-UKCore-SampleCategory

Context of Use

Canonical_URL	Status	Current_Version	Last_Updated	Description	Profile_Purpose
https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory	active	1.1.0	2023-12-12	An extension to record the category of genome sequencing sample.	This extension is a Genomics use case to categorise the genome sequencing sample type, whether it is a tumour or germline Sample. This is different to Specimen.type which, for genomics, records the tissue of origin.

Tree View

Extension	I		Extension	Element id Extension Short description An extension to record the category of the sample. Definition This extension allows the recording of the category of a sample for use within Genomics, whether it is a tumour or germline sample. Data type Extension Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
id		0..1	string	There are no (further) constraints on this element Element id Extension.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Extension.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
url		1..1	uriFixed Value	Element id Extension.url Short description identifies the meaning of the extension Definition Source of the definition for the extension code - a logical name or a URL. Comments 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. Data type uri Fixed value https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory Mappings rim: N/A
value[x]		1..1	Binding	Element id Extension.value[x] Short description A set of codes to record the category of the sample Definition Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). Binding A set of codes to record the category of the sample UKCoreSampleCategory (extensible) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
valueCodeableConcept			CodeableConcept	Data type CodeableConcept

Detailed Descriptions

Extension
Definition	This extension allows the recording of the category of a sample for use within Genomics, whether it is a tumour or germline sample.
Cardinality	0...*
Invariants	ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()`
Mappings	rim: n/a rim: N/A
Extension.id
Definition	Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Cardinality	0...1
Type	string
Mappings	rim: n/a
Extension.extension
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.
Cardinality	0...*
Type	Extension
Alias	extensions, user content
Comments	There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Slicing	Unordered, Open, by url(Value)
Invariants	ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()`
Mappings	rim: n/a rim: N/A
Extension.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Cardinality	1...1
Type	uri
Comments	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.
Fixed Value	https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory
Mappings	rim: N/A
Extension.value[x]
Definition	Value of extension - must be one of a constrained set of the data types (see [Extensibility](extensibility.html) for a list).
Cardinality	1...1
Type	CodeableConcept
Binding	A set of codes to record the category of the sample UKCoreSampleCategory (extensible)
Invariants	ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())`
Mappings	rim: n/a rim: N/A

Table View

Extension		..
Extension.url		..
Extension.value[x]	CodeableConcept	1..

XML View

<StructureDefinition xmlns="http://hl7.org/fhir">
    <id value="Extension-UKCore-SampleCategory" />
    <url value="https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory" />
    <version value="1.1.0" />
    <name value="ExtensionUKCoreSampleCategory" />
    <title value="Extension UK Core Sample Category" />
    <status value="active" />
    <date value="2023-12-12" />
    <publisher value="HL7 UK" />
    <contact>
        <name value="HL7 UK" />
        <telecom>
            <system value="email" />
            <value value="ukcore@hl7.org.uk" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <description value="An extension to record the category of genome sequencing sample." />
    <purpose value="This extension is a Genomics use case to categorise the genome sequencing sample type, whether it is a tumour or germline Sample. This is different to Specimen.type which, for genomics, records the tissue of origin." />
    <copyright value="Copyright &#169; 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); 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 &quot;AS IS&quot; 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&#174; FHIR&#174; standard Copyright &#169; 2011+ HL7 The HL7&#174; FHIR&#174; standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html." />
    <fhirVersion value="4.0.1" />
    <kind value="complex-type" />
    <abstract value="false" />
    <context>
        <type value="element" />
        <expression value="Specimen" />
    </context>
    <type value="Extension" />
    <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Extension" />
    <derivation value="constraint" />
    <differential>
        <element id="Extension">
            <path value="Extension" />
            <short value="An extension to record the category of the sample." />
            <definition value="This extension allows the recording of the category of a sample for use within Genomics, whether it is a tumour or germline sample." />
        </element>
        <element id="Extension.url">
            <path value="Extension.url" />
            <fixedUri value="https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory" />
        </element>
        <element id="Extension.value[x]">
            <path value="Extension.value[x]" />
            <short value="A set of codes to record the category of the sample" />
            <min value="1" />
            <type>
                <code value="CodeableConcept" />
            </type>
            <binding>
                <strength value="extensible" />
                <description value="A set of codes to record the category of the sample" />
                <valueSet value="https://fhir.hl7.org.uk/ValueSet/UKCore-SampleCategory" />
            </binding>
        </element>
    </differential>
</StructureDefinition>

JSON View

{
    "resourceType": "StructureDefinition",
    "id": "Extension-UKCore-SampleCategory",
    "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory",
    "version": "1.1.0",
    "name": "ExtensionUKCoreSampleCategory",
    "title": "Extension UK Core Sample Category",
    "status": "active",
    "date": "2023-12-12",
    "publisher": "HL7 UK",
    "contact":  [
        {
            "name": "HL7 UK",
            "telecom":  [
                {
                    "system": "email",
                    "value": "ukcore@hl7.org.uk",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "description": "An extension to record the category of genome sequencing sample.",
    "purpose": "This extension is a Genomics use case to categorise the genome sequencing sample type, whether it is a tumour or germline Sample. This is different to Specimen.type which, for genomics, records the tissue of origin.",
    "copyright": "Copyright © 2021+ HL7 UK 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.",
    "fhirVersion": "4.0.1",
    "kind": "complex-type",
    "abstract": false,
    "context":  [
        {
            "type": "element",
            "expression": "Specimen"
        }
    ],
    "type": "Extension",
    "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension",
    "derivation": "constraint",
    "differential": {
        "element":  [
            {
                "id": "Extension",
                "path": "Extension",
                "short": "An extension to record the category of the sample.",
                "definition": "This extension allows the recording of the category of a sample for use within Genomics, whether it is a tumour or germline sample."
            },
            {
                "id": "Extension.url",
                "path": "Extension.url",
                "fixedUri": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory"
            },
            {
                "id": "Extension.value[x]",
                "path": "Extension.value[x]",
                "short": "A set of codes to record the category of the sample",
                "min": 1,
                "type":  [
                    {
                        "code": "CodeableConcept"
                    }
                ],
                "binding": {
                    "strength": "extensible",
                    "description": "A set of codes to record the category of the sample",
                    "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-SampleCategory"
                }
            }
        ]
    }
}

Feedback

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Report issue for Extension-UKCore-SampleCategory

Examples

Sample Category- An example to illustrate the extension to show the Genomics classification of a sample.
Example UKCore-Extension-SampleCategory

Extension Specific Guidance

There is a binding within this extension to a ValueSet UKCore-SampleCategory.