Genomics Clinical Picture Repository Implementation Guide
0.1.0 - ci-build
Genomics Clinical Picture Repository Implementation Guide - Local Development build (v0.1.0). See the Directory of published versions
Active as of 2022-03-21 |
Definitions for the GencliprResearchSubject resource profile.
1. ResearchSubject | |
Definition | A physical entity which is the primary unit of operational and/or administrative interest in a study. |
Control | 0..* |
Alternate Names | Study Subject |
Comments | Need to make sure we encompass public health studies. |
Invariants | Defined on this element dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (: contained.contained.empty()) dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource (: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()) dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated (: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()) dom-5: If a resource is contained in another resource, it SHALL NOT have a security label (: contained.meta.security.empty()) dom-6: A resource should have narrative for robust management (: text.`div`.exists()) |
2. ResearchSubject.id | |
Definition | The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. |
Control | 0..1 |
Type | string |
Comments | The only time that a resource does not have an id is when it is being submitted to the server using a create operation. |
3. ResearchSubject.meta | |
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. |
Control | 0..1 |
Type | Meta |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
4. ResearchSubject.implicitRules | |
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. |
Control | 0..1 |
Type | uri |
Is Modifier | true |
Comments | Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc. |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
5. ResearchSubject.language | |
Definition | The base language in which the resource is written. |
Control | 0..1 |
Binding | The codes SHOULD be taken from CommonLanguages Max Binding: AllLanguages A human language. |
Type | code |
Comments | Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute). |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
6. ResearchSubject.text | |
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. |
Control | 0..1 |
Type | Narrative |
Alternate Names | narrative, html, xhtml, display |
Comments | Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later. |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
7. ResearchSubject.contained | |
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. |
Control | 0..* |
Type | Resource |
Alternate Names | inline resources, anonymous resources, contained resources |
Comments | This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels. |
8. ResearchSubject.extension | |
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. |
Control | 0..* |
Type | Extension |
Alternate Names | 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. |
Invariants | Defined on this element 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()) |
9. ResearchSubject.modifierExtension | |
Definition | May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). |
Control | 0..* |
Type | Extension |
Is Modifier | true |
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. |
Alternate Names | 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. |
Invariants | Defined on this element 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()) |
10. ResearchSubject.identifier | |
Definition | Identifiers assigned to this research subject for a study. |
Note | This is a business identifier, not a resource identifier (see discussion) |
Control | 1..* |
Type | Identifier |
Must Support | true |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
11. ResearchSubject.identifier.id | |
Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
Control | 0..1 |
Type | string |
12. ResearchSubject.identifier.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. |
Control | 0..* |
Type | Extension |
Alternate Names | 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. |
Invariants | Defined on this element 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()) |
Slicing | This element introduces a set of slices on ResearchSubject.identifier.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
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13. ResearchSubject.identifier.use | |
Definition | The purpose of this identifier. |
Control | 0..1 |
Binding | The codes SHALL be taken from IdentifierUse Identifies the purpose for this identifier, if known . |
Type | code |
Is Modifier | true |
Requirements | Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers. |
Comments | Applications can assume that an identifier is permanent unless it explicitly says that it is temporary. |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
14. ResearchSubject.identifier.type | |
Definition | A coded type for the identifier that can be used to determine which identifier to use for a specific purpose. |
Control | 0..1 |
Binding | The codes SHALL be taken from Identifier Type Codes; other codes may be used where these codes are not suitable A coded type for an identifier that can be used to determine which identifier to use for a specific purpose. |
Type | CodeableConcept |
Requirements | Allows users to make use of identifiers when the identifier system is not known. |
Comments | 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. |
Pattern Value | <valueCodeableConcept xmlns="http://hl7.org/fhir"> <coding> <system value="http://terminology.hl7.org/CodeSystem/v2-0203"/> <code value="PI"/> </coding> </valueCodeableConcept> |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
15. ResearchSubject.identifier.system | |
Definition | Establishes the namespace for the value - that is, a URL that describes a set values that are unique. |
Control | 0..1 |
Type | uri |
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. |
Comments | Identifier.system is always case sensitive. |
Example | General:http://www.acme.com/identifiers/patient |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
16. ResearchSubject.identifier.value | |
Definition | The portion of the identifier typically relevant to the user and which is unique within the context of the system. |
Control | 0..1 |
Type | string |
Comments | 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. 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 | General:123456 |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
17. ResearchSubject.identifier.period | |
Definition | Time period during which identifier is/was valid for use. |
Control | 0..1 |
Type | Period |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
18. ResearchSubject.identifier.assigner | |
Definition | Organization that issued/manages the identifier. |
Control | 0..1 |
Type | Reference(Organization) |
Comments | 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. |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
19. ResearchSubject.status | |
Definition | The current state of the subject. |
Control | 1..1 |
Binding | The codes SHALL be taken from ResearchSubjectStatus Indicates the progression of a study subject through a study. |
Type | code |
Is Modifier | true |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
20. ResearchSubject.period | |
Definition | The dates the subject began and ended their participation in the study. |
Control | 0..1 |
Type | Period |
Alternate Names | timing |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
21. ResearchSubject.study | |
Definition | Reference to the study the subject is participating in. |
Control | 1..1 |
Type | Reference(GencliprResearchStudy) |
Must Support | true |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
22. ResearchSubject.individual | |
Definition | The record of the person or animal who is involved in the study. |
Control | 1..1 |
Type | Reference(DeidentifiedPatient) |
Must Support | true |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
23. ResearchSubject.assignedArm | |
Definition | The name of the arm in the study the subject is expected to follow as part of this study. |
Control | 0..1 |
Type | string |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
24. ResearchSubject.actualArm | |
Definition | The name of the arm in the study the subject actually followed as part of this study. |
Control | 0..1 |
Type | string |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |
25. ResearchSubject.consent | |
Definition | A record of the patient's informed agreement to participate in the study. |
Control | 0..1 |
Type | Reference(Consent) |
Invariants | Defined on this element ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count())) |