FHIR IG analytics| Package | hl7.fhir.uv.cg-incubator |
| Resource Type | StructureDefinition |
| Id | StructureDefinition-GenomicStudy.json |
| FHIR Version | R6 |
| Source | https://build.fhir.org/ig/HL7/cg-incubator/StructureDefinition-GenomicStudy.html |
| URL | http://hl7.org/fhir/StructureDefinition/GenomicStudy |
| Version | 0.1.0-ci-build |
| Status | draft |
| Date | 2021-01-02T08:58:31+11:00 |
| Name | GenomicStudy |
| Title | Genomic Study |
| Realm | uv |
| Authority | hl7 |
| Description | A set of analyses performed to analyze and generate genomic data. |
| Type | GenomicStudy |
| Kind | resource |
No resources found
| ValueSet | ||
| hl7.fhir.uv.cg-incubator#current | genomicstudy-changetype | Genomic Study Change Type VS |
| hl7.fhir.uv.cg-incubator#current | genomicstudy-dataformat | Genomic Study Data Format VS |
| hl7.fhir.uv.cg-incubator#current | genomicstudy-methodtype | Genomic Study Method Type VS |
| hl7.fhir.uv.cg-incubator#current | genomicstudy-regiontype | Genomic Study Region Type VS |
| hl7.fhir.uv.cg-incubator#current | genomicstudy-status | Genomic Study Status VS |
| hl7.fhir.uv.cg-incubator#current | genomicstudy-type | Genomic Study Type VS |
| hl7.fhir.uv.cg-incubator#current | hgnc-vs | HUGO Gene Nomenclature Committee Gene Names (HGNC) |
Note: links and images are rebased to the (stated) source
Generated Narrative: StructureDefinition GenomicStudy
Last updated: 2021-01-02 08:58:31+1100
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  GenomicStudy | 0..* | DomainResource | Genomic Study Elements defined in Ancestors:id, meta, implicitRules, language, text, contained, extension, modifierExtension | |
  identifier | Σ | 0..* | Identifier | Identifiers for this genomic study |
 status | ?!Σ | 1..1 | code | registered | available | cancelled | entered-in-error | unknown Binding: Genomic Study Status VS (required): The status of the GenomicStudy. |
| type | Σ | 0..* | CodeableConcept | The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling) Binding: Genomic Study Type VS (example): The type relevant to GenomicStudy. |
 subject | Σ | 1..1 | Reference(Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct) | The primary subject of the genomic study |
| encounter | Σ | 0..1 | Reference(Encounter) | The healthcare event with which this genomics study is associated |
| startDate | 0..1 | dateTime | When the genomic study was started | |
| basedOn | 0..* | Reference(ServiceRequest | Task) | Event resources that the genomic study is based on | |
| referrer | 0..1 | Reference(Practitioner | PractitionerRole) | Healthcare professional who requested or referred the genomic study | |
| interpreter | 0..* | Reference(Practitioner | PractitionerRole) | Healthcare professionals who interpreted the genomic study | |
| reason | 0..* | CodeableReference(Condition | Observation) | Why the genomic study was performed | |
| instantiatesCanonical | 0..1 | canonical(PlanDefinition) | The defined protocol that describes the study | |
| instantiatesUri | 0..1 | uri | The URL pointing to an externally maintained protocol that describes the study | |
| note | 0..* | Annotation | Comments related to the genomic study | |
| description | 0..1 | markdown | Description of the genomic study | |
 analysis | C | 0..* | BackboneElement | Genomic Analysis Event Constraints: gs-regions-1, gs-regions-2 |
 identifier | Σ | 0..* | Identifier | Identifiers for the analysis event |
| methodType | Σ | 0..* | CodeableConcept | Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI) Binding: Genomic Study Method Type VS (preferred): The method type of the GenomicStudy analysis. |
| changeType | 0..* | CodeableConcept | Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change) Binding: Genomic Study Change Type VS (preferred): The change type relevant to GenomicStudy analysis. | |
| genomeBuild | 0..1 | CodeableConcept | Genome build that is used in this analysis Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build ID | |
| genomicSourceClass | 0..1 | CodeableConcept | The genomic source class of the specimens used in the analysis (e.g., somatic, germline) Binding: LOINC Answer List LL378-1 (extensible): The genomic source class (e.g., somatic, germline) of the specimens being analyzed. | |
| instantiatesCanonical | 0..1 | canonical(PlanDefinition | ActivityDefinition) | The defined protocol that describes the analysis | |
| instantiatesUri | 0..1 | uri | The URL pointing to an externally maintained protocol that describes the analysis | |
| title | Σ | 0..1 | string | Name of the analysis event (human friendly) |
| focus | Σ | 0..* | Reference(Resource) | What the genomic analysis is about, when it is not about the subject of record |
| specimen | Σ | 0..* | Reference(Specimen) | The specimen used in the analysis event |
| date | 0..1 | dateTime | The date of the analysis event | |
| note | 0..* | Annotation | Any notes capture with the analysis event | |
| metrics | 0..1 | BackboneElement | Quality metrics for the analysis | |
 readDepth | 0..1 | SimpleQuantity | Average read depth (e.g., 30x, 100x) | |
| sequencingCoverage | 0..1 | SimpleQuantity | Percentage of studied regions sequenced (e.g., 95%) | |
| description | 0..1 | string | Freetext coverage metrics description | |
| protocolPerformed | 0..1 | Reference(Procedure | Task) | The protocol that was performed for the analysis event | |
| genomicRegion | 0..* | BackboneElement | Genomic regions relevant to the analysis, grouped by type | |
| type | 1..1 | CodeableConcept | studied | called | uncalled Binding: Genomic Study Region Type VS (extensible): The type of genomic region group. Use studied, called, or uncalled where applicable; other codes may be used for methodology-specific region classifications not covered by this value set. | |
| locus | 0..* | CodeableReference(DocumentReference) | Genomic regions in this group (coded genes or BED file) Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible): HGNC gene names for coded gene lists. | |
| description | 0..1 | string | Additional details about this region group | |
| input | 0..* | BackboneElement | Inputs for the analysis event | |
| file | Σ | 0..1 | Reference(DocumentReference) | File containing input data |
| type | 0..1 | CodeableConcept | Type of input data (e.g., BAM, CRAM, or FASTA) Binding: Genomic Study Data Format VS (example): The data format of the data file. | |
 generatedBy[x] | 0..1 | The analysis event or other GenomicStudy that generated this input file | ||
| generatedByIdentifier | Identifier | |||
| generatedByReference | Reference(Genomic Study) | |||
| output | 0..* | BackboneElement | Outputs for the analysis event | |
| file | Σ | 0..1 | Reference(DocumentReference) | File containing output data |
| type | Σ | 0..1 | CodeableConcept | Type of output data (e.g., VCF, MAF, or BAM) Binding: Genomic Study Data Format VS (example): The data format of the data file. |
| performer | 0..* | BackboneElement | Performer for the analysis event | |
| actor | 0..1 | Reference(Practitioner | PractitionerRole | Organization | Device) | The organization, healthcare professional, or others who participated in performing this analysis | |
| role | 0..1 | CodeableConcept | Role of the actor for this analysis | |
| device | 0..* | BackboneElement | Devices used for the analysis (e.g., instruments, software), with settings and parameters | |
| device | 0..1 | Reference(Device) | Device used for the analysis | |
| function | 0..1 | CodeableConcept | Specific function for the device used for the analysis | |
| Documentation for this format | ||||
FHIR
FHIRsmith{
"resourceType": "StructureDefinition",
"id": "GenomicStudy",
"meta": {
"lastUpdated": "2021-01-02T08:58:31.578+11:00"
},
"text": {
"status": "extensions",
"div": "<!-- snip (see above) -->"
},
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-category",
"valueString": "Clinical.Diagnostics"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode": "draft"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger": 1
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category",
"valueCode": "patient"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode": "cg"
},
{
"url": "http://hl7.org/fhir/build/StructureDefinition/entered-in-error-status",
"valueCode": ".status = entered-in-error"
},
{
"url": "http://hl7.org/fhir/tools/StructureDefinition/additional-resource",
"valueBoolean": true
}
],
"url": "http://hl7.org/fhir/StructureDefinition/GenomicStudy",
"identifier": [
{
"system": "urn:ietf:rfc:3986",
"value": "urn:oid:2.16.840.1.113883.4.642.5.1109"
}
],
"version": "0.1.0-ci-build",
"name": "GenomicStudy",
"title": "Genomic Study",
"status": "draft",
"experimental": true,
"date": "2021-01-02T08:58:31+11:00",
"publisher": "HL7 International / Clinical Genomics",
"contact": [
{
"name": "HL7 International / Clinical Genomics",
"telecom": [
{
"system": "url",
"value": "http://www.hl7.org/Special/committees/clingenomics"
},
{
"system": "email",
"value": "clingenomics@lists.hl7.org"
}
]
}
],
"description": "A set of analyses performed to analyze and generate genomic data.",
"jurisdiction": [
{
"coding": [
{
"system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code": "001",
"display": "World"
}
]
}
],
"fhirVersion": "6.0.0-ballot5",
"mapping": [
{
"identity": "workflow",
"uri": "http://hl7.org/fhir/workflow",
"name": "Workflow Pattern"
},
{
"identity": "rim",
"uri": "http://hl7.org/v3",
"name": "RIM Mapping"
},
{
"identity": "w5",
"uri": "http://hl7.org/fhir/fivews",
"name": "FiveWs Pattern Mapping"
},
{
"identity": "v2",
"uri": "http://hl7.org/v2",
"name": "HL7 V2 Mapping"
}
],
"kind": "resource",
"abstract": false,
"type": "GenomicStudy",
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/DomainResource",
"derivation": "specialization",
"snapshot": {
"extension": [
{
"url": "http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version",
"valueString": "6.0.0-ballot5"
}
],
"element": [
{
"id": "GenomicStudy",
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/svg",
"valueCode": "0,0"
}
],
"path": "GenomicStudy",
"short": "Genomic Study",
"definition": "A GenomicStudy is a set of analyses performed to analyze and generate genomic data.",
"min": 0,
"max": "*",
"base": {
"path": "DomainResource",
"min": 0,
"max": "*"
},
"constraint": [
{
"key": "dom-2",
"severity": "error",
"human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources",
"expression": "contained.contained.empty()",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key": "dom-3",
"severity": "error",
"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",
"expression": "contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key": "dom-4",
"severity": "error",
"human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated",
"expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key": "dom-5",
"severity": "error",
"human": "If a resource is contained in another resource, it SHALL NOT have a security label",
"expression": "contained.meta.security.empty()",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"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."
}
],
"key": "dom-6",
"severity": "warning",
"human": "A resource should have narrative for robust management",
"expression": "text.`div`.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "workflow",
"map": "Event"
},
{
"identity": "w5",
"map": "clinical.diagnostics"
},
{
"identity": "rim",
"map": "Entity. Role, or Act,Entity, Role, or Act"
}
]
},
{
"id": "GenomicStudy.id",
"path": "GenomicStudy.id",
"short": "Logical id of this artifact",
"definition": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.",
"comment": "Within the context of the FHIR RESTful interactions, the resource has an id except for cases like the create and conditional update. Otherwise, the use of the resource id depends on the given use case.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "GenomicStudy.meta",
"path": "GenomicStudy.meta",
"short": "Metadata about the resource",
"definition": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.meta",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Meta"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "GenomicStudy.implicitRules",
"path": "GenomicStudy.implicitRules",
"short": "A set of rules under which this content was created",
"definition": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. For DomainResources, if more than one implicitRules policy applies, additional policies may be conveyed using the [additionalImplicitRules](https://build.fhir.org/ig/HL7/fhir-extensions/StructureDefinition-additionalImplicitRules.html) extension.",
"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 its narrative along with other profiles, value sets, etc.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.implicitRules",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"mustSupport": false,
"isModifier": true,
"isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies its meaning or interpretation",
"isSummary": true
},
{
"id": "GenomicStudy.language",
"path": "GenomicStudy.language",
"short": "Language of the resource content",
"definition": "The base language in which the resource is written.",
"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).",
"min": 0,
"max": "1",
"base": {
"path": "Resource.language",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "Language"
}
],
"strength": "required",
"description": "IETF language tag for a human language",
"valueSet": "http://hl7.org/fhir/ValueSet/all-languages|6.0.0-ballot5",
"additional": [
{
"purpose": "starter",
"valueSet": "http://hl7.org/fhir/ValueSet/languages|6.0.0-ballot5"
}
]
}
},
{
"id": "GenomicStudy.text",
"path": "GenomicStudy.text",
"short": "Text summary of the resource, for human interpretation",
"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.",
"comment": "Contained resources do not have a 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.",
"alias": [
"narrative",
"html",
"xhtml",
"display"
],
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.text",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Narrative"
}
],
"condition": [
"dom-6"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "Act.text?"
}
]
},
{
"id": "GenomicStudy.contained",
"path": "GenomicStudy.contained",
"short": "Contained, inline Resources",
"definition": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, nor can they have their own independent transaction scope. This is allowed to be a Parameters resource if and only if it is referenced by a resource that provides context/meaning.",
"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. Contained resources may be a resource type defined in the FHIR specification, or an [additional resource](http://build.fhir.org/resource.html#additional).",
"alias": [
"inline resources",
"anonymous resources",
"contained resources"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.contained",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Resource"
}
],
"condition": [
"dom-2",
"dom-4",
"dom-3",
"dom-5"
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.extension",
"path": "GenomicStudy.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"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 managable, 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.",
"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.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.modifierExtension",
"path": "GenomicStudy.modifierExtension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Extensions that cannot be ignored",
"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 managable, 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).",
"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.",
"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](http://build.fhir.org/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"mustSupport": false,
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.identifier",
"path": "GenomicStudy.identifier",
"short": "Identifiers for this genomic study",
"definition": "Identifiers for this genomic study.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.identifier",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true
},
{
"id": "GenomicStudy.status",
"path": "GenomicStudy.status",
"short": "registered | available | cancelled | entered-in-error | unknown",
"definition": "The status of the genomic study.",
"min": 1,
"max": "1",
"base": {
"path": "GenomicStudy.status",
"min": 1,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"isModifier": true,
"isModifierReason": "This element is labeled 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,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyStatus"
}
],
"strength": "required",
"description": "The status of the GenomicStudy.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-status"
},
"mapping": [
{
"identity": "workflow",
"map": "Event.status"
},
{
"identity": "w5",
"map": "FiveWs.status"
},
{
"identity": "v2",
"map": "Varies by domain"
},
{
"identity": "rim",
"map": ".status"
}
]
},
{
"id": "GenomicStudy.type",
"path": "GenomicStudy.type",
"short": "The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling)",
"definition": "The type of the study, e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.type",
"min": 0,
"max": "*"
},
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyType"
}
],
"strength": "example",
"description": "The type relevant to GenomicStudy.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-type"
}
},
{
"id": "GenomicStudy.subject",
"path": "GenomicStudy.subject",
"short": "The primary subject of the genomic study",
"definition": "The primary subject of the genomic study.",
"min": 1,
"max": "1",
"base": {
"path": "GenomicStudy.subject",
"min": 1,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Patient",
"http://hl7.org/fhir/StructureDefinition/Group",
"http://hl7.org/fhir/StructureDefinition/Substance",
"http://hl7.org/fhir/StructureDefinition/BiologicallyDerivedProduct",
"http://hl7.org/fhir/StructureDefinition/NutritionProduct"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.encounter",
"path": "GenomicStudy.encounter",
"short": "The healthcare event with which this genomics study is associated",
"definition": "The healthcare event with which this genomics study is associated.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.encounter",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Encounter"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.startDate",
"path": "GenomicStudy.startDate",
"short": "When the genomic study was started",
"definition": "When the genomic study was started.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.startDate",
"min": 0,
"max": "1"
},
"type": [
{
"code": "dateTime"
}
]
},
{
"id": "GenomicStudy.basedOn",
"path": "GenomicStudy.basedOn",
"short": "Event resources that the genomic study is based on",
"definition": "Event resources that the genomic study is based on.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.basedOn",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/ServiceRequest",
"http://hl7.org/fhir/StructureDefinition/Task"
]
}
]
},
{
"id": "GenomicStudy.referrer",
"path": "GenomicStudy.referrer",
"short": "Healthcare professional who requested or referred the genomic study",
"definition": "Healthcare professional who requested or referred the genomic study.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.referrer",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Practitioner",
"http://hl7.org/fhir/StructureDefinition/PractitionerRole"
]
}
]
},
{
"id": "GenomicStudy.interpreter",
"path": "GenomicStudy.interpreter",
"short": "Healthcare professionals who interpreted the genomic study",
"definition": "Healthcare professionals who interpreted the genomic study.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.interpreter",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Practitioner",
"http://hl7.org/fhir/StructureDefinition/PractitionerRole"
]
}
]
},
{
"id": "GenomicStudy.reason",
"path": "GenomicStudy.reason",
"short": "Why the genomic study was performed",
"definition": "Why the genomic study was performed.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.reason",
"min": 0,
"max": "*"
},
"type": [
{
"code": "CodeableReference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Condition",
"http://hl7.org/fhir/StructureDefinition/Observation"
]
}
]
},
{
"id": "GenomicStudy.instantiatesCanonical",
"path": "GenomicStudy.instantiatesCanonical",
"short": "The defined protocol that describes the study",
"definition": "The defined protocol that describes the study.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.instantiatesCanonical",
"min": 0,
"max": "1"
},
"type": [
{
"code": "canonical",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/PlanDefinition"
]
}
]
},
{
"id": "GenomicStudy.instantiatesUri",
"path": "GenomicStudy.instantiatesUri",
"short": "The URL pointing to an externally maintained protocol that describes the study",
"definition": "The URL pointing to an externally maintained protocol that describes the study.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.instantiatesUri",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
]
},
{
"id": "GenomicStudy.note",
"path": "GenomicStudy.note",
"short": "Comments related to the genomic study",
"definition": "Comments related to the genomic study.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.note",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Annotation"
}
]
},
{
"id": "GenomicStudy.description",
"path": "GenomicStudy.description",
"short": "Description of the genomic study",
"definition": "Description of the genomic study.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.description",
"min": 0,
"max": "1"
},
"type": [
{
"code": "markdown"
}
]
},
{
"id": "GenomicStudy.analysis",
"path": "GenomicStudy.analysis",
"short": "Genomic Analysis Event",
"definition": "The details about a specific analysis that was performed in this GenomicStudy.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "gs-regions-1",
"severity": "warning",
"human": "When genomicRegion.studied entries use coded concepts, every code in genomicRegion.called and genomicRegion.uncalled entries should also appear in genomicRegion.studied. This constraint cannot be evaluated when BED file references (DocumentReference) are used instead of coded concepts.",
"expression": "genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and code = 'studied').exists()).locus.concept.exists() implies genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and (code = 'called' or code = 'uncalled')).exists()).locus.concept.coding.where(system.exists()).all((system & '|' & code) in %context.genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and code = 'studied').exists()).locus.concept.coding.select(system & '|' & code))"
},
{
"key": "gs-regions-2",
"severity": "error",
"human": "If all studied genomicRegion entries use coded concepts (none use DocumentReference), then all called and uncalled genomicRegion entries must also use coded concepts and not DocumentReference. This ensures a consistent representation when the studied scope is fully expressed as coded identifiers. Note: this constraint is intentionally one-directional — when studied uses DocumentReference (e.g., a BED file), called and uncalled entries may legitimately use coded concepts to name specific genes, since enumerating a full BED file as coded genes is impractical.",
"expression": "(genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and code = 'studied').exists()).locus.reference.exists().not() and genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and code = 'studied').exists()).locus.concept.exists()) implies genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and (code = 'called' or code = 'uncalled')).exists()).locus.reference.exists().not()"
},
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children or both",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
]
},
{
"id": "GenomicStudy.analysis.id",
"path": "GenomicStudy.analysis.id",
"representation": [
"xmlAttr"
],
"short": "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.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.extension",
"path": "GenomicStudy.analysis.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"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 managable, 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.",
"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.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.modifierExtension",
"path": "GenomicStudy.analysis.modifierExtension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Extensions that cannot be ignored even if unrecognized",
"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 managable, 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).",
"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.",
"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](http://build.fhir.org/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.analysis.identifier",
"path": "GenomicStudy.analysis.identifier",
"short": "Identifiers for the analysis event",
"definition": "Identifiers for the analysis event.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.identifier",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.methodType",
"path": "GenomicStudy.analysis.methodType",
"short": "Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI)",
"definition": "Type of the methods used in the analysis, e.g., Fluorescence in situ hybridization (FISH), Karyotyping, or Microsatellite instability testing (MSI).",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.methodType",
"min": 0,
"max": "*"
},
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyMethodType"
}
],
"strength": "preferred",
"description": "The method type of the GenomicStudy analysis.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-methodtype"
}
},
{
"id": "GenomicStudy.analysis.changeType",
"path": "GenomicStudy.analysis.changeType",
"short": "Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change)",
"definition": "Type of the genomic changes studied in the analysis, e.g., DNA, RNA, or amino acid change.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.changeType",
"min": 0,
"max": "*"
},
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyChangeType"
}
],
"strength": "preferred",
"description": "The change type relevant to GenomicStudy analysis.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-changetype"
}
},
{
"id": "GenomicStudy.analysis.genomeBuild",
"path": "GenomicStudy.analysis.genomeBuild",
"short": "Genome build that is used in this analysis",
"definition": "The reference genome build that is used in this analysis.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.genomeBuild",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "HumanRefSeqNCBIBuildId"
},
{
"url": "http://hl7.org/fhir/build/StructureDefinition/copyright",
"valueString": "Copyright © 2022 Regenstrief Institute, Inc. All Rights Reserved."
}
],
"strength": "extensible",
"description": "Human reference sequence NCBI build ID",
"valueSet": "http://loinc.org/vs/LL1040-6"
}
},
{
"id": "GenomicStudy.analysis.genomicSourceClass",
"path": "GenomicStudy.analysis.genomicSourceClass",
"short": "The genomic source class of the specimens used in the analysis (e.g., somatic, germline)",
"definition": "The genomic source class of the specimens used in the analysis, e.g., somatic or germline.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.genomicSourceClass",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyGenomicSourceClass"
},
{
"url": "http://hl7.org/fhir/build/StructureDefinition/copyright",
"valueString": "Copyright © 2022 Regenstrief Institute, Inc. All Rights Reserved."
}
],
"strength": "extensible",
"description": "The genomic source class (e.g., somatic, germline) of the specimens being analyzed.",
"valueSet": "http://loinc.org/vs/LL378-1"
}
},
{
"id": "GenomicStudy.analysis.instantiatesCanonical",
"path": "GenomicStudy.analysis.instantiatesCanonical",
"short": "The defined protocol that describes the analysis",
"definition": "The defined protocol that describes the analysis.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.instantiatesCanonical",
"min": 0,
"max": "1"
},
"type": [
{
"code": "canonical",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/PlanDefinition",
"http://hl7.org/fhir/StructureDefinition/ActivityDefinition"
]
}
]
},
{
"id": "GenomicStudy.analysis.instantiatesUri",
"path": "GenomicStudy.analysis.instantiatesUri",
"short": "The URL pointing to an externally maintained protocol that describes the analysis",
"definition": "The URL pointing to an externally maintained protocol that describes the analysis.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.instantiatesUri",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
]
},
{
"id": "GenomicStudy.analysis.title",
"path": "GenomicStudy.analysis.title",
"short": "Name of the analysis event (human friendly)",
"definition": "Name of the analysis event (human friendly).",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.title",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.focus",
"path": "GenomicStudy.analysis.focus",
"short": "What the genomic analysis is about, when it is not about the subject of record",
"definition": "The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parent.",
"comment": "If the focus of the analysis is not known, the value of this field SHALL use the data absent extension.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.focus",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Resource"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.specimen",
"path": "GenomicStudy.analysis.specimen",
"short": "The specimen used in the analysis event",
"definition": "The specimen used in the analysis event.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.specimen",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Specimen"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.date",
"path": "GenomicStudy.analysis.date",
"short": "The date of the analysis event",
"definition": "The date of the analysis event.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.date",
"min": 0,
"max": "1"
},
"type": [
{
"code": "dateTime"
}
]
},
{
"id": "GenomicStudy.analysis.note",
"path": "GenomicStudy.analysis.note",
"short": "Any notes capture with the analysis event",
"definition": "Any notes capture with the analysis event.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.note",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Annotation"
}
]
},
{
"id": "GenomicStudy.analysis.metrics",
"path": "GenomicStudy.analysis.metrics",
"short": "Quality metrics for the analysis",
"definition": "High-level quality metrics about the sequencing analysis that was performed.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.metrics",
"min": 0,
"max": "1"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children or both",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
]
},
{
"id": "GenomicStudy.analysis.metrics.id",
"path": "GenomicStudy.analysis.metrics.id",
"representation": [
"xmlAttr"
],
"short": "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.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.metrics.extension",
"path": "GenomicStudy.analysis.metrics.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"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 managable, 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.",
"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.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.metrics.modifierExtension",
"path": "GenomicStudy.analysis.metrics.modifierExtension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Extensions that cannot be ignored even if unrecognized",
"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 managable, 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).",
"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.",
"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](http://build.fhir.org/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.analysis.metrics.readDepth",
"path": "GenomicStudy.analysis.metrics.readDepth",
"short": "Average read depth (e.g., 30x, 100x)",
"definition": "The average read depth (number of reads for a position) for the sequencing analysis.",
"comment": "This value is typically represented with an 'x' after the number (30x). Share the quantity value only.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.metrics.readDepth",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Quantity",
"profile": [
"http://hl7.org/fhir/StructureDefinition/SimpleQuantity"
]
}
]
},
{
"id": "GenomicStudy.analysis.metrics.sequencingCoverage",
"path": "GenomicStudy.analysis.metrics.sequencingCoverage",
"short": "Percentage of studied regions sequenced (e.g., 95%)",
"definition": "The percentage of the studied regions that were sequenced.",
"comment": "This value is typically represented with a '%' after the number (95%). Share the quantity value only.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.metrics.sequencingCoverage",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Quantity",
"profile": [
"http://hl7.org/fhir/StructureDefinition/SimpleQuantity"
]
}
]
},
{
"id": "GenomicStudy.analysis.metrics.description",
"path": "GenomicStudy.analysis.metrics.description",
"short": "Freetext coverage metrics description",
"definition": "Freetext description of the coverage and quality metrics for the sequencing analysis.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.metrics.description",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
]
},
{
"id": "GenomicStudy.analysis.protocolPerformed",
"path": "GenomicStudy.analysis.protocolPerformed",
"short": "The protocol that was performed for the analysis event",
"definition": "The protocol that was performed for the analysis event.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.protocolPerformed",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Procedure",
"http://hl7.org/fhir/StructureDefinition/Task"
]
}
]
},
{
"id": "GenomicStudy.analysis.genomicRegion",
"path": "GenomicStudy.analysis.genomicRegion",
"short": "Genomic regions relevant to the analysis, grouped by type",
"definition": "A set of genomic regions associated with this analysis, classified by their relationship to the analysis outcome (studied, called, or uncalled). Each repetition represents one group of regions sharing the same type.",
"comment": "Use one repetition per region type. For example, include one entry with type=studied for the full panel scope, one with type=called for regions with sufficient coverage to produce calls, and one with type=uncalled for regions where calls could not be produced. All three types may be present in a single analysis, or only a subset, as appropriate.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.genomicRegion",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children or both",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
]
},
{
"id": "GenomicStudy.analysis.genomicRegion.id",
"path": "GenomicStudy.analysis.genomicRegion.id",
"representation": [
"xmlAttr"
],
"short": "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.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.genomicRegion.extension",
"path": "GenomicStudy.analysis.genomicRegion.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"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 managable, 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.",
"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.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.genomicRegion.modifierExtension",
"path": "GenomicStudy.analysis.genomicRegion.modifierExtension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Extensions that cannot be ignored even if unrecognized",
"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 managable, 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).",
"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.",
"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](http://build.fhir.org/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.analysis.genomicRegion.type",
"path": "GenomicStudy.analysis.genomicRegion.type",
"short": "studied | called | uncalled",
"definition": "The type of this region group, indicating the relationship of these regions to the analysis outcome.",
"comment": "Use 'studied' for the full intended scope of the analysis. Use 'called' for regions where sufficient coverage and data quality enabled variant calling. Use 'uncalled' for regions within the studied scope where calls could not be produced (e.g., due to low coverage or poor mapping quality). An 'uncalled' entry does not imply that a pathogenic variant is present or was missed; it indicates a technical limitation. Use genomicRegion.description to document the reason.",
"min": 1,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.genomicRegion.type",
"min": 1,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyRegionType"
}
],
"strength": "extensible",
"description": "The type of genomic region group. Use studied, called, or uncalled where applicable; other codes may be used for methodology-specific region classifications not covered by this value set.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-regiontype"
}
},
{
"id": "GenomicStudy.analysis.genomicRegion.locus",
"path": "GenomicStudy.analysis.genomicRegion.locus",
"short": "Genomic regions in this group (coded genes or BED file)",
"definition": "The genomic regions belonging to this group. May be expressed as a coded list of HGNC gene symbols (using CodeableReference.concept) or as a reference to a BED file (using CodeableReference.reference to a DocumentReference).",
"comment": "For coded genes, use the HGNC gene symbol as display text and the HGNC gene ID as the code. If no HGNC code has been issued, use NCBI gene IDs. If region details beyond a coded gene list are needed (e.g., sub-gene coordinates), reference a BED file via DocumentReference. Multiple repetitions may be used to list individual genes or to combine a BED file reference with supplementary coded entries.",
"requirements": "Expressed as a coded list of HGNC gene symbols or a reference to a BED file (DocumentReference).",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.genomicRegion.locus",
"min": 0,
"max": "*"
},
"type": [
{
"code": "CodeableReference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/DocumentReference"
]
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "HGNCGeneNames"
}
],
"strength": "extensible",
"description": "HGNC gene names for coded gene lists.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/hgnc-vs"
}
},
{
"id": "GenomicStudy.analysis.genomicRegion.description",
"path": "GenomicStudy.analysis.genomicRegion.description",
"short": "Additional details about this region group",
"definition": "Free-text notes providing additional context about this group of regions. Particularly useful for 'uncalled' entries to document the reason calls could not be produced (e.g., 'low coverage <20x', 'poor mapping due to repetitive sequence', 'homopolymer region exceeding assay limit').",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.genomicRegion.description",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
]
},
{
"id": "GenomicStudy.analysis.input",
"path": "GenomicStudy.analysis.input",
"short": "Inputs for the analysis event",
"definition": "Inputs for the analysis event.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.input",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children or both",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
]
},
{
"id": "GenomicStudy.analysis.input.id",
"path": "GenomicStudy.analysis.input.id",
"representation": [
"xmlAttr"
],
"short": "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.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.input.extension",
"path": "GenomicStudy.analysis.input.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"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 managable, 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.",
"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.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.input.modifierExtension",
"path": "GenomicStudy.analysis.input.modifierExtension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Extensions that cannot be ignored even if unrecognized",
"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 managable, 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).",
"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.",
"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](http://build.fhir.org/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.analysis.input.file",
"path": "GenomicStudy.analysis.input.file",
"short": "File containing input data",
"definition": "File containing input data.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.input.file",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/DocumentReference"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.input.type",
"path": "GenomicStudy.analysis.input.type",
"short": "Type of input data (e.g., BAM, CRAM, or FASTA)",
"definition": "Type of input data, e.g., BAM, CRAM, or FASTA.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.input.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyDataFormat"
}
],
"strength": "example",
"description": "The data format of the data file.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-dataformat"
}
},
{
"id": "GenomicStudy.analysis.input.generatedBy[x]",
"path": "GenomicStudy.analysis.input.generatedBy[x]",
"short": "The analysis event or other GenomicStudy that generated this input file",
"definition": "The analysis event or other GenomicStudy that generated this input file.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.input.generatedBy[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
},
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/GenomicStudy"
]
}
]
},
{
"id": "GenomicStudy.analysis.output",
"path": "GenomicStudy.analysis.output",
"short": "Outputs for the analysis event",
"definition": "Outputs for the analysis event.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.output",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children or both",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
]
},
{
"id": "GenomicStudy.analysis.output.id",
"path": "GenomicStudy.analysis.output.id",
"representation": [
"xmlAttr"
],
"short": "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.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.output.extension",
"path": "GenomicStudy.analysis.output.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"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 managable, 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.",
"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.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.output.modifierExtension",
"path": "GenomicStudy.analysis.output.modifierExtension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Extensions that cannot be ignored even if unrecognized",
"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 managable, 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).",
"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.",
"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](http://build.fhir.org/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.analysis.output.file",
"path": "GenomicStudy.analysis.output.file",
"short": "File containing output data",
"definition": "File containing output data.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.output.file",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/DocumentReference"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.output.type",
"path": "GenomicStudy.analysis.output.type",
"short": "Type of output data (e.g., VCF, MAF, or BAM)",
"definition": "Type of output data, e.g., VCF, MAF, or BAM.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.output.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyDataFormat"
}
],
"strength": "example",
"description": "The data format of the data file.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-dataformat"
}
},
{
"id": "GenomicStudy.analysis.performer",
"path": "GenomicStudy.analysis.performer",
"short": "Performer for the analysis event",
"definition": "Performer for the analysis event.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.performer",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children or both",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
]
},
{
"id": "GenomicStudy.analysis.performer.id",
"path": "GenomicStudy.analysis.performer.id",
"representation": [
"xmlAttr"
],
"short": "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.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.performer.extension",
"path": "GenomicStudy.analysis.performer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"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 managable, 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.",
"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.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.performer.modifierExtension",
"path": "GenomicStudy.analysis.performer.modifierExtension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Extensions that cannot be ignored even if unrecognized",
"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 managable, 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).",
"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.",
"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](http://build.fhir.org/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.analysis.performer.actor",
"path": "GenomicStudy.analysis.performer.actor",
"short": "The organization, healthcare professional, or others who participated in performing this analysis",
"definition": "The organization, healthcare professional, or others who participated in performing this analysis.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.performer.actor",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Practitioner",
"http://hl7.org/fhir/StructureDefinition/PractitionerRole",
"http://hl7.org/fhir/StructureDefinition/Organization",
"http://hl7.org/fhir/StructureDefinition/Device"
]
}
]
},
{
"id": "GenomicStudy.analysis.performer.role",
"path": "GenomicStudy.analysis.performer.role",
"short": "Role of the actor for this analysis",
"definition": "Role of the actor for this analysis.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.performer.role",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "GenomicStudy.analysis.device",
"path": "GenomicStudy.analysis.device",
"short": "Devices used for the analysis (e.g., instruments, software), with settings and parameters",
"definition": "Devices used for the analysis (e.g., instruments, software), with settings and parameters.",
"min": 0,
"max": "*",
"base": {
"path": "GenomicStudy.analysis.device",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children or both",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
]
},
{
"id": "GenomicStudy.analysis.device.id",
"path": "GenomicStudy.analysis.device.id",
"representation": [
"xmlAttr"
],
"short": "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.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.device.extension",
"path": "GenomicStudy.analysis.device.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"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 managable, 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.",
"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.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "GenomicStudy.analysis.device.modifierExtension",
"path": "GenomicStudy.analysis.device.modifierExtension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Extensions that cannot be ignored even if unrecognized",
"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 managable, 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).",
"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.",
"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](http://build.fhir.org/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "GenomicStudy.analysis.device.device",
"path": "GenomicStudy.analysis.device.device",
"short": "Device used for the analysis",
"definition": "Device used for the analysis.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.device.device",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Device"
]
}
]
},
{
"id": "GenomicStudy.analysis.device.function",
"path": "GenomicStudy.analysis.device.function",
"short": "Specific function for the device used for the analysis",
"definition": "Specific function for the device used for the analysis.",
"min": 0,
"max": "1",
"base": {
"path": "GenomicStudy.analysis.device.function",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
]
}
]
},
"differential": {
"element": [
{
"id": "GenomicStudy",
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/svg",
"valueCode": "0,0"
}
],
"path": "GenomicStudy",
"short": "Genomic Study",
"definition": "A GenomicStudy is a set of analyses performed to analyze and generate genomic data.",
"min": 0,
"max": "*",
"mapping": [
{
"identity": "workflow",
"map": "Event"
},
{
"identity": "w5",
"map": "clinical.diagnostics"
}
]
},
{
"id": "GenomicStudy.identifier",
"path": "GenomicStudy.identifier",
"short": "Identifiers for this genomic study",
"definition": "Identifiers for this genomic study.",
"min": 0,
"max": "*",
"type": [
{
"code": "Identifier"
}
],
"isSummary": true
},
{
"id": "GenomicStudy.status",
"path": "GenomicStudy.status",
"short": "registered | available | cancelled | entered-in-error | unknown",
"definition": "The status of the genomic study.",
"min": 1,
"max": "1",
"type": [
{
"code": "code"
}
],
"isModifier": true,
"isModifierReason": "This element is labeled 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,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyStatus"
}
],
"strength": "required",
"description": "The status of the GenomicStudy.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-status"
},
"mapping": [
{
"identity": "workflow",
"map": "Event.status"
},
{
"identity": "w5",
"map": "FiveWs.status"
},
{
"identity": "v2",
"map": "Varies by domain"
},
{
"identity": "rim",
"map": ".status"
}
]
},
{
"id": "GenomicStudy.type",
"path": "GenomicStudy.type",
"short": "The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling)",
"definition": "The type of the study, e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling.",
"min": 0,
"max": "*",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyType"
}
],
"strength": "example",
"description": "The type relevant to GenomicStudy.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-type"
}
},
{
"id": "GenomicStudy.subject",
"path": "GenomicStudy.subject",
"short": "The primary subject of the genomic study",
"definition": "The primary subject of the genomic study.",
"min": 1,
"max": "1",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Patient",
"http://hl7.org/fhir/StructureDefinition/Group",
"http://hl7.org/fhir/StructureDefinition/Substance",
"http://hl7.org/fhir/StructureDefinition/BiologicallyDerivedProduct",
"http://hl7.org/fhir/StructureDefinition/NutritionProduct"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.encounter",
"path": "GenomicStudy.encounter",
"short": "The healthcare event with which this genomics study is associated",
"definition": "The healthcare event with which this genomics study is associated.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Encounter"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.startDate",
"path": "GenomicStudy.startDate",
"short": "When the genomic study was started",
"definition": "When the genomic study was started.",
"min": 0,
"max": "1",
"type": [
{
"code": "dateTime"
}
]
},
{
"id": "GenomicStudy.basedOn",
"path": "GenomicStudy.basedOn",
"short": "Event resources that the genomic study is based on",
"definition": "Event resources that the genomic study is based on.",
"min": 0,
"max": "*",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/ServiceRequest",
"http://hl7.org/fhir/StructureDefinition/Task"
]
}
]
},
{
"id": "GenomicStudy.referrer",
"path": "GenomicStudy.referrer",
"short": "Healthcare professional who requested or referred the genomic study",
"definition": "Healthcare professional who requested or referred the genomic study.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Practitioner",
"http://hl7.org/fhir/StructureDefinition/PractitionerRole"
]
}
]
},
{
"id": "GenomicStudy.interpreter",
"path": "GenomicStudy.interpreter",
"short": "Healthcare professionals who interpreted the genomic study",
"definition": "Healthcare professionals who interpreted the genomic study.",
"min": 0,
"max": "*",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Practitioner",
"http://hl7.org/fhir/StructureDefinition/PractitionerRole"
]
}
]
},
{
"id": "GenomicStudy.reason",
"path": "GenomicStudy.reason",
"short": "Why the genomic study was performed",
"definition": "Why the genomic study was performed.",
"min": 0,
"max": "*",
"type": [
{
"code": "CodeableReference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Condition",
"http://hl7.org/fhir/StructureDefinition/Observation"
]
}
]
},
{
"id": "GenomicStudy.instantiatesCanonical",
"path": "GenomicStudy.instantiatesCanonical",
"short": "The defined protocol that describes the study",
"definition": "The defined protocol that describes the study.",
"min": 0,
"max": "1",
"type": [
{
"code": "canonical",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/PlanDefinition"
]
}
]
},
{
"id": "GenomicStudy.instantiatesUri",
"path": "GenomicStudy.instantiatesUri",
"short": "The URL pointing to an externally maintained protocol that describes the study",
"definition": "The URL pointing to an externally maintained protocol that describes the study.",
"min": 0,
"max": "1",
"type": [
{
"code": "uri"
}
]
},
{
"id": "GenomicStudy.note",
"path": "GenomicStudy.note",
"short": "Comments related to the genomic study",
"definition": "Comments related to the genomic study.",
"min": 0,
"max": "*",
"type": [
{
"code": "Annotation"
}
]
},
{
"id": "GenomicStudy.description",
"path": "GenomicStudy.description",
"short": "Description of the genomic study",
"definition": "Description of the genomic study.",
"min": 0,
"max": "1",
"type": [
{
"code": "markdown"
}
]
},
{
"id": "GenomicStudy.analysis",
"path": "GenomicStudy.analysis",
"short": "Genomic Analysis Event",
"definition": "The details about a specific analysis that was performed in this GenomicStudy.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "gs-regions-1",
"severity": "warning",
"human": "When genomicRegion.studied entries use coded concepts, every code in genomicRegion.called and genomicRegion.uncalled entries should also appear in genomicRegion.studied. This constraint cannot be evaluated when BED file references (DocumentReference) are used instead of coded concepts.",
"expression": "genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and code = 'studied').exists()).locus.concept.exists() implies genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and (code = 'called' or code = 'uncalled')).exists()).locus.concept.coding.where(system.exists()).all((system & '|' & code) in %context.genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and code = 'studied').exists()).locus.concept.coding.select(system & '|' & code))"
},
{
"key": "gs-regions-2",
"severity": "error",
"human": "If all studied genomicRegion entries use coded concepts (none use DocumentReference), then all called and uncalled genomicRegion entries must also use coded concepts and not DocumentReference. This ensures a consistent representation when the studied scope is fully expressed as coded identifiers. Note: this constraint is intentionally one-directional — when studied uses DocumentReference (e.g., a BED file), called and uncalled entries may legitimately use coded concepts to name specific genes, since enumerating a full BED file as coded genes is impractical.",
"expression": "(genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and code = 'studied').exists()).locus.reference.exists().not() and genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and code = 'studied').exists()).locus.concept.exists()) implies genomicRegion.where(type.coding.where(system = 'http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype' and (code = 'called' or code = 'uncalled')).exists()).locus.reference.exists().not()"
}
]
},
{
"id": "GenomicStudy.analysis.identifier",
"path": "GenomicStudy.analysis.identifier",
"short": "Identifiers for the analysis event",
"definition": "Identifiers for the analysis event.",
"min": 0,
"max": "*",
"type": [
{
"code": "Identifier"
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.methodType",
"path": "GenomicStudy.analysis.methodType",
"short": "Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI)",
"definition": "Type of the methods used in the analysis, e.g., Fluorescence in situ hybridization (FISH), Karyotyping, or Microsatellite instability testing (MSI).",
"min": 0,
"max": "*",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyMethodType"
}
],
"strength": "preferred",
"description": "The method type of the GenomicStudy analysis.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-methodtype"
}
},
{
"id": "GenomicStudy.analysis.changeType",
"path": "GenomicStudy.analysis.changeType",
"short": "Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change)",
"definition": "Type of the genomic changes studied in the analysis, e.g., DNA, RNA, or amino acid change.",
"min": 0,
"max": "*",
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyChangeType"
}
],
"strength": "preferred",
"description": "The change type relevant to GenomicStudy analysis.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-changetype"
}
},
{
"id": "GenomicStudy.analysis.genomeBuild",
"path": "GenomicStudy.analysis.genomeBuild",
"short": "Genome build that is used in this analysis",
"definition": "The reference genome build that is used in this analysis.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "HumanRefSeqNCBIBuildId"
},
{
"url": "http://hl7.org/fhir/build/StructureDefinition/copyright",
"valueString": "Copyright © 2022 Regenstrief Institute, Inc. All Rights Reserved."
}
],
"strength": "extensible",
"description": "Human reference sequence NCBI build ID",
"valueSet": "http://loinc.org/vs/LL1040-6"
}
},
{
"id": "GenomicStudy.analysis.genomicSourceClass",
"path": "GenomicStudy.analysis.genomicSourceClass",
"short": "The genomic source class of the specimens used in the analysis (e.g., somatic, germline)",
"definition": "The genomic source class of the specimens used in the analysis, e.g., somatic or germline.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyGenomicSourceClass"
},
{
"url": "http://hl7.org/fhir/build/StructureDefinition/copyright",
"valueString": "Copyright © 2022 Regenstrief Institute, Inc. All Rights Reserved."
}
],
"strength": "extensible",
"description": "The genomic source class (e.g., somatic, germline) of the specimens being analyzed.",
"valueSet": "http://loinc.org/vs/LL378-1"
}
},
{
"id": "GenomicStudy.analysis.instantiatesCanonical",
"path": "GenomicStudy.analysis.instantiatesCanonical",
"short": "The defined protocol that describes the analysis",
"definition": "The defined protocol that describes the analysis.",
"min": 0,
"max": "1",
"type": [
{
"code": "canonical",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/PlanDefinition",
"http://hl7.org/fhir/StructureDefinition/ActivityDefinition"
]
}
]
},
{
"id": "GenomicStudy.analysis.instantiatesUri",
"path": "GenomicStudy.analysis.instantiatesUri",
"short": "The URL pointing to an externally maintained protocol that describes the analysis",
"definition": "The URL pointing to an externally maintained protocol that describes the analysis.",
"min": 0,
"max": "1",
"type": [
{
"code": "uri"
}
]
},
{
"id": "GenomicStudy.analysis.title",
"path": "GenomicStudy.analysis.title",
"short": "Name of the analysis event (human friendly)",
"definition": "Name of the analysis event (human friendly).",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.focus",
"path": "GenomicStudy.analysis.focus",
"short": "What the genomic analysis is about, when it is not about the subject of record",
"definition": "The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parent.",
"comment": "If the focus of the analysis is not known, the value of this field SHALL use the data absent extension.",
"min": 0,
"max": "*",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Resource"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.specimen",
"path": "GenomicStudy.analysis.specimen",
"short": "The specimen used in the analysis event",
"definition": "The specimen used in the analysis event.",
"min": 0,
"max": "*",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Specimen"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.date",
"path": "GenomicStudy.analysis.date",
"short": "The date of the analysis event",
"definition": "The date of the analysis event.",
"min": 0,
"max": "1",
"type": [
{
"code": "dateTime"
}
]
},
{
"id": "GenomicStudy.analysis.note",
"path": "GenomicStudy.analysis.note",
"short": "Any notes capture with the analysis event",
"definition": "Any notes capture with the analysis event.",
"min": 0,
"max": "*",
"type": [
{
"code": "Annotation"
}
]
},
{
"id": "GenomicStudy.analysis.metrics",
"path": "GenomicStudy.analysis.metrics",
"short": "Quality metrics for the analysis",
"definition": "High-level quality metrics about the sequencing analysis that was performed.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
]
},
{
"id": "GenomicStudy.analysis.metrics.readDepth",
"path": "GenomicStudy.analysis.metrics.readDepth",
"short": "Average read depth (e.g., 30x, 100x)",
"definition": "The average read depth (number of reads for a position) for the sequencing analysis.",
"comment": "This value is typically represented with an 'x' after the number (30x). Share the quantity value only.",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity",
"profile": [
"http://hl7.org/fhir/StructureDefinition/SimpleQuantity"
]
}
]
},
{
"id": "GenomicStudy.analysis.metrics.sequencingCoverage",
"path": "GenomicStudy.analysis.metrics.sequencingCoverage",
"short": "Percentage of studied regions sequenced (e.g., 95%)",
"definition": "The percentage of the studied regions that were sequenced.",
"comment": "This value is typically represented with a '%' after the number (95%). Share the quantity value only.",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity",
"profile": [
"http://hl7.org/fhir/StructureDefinition/SimpleQuantity"
]
}
]
},
{
"id": "GenomicStudy.analysis.metrics.description",
"path": "GenomicStudy.analysis.metrics.description",
"short": "Freetext coverage metrics description",
"definition": "Freetext description of the coverage and quality metrics for the sequencing analysis.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
]
},
{
"id": "GenomicStudy.analysis.protocolPerformed",
"path": "GenomicStudy.analysis.protocolPerformed",
"short": "The protocol that was performed for the analysis event",
"definition": "The protocol that was performed for the analysis event.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Procedure",
"http://hl7.org/fhir/StructureDefinition/Task"
]
}
]
},
{
"id": "GenomicStudy.analysis.genomicRegion",
"path": "GenomicStudy.analysis.genomicRegion",
"short": "Genomic regions relevant to the analysis, grouped by type",
"definition": "A set of genomic regions associated with this analysis, classified by their relationship to the analysis outcome (studied, called, or uncalled). Each repetition represents one group of regions sharing the same type.",
"comment": "Use one repetition per region type. For example, include one entry with type=studied for the full panel scope, one with type=called for regions with sufficient coverage to produce calls, and one with type=uncalled for regions where calls could not be produced. All three types may be present in a single analysis, or only a subset, as appropriate.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
]
},
{
"id": "GenomicStudy.analysis.genomicRegion.type",
"path": "GenomicStudy.analysis.genomicRegion.type",
"short": "studied | called | uncalled",
"definition": "The type of this region group, indicating the relationship of these regions to the analysis outcome.",
"comment": "Use 'studied' for the full intended scope of the analysis. Use 'called' for regions where sufficient coverage and data quality enabled variant calling. Use 'uncalled' for regions within the studied scope where calls could not be produced (e.g., due to low coverage or poor mapping quality). An 'uncalled' entry does not imply that a pathogenic variant is present or was missed; it indicates a technical limitation. Use genomicRegion.description to document the reason.",
"min": 1,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyRegionType"
}
],
"strength": "extensible",
"description": "The type of genomic region group. Use studied, called, or uncalled where applicable; other codes may be used for methodology-specific region classifications not covered by this value set.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-regiontype"
}
},
{
"id": "GenomicStudy.analysis.genomicRegion.locus",
"path": "GenomicStudy.analysis.genomicRegion.locus",
"short": "Genomic regions in this group (coded genes or BED file)",
"definition": "The genomic regions belonging to this group. May be expressed as a coded list of HGNC gene symbols (using CodeableReference.concept) or as a reference to a BED file (using CodeableReference.reference to a DocumentReference).",
"comment": "For coded genes, use the HGNC gene symbol as display text and the HGNC gene ID as the code. If no HGNC code has been issued, use NCBI gene IDs. If region details beyond a coded gene list are needed (e.g., sub-gene coordinates), reference a BED file via DocumentReference. Multiple repetitions may be used to list individual genes or to combine a BED file reference with supplementary coded entries.",
"requirements": "Expressed as a coded list of HGNC gene symbols or a reference to a BED file (DocumentReference).",
"min": 0,
"max": "*",
"type": [
{
"code": "CodeableReference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/DocumentReference"
]
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "HGNCGeneNames"
}
],
"strength": "extensible",
"description": "HGNC gene names for coded gene lists.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/hgnc-vs"
}
},
{
"id": "GenomicStudy.analysis.genomicRegion.description",
"path": "GenomicStudy.analysis.genomicRegion.description",
"short": "Additional details about this region group",
"definition": "Free-text notes providing additional context about this group of regions. Particularly useful for 'uncalled' entries to document the reason calls could not be produced (e.g., 'low coverage <20x', 'poor mapping due to repetitive sequence', 'homopolymer region exceeding assay limit').",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
]
},
{
"id": "GenomicStudy.analysis.input",
"path": "GenomicStudy.analysis.input",
"short": "Inputs for the analysis event",
"definition": "Inputs for the analysis event.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
]
},
{
"id": "GenomicStudy.analysis.input.file",
"path": "GenomicStudy.analysis.input.file",
"short": "File containing input data",
"definition": "File containing input data.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/DocumentReference"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.input.type",
"path": "GenomicStudy.analysis.input.type",
"short": "Type of input data (e.g., BAM, CRAM, or FASTA)",
"definition": "Type of input data, e.g., BAM, CRAM, or FASTA.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyDataFormat"
}
],
"strength": "example",
"description": "The data format of the data file.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-dataformat"
}
},
{
"id": "GenomicStudy.analysis.input.generatedBy[x]",
"path": "GenomicStudy.analysis.input.generatedBy[x]",
"short": "The analysis event or other GenomicStudy that generated this input file",
"definition": "The analysis event or other GenomicStudy that generated this input file.",
"min": 0,
"max": "1",
"type": [
{
"code": "Identifier"
},
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/GenomicStudy"
]
}
]
},
{
"id": "GenomicStudy.analysis.output",
"path": "GenomicStudy.analysis.output",
"short": "Outputs for the analysis event",
"definition": "Outputs for the analysis event.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
]
},
{
"id": "GenomicStudy.analysis.output.file",
"path": "GenomicStudy.analysis.output.file",
"short": "File containing output data",
"definition": "File containing output data.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/DocumentReference"
]
}
],
"isSummary": true
},
{
"id": "GenomicStudy.analysis.output.type",
"path": "GenomicStudy.analysis.output.type",
"short": "Type of output data (e.g., VCF, MAF, or BAM)",
"definition": "Type of output data, e.g., VCF, MAF, or BAM.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "GenomicStudyDataFormat"
}
],
"strength": "example",
"description": "The data format of the data file.",
"valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-dataformat"
}
},
{
"id": "GenomicStudy.analysis.performer",
"path": "GenomicStudy.analysis.performer",
"short": "Performer for the analysis event",
"definition": "Performer for the analysis event.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
]
},
{
"id": "GenomicStudy.analysis.performer.actor",
"path": "GenomicStudy.analysis.performer.actor",
"short": "The organization, healthcare professional, or others who participated in performing this analysis",
"definition": "The organization, healthcare professional, or others who participated in performing this analysis.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Practitioner",
"http://hl7.org/fhir/StructureDefinition/PractitionerRole",
"http://hl7.org/fhir/StructureDefinition/Organization",
"http://hl7.org/fhir/StructureDefinition/Device"
]
}
]
},
{
"id": "GenomicStudy.analysis.performer.role",
"path": "GenomicStudy.analysis.performer.role",
"short": "Role of the actor for this analysis",
"definition": "Role of the actor for this analysis.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "GenomicStudy.analysis.device",
"path": "GenomicStudy.analysis.device",
"short": "Devices used for the analysis (e.g., instruments, software), with settings and parameters",
"definition": "Devices used for the analysis (e.g., instruments, software), with settings and parameters.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
]
},
{
"id": "GenomicStudy.analysis.device.device",
"path": "GenomicStudy.analysis.device.device",
"short": "Device used for the analysis",
"definition": "Device used for the analysis.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Device"
]
}
]
},
{
"id": "GenomicStudy.analysis.device.function",
"path": "GenomicStudy.analysis.device.function",
"short": "Specific function for the device used for the analysis",
"definition": "Specific function for the device used for the analysis.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
]
}
]
}
}