This page is part of the FHIR Specification (v3.0.2: STU 3). The current version which supercedes this version is 4.0.1. For a full list of available versions, see the Directory of published versions
Clinical Genomics Work Group | Maturity Level: N/A | Ballot Status: Informative | Compartments: Not linked to any defined compartments |
Generated Questionnaire for Sequence
{ "resourceType": "Questionnaire", "id": "qs1", "identifier": [ { "system": "urn:ietf:rfc:3986" } ], "status": "draft", "date": "2019-10-24T11:53:00+11:00", "publisher": "Health Level Seven International (Clinical Genomics)", "item": [ { "linkId": "Sequence", "text": "Information about a biological sequence", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Raw data describing a biological sequence.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.id", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. The only time that a resource does not have an id is when it is being submitted to the server using a create operation.", "type": "display" }, { "linkId": "Sequence.id.value", "text": "Logical id of this artifact", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 } ], "linkId": "Sequence.meta", "text": "Metadata about the resource", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content may not always be associated with version changes to the resource.", "type": "display" } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "uri" } ], "linkId": "Sequence.implicitRules", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. 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. \n\nThis element is labelled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation.", "type": "display" }, { "linkId": "Sequence.implicitRules.value", "text": "A set of rules under which this content was created", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "code" } ], "linkId": "Sequence.language", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The base language in which the resource is written. 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).", "type": "display" }, { "linkId": "Sequence.language.value", "text": "language", "type": "choice", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 } ], "linkId": "Sequence.text", "text": "Text summary of the resource, for human interpretation", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "A human-readable narrative that contains a summary of the resource, and may 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. Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded in formation is added later.", "type": "display" } ] }, { "linkId": "Sequence.contained", "text": "Contained, inline Resources", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. 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.", "type": "display" } ] }, { "linkId": "Sequence.extension", "text": "Additional Content defined by implementations", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "May be used to represent additional information that is not part of the basic definition of the resource. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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.", "type": "display" } ] }, { "linkId": "Sequence.modifierExtension", "text": "Extensions that cannot be ignored", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "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. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. 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.", "type": "display" } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Identifier" } ], "linkId": "Sequence.identifier", "text": "Unique ID for this particular sequence. This is a FHIR-defined id", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "A unique identifier for this particular sequence instance. This is a FHIR-defined id.", "type": "display" }, { "linkId": "Sequence.identifier.label", "text": "label:", "type": "string", "required": false, "repeats": false }, { "linkId": "Sequence.identifier.system", "text": "system:", "type": "string", "required": false, "repeats": false }, { "linkId": "Sequence.identifier.value", "text": "value:", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "code" } ], "linkId": "Sequence.type", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Amino Acid Sequence/ DNA Sequence / RNA Sequence.", "type": "display" }, { "linkId": "Sequence.type.value", "text": "type", "type": "choice", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-minOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.coordinateSystem", "type": "group", "required": true, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).", "type": "display" }, { "linkId": "Sequence.coordinateSystem.value", "text": "Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)", "type": "integer", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Reference" } ], "linkId": "Sequence.patient", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The patient whose sequencing results are described by this resource.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-allowedResource", "valueCode": "Patient" }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-referenceFilter", "valueString": "subject=$subj&patient=$subj&encounter=$encounter" } ], "linkId": "Sequence.patient.value", "text": "Who and/or what this is about", "type": "reference", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Reference" } ], "linkId": "Sequence.specimen", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Specimen used for sequencing.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-allowedResource", "valueCode": "Specimen" }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-referenceFilter", "valueString": "subject=$subj&patient=$subj&encounter=$encounter" } ], "linkId": "Sequence.specimen.value", "text": "Specimen used for sequencing", "type": "reference", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Reference" } ], "linkId": "Sequence.device", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The method for sequencing, for example, chip information.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-allowedResource", "valueCode": "Device" }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-referenceFilter", "valueString": "subject=$subj&patient=$subj&encounter=$encounter" } ], "linkId": "Sequence.device.value", "text": "The method for sequencing", "type": "reference", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Reference" } ], "linkId": "Sequence.performer", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The organization or lab that should be responsible for this result.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-allowedResource", "valueCode": "Organization" }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-referenceFilter", "valueString": "subject=$subj&patient=$subj&encounter=$encounter" } ], "linkId": "Sequence.performer.value", "text": "Who should be responsible for test result", "type": "reference", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Quantity" } ], "linkId": "Sequence.quantity", "text": "The number of copies of the seqeunce of interest. (RNASeq)", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The number of copies of the seqeunce of interest. (RNASeq).", "type": "display" }, { "linkId": "Sequence.quantity.comparator", "text": "comp:", "type": "choice", "required": false, "repeats": false }, { "linkId": "Sequence.quantity.value", "text": "value:", "type": "decimal", "required": false, "repeats": false }, { "linkId": "Sequence.quantity.units", "text": "units:", "type": "string", "required": false, "repeats": false }, { "linkId": "Sequence.quantity.code", "text": "coded units:", "type": "string", "required": false, "repeats": false }, { "linkId": "Sequence.quantity.system", "text": "units system:", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 } ], "linkId": "Sequence.referenceSeq", "text": "A sequence used as reference", "type": "group", "required": false, "repeats": false, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "A sequence that is used as a reference to describe variants that are present in a sequence analyzed.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.referenceSeq.id", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", "type": "display" }, { "linkId": "Sequence.referenceSeq.id.value", "text": "xml:id (or equivalent in JSON)", "type": "string", "required": false, "repeats": false } ] }, { "linkId": "Sequence.referenceSeq.extension", "text": "Additional Content defined by implementations", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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.", "type": "display" } ] }, { "linkId": "Sequence.referenceSeq.modifierExtension", "text": "Extensions that cannot be ignored", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "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 that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. 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.", "type": "display" } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "CodeableConcept" } ], "linkId": "Sequence.referenceSeq.chromosome", "text": "Chromosome containing genetic finding", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).", "type": "display" }, { "linkId": "Sequence.referenceSeq.chromosome.coding", "text": "code:", "type": "open-choice", "required": false, "repeats": false }, { "linkId": "Sequence.referenceSeq.chromosome.text", "text": "text:", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.referenceSeq.genomeBuild", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.", "type": "display" }, { "linkId": "Sequence.referenceSeq.genomeBuild.value", "text": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "CodeableConcept" } ], "linkId": "Sequence.referenceSeq.referenceSeqId", "text": "Reference identifier", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.", "type": "display" }, { "linkId": "Sequence.referenceSeq.referenceSeqId.coding", "text": "code:", "type": "open-choice", "required": false, "repeats": false }, { "linkId": "Sequence.referenceSeq.referenceSeqId.text", "text": "text:", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Reference" } ], "linkId": "Sequence.referenceSeq.referenceSeqPointer", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "A Pointer to another Sequence entity as reference sequence.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-allowedResource", "valueCode": "Sequence" }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-referenceFilter", "valueString": "subject=$subj&patient=$subj&encounter=$encounter" } ], "linkId": "Sequence.referenceSeq.referenceSeqPointer.value", "text": "A Pointer to another Sequence entity as reference sequence", "type": "reference", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.referenceSeq.referenceSeqString", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "A string like \"ACGT\".", "type": "display" }, { "linkId": "Sequence.referenceSeq.referenceSeqString.value", "text": "A string to represent reference sequence", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.referenceSeq.strand", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Directionality of DNA sequence. Available values are \"1\" for the plus strand (5' to 3')/Watson/Sense/positive and \"-1\" for the minus strand(3' to 5')/Crick/Antisense/negative.", "type": "display" }, { "linkId": "Sequence.referenceSeq.strand.value", "text": "Directionality of DNA ( +1/-1)", "type": "integer", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-minOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.referenceSeq.windowStart", "type": "group", "required": true, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "type": "display" }, { "linkId": "Sequence.referenceSeq.windowStart.value", "text": "Start position of the window on the reference sequence", "type": "integer", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-minOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.referenceSeq.windowEnd", "type": "group", "required": true, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "End position of the window on the reference sequence. If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "type": "display" }, { "linkId": "Sequence.referenceSeq.windowEnd.value", "text": "End position of the window on the reference sequence", "type": "integer", "required": false, "repeats": false } ] } ] }, { "linkId": "Sequence.variant", "text": "Variant in sequence", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.variant.id", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", "type": "display" }, { "linkId": "Sequence.variant.id.value", "text": "xml:id (or equivalent in JSON)", "type": "string", "required": false, "repeats": false } ] }, { "linkId": "Sequence.variant.extension", "text": "Additional Content defined by implementations", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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.", "type": "display" } ] }, { "linkId": "Sequence.variant.modifierExtension", "text": "Extensions that cannot be ignored", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "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 that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. 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.", "type": "display" } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.variant.start", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Start position of the variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "type": "display" }, { "linkId": "Sequence.variant.start.value", "text": "Start position of the variant on the reference sequence", "type": "integer", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.variant.end", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "type": "display" }, { "linkId": "Sequence.variant.end.value", "text": "End position of the variant on the reference sequence", "type": "integer", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.variant.observedAllele", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.", "type": "display" }, { "linkId": "Sequence.variant.observedAllele.value", "text": "Allele that was observed", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.variant.referenceAllele", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.", "type": "display" }, { "linkId": "Sequence.variant.referenceAllele.value", "text": "Allele in the reference sequence", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.variant.cigar", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).", "type": "display" }, { "linkId": "Sequence.variant.cigar.value", "text": "Extended CIGAR string for aligning the sequence with reference bases", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Reference" } ], "linkId": "Sequence.variant.variantPointer", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "A pointer to an Observation containing variant information.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-allowedResource", "valueCode": "Observation" }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-referenceFilter", "valueString": "subject=$subj&patient=$subj&encounter=$encounter" } ], "linkId": "Sequence.variant.variantPointer.value", "text": "Pointer to observed variant information", "type": "reference", "required": false, "repeats": false } ] } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.observedSeq", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.", "type": "display" }, { "linkId": "Sequence.observedSeq.value", "text": "Sequence that was observed", "type": "string", "required": false, "repeats": false } ] }, { "linkId": "Sequence.quality", "text": "An set of value as quality of sequence", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.quality.id", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", "type": "display" }, { "linkId": "Sequence.quality.id.value", "text": "xml:id (or equivalent in JSON)", "type": "string", "required": false, "repeats": false } ] }, { "linkId": "Sequence.quality.extension", "text": "Additional Content defined by implementations", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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.", "type": "display" } ] }, { "linkId": "Sequence.quality.modifierExtension", "text": "Extensions that cannot be ignored", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "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 that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. 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.", "type": "display" } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-minOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "code" } ], "linkId": "Sequence.quality.type", "type": "group", "required": true, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "INDEL / SNP / Undefined variant.", "type": "display" }, { "linkId": "Sequence.quality.type.value", "text": "type", "type": "choice", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "CodeableConcept" } ], "linkId": "Sequence.quality.standardSequence", "text": "Standard sequence for comparison", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Gold standard sequence used for comparing against.", "type": "display" }, { "linkId": "Sequence.quality.standardSequence.coding", "text": "code:", "type": "open-choice", "required": false, "repeats": false }, { "linkId": "Sequence.quality.standardSequence.text", "text": "text:", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.quality.start", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "type": "display" }, { "linkId": "Sequence.quality.start.value", "text": "Start position of the sequence", "type": "integer", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.quality.end", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "End position of the sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "type": "display" }, { "linkId": "Sequence.quality.end.value", "text": "End position of the sequence", "type": "integer", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Quantity" } ], "linkId": "Sequence.quality.score", "text": "Quality score for the comparison", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).", "type": "display" }, { "linkId": "Sequence.quality.score.comparator", "text": "comp:", "type": "choice", "required": false, "repeats": false }, { "linkId": "Sequence.quality.score.value", "text": "value:", "type": "decimal", "required": false, "repeats": false }, { "linkId": "Sequence.quality.score.units", "text": "units:", "type": "string", "required": false, "repeats": false }, { "linkId": "Sequence.quality.score.code", "text": "coded units:", "type": "string", "required": false, "repeats": false }, { "linkId": "Sequence.quality.score.system", "text": "units system:", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "CodeableConcept" } ], "linkId": "Sequence.quality.method", "text": "Method to get quality", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Which method is used to get sequence quality.", "type": "display" }, { "linkId": "Sequence.quality.method.coding", "text": "code:", "type": "open-choice", "required": false, "repeats": false }, { "linkId": "Sequence.quality.method.text", "text": "text:", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "decimal" } ], "linkId": "Sequence.quality.truthTP", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.", "type": "display" }, { "linkId": "Sequence.quality.truthTP.value", "text": "True positives from the perspective of the truth data", "type": "decimal", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "decimal" } ], "linkId": "Sequence.quality.queryTP", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.", "type": "display" }, { "linkId": "Sequence.quality.queryTP.value", "text": "True positives from the perspective of the query data", "type": "decimal", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "decimal" } ], "linkId": "Sequence.quality.truthFN", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.", "type": "display" }, { "linkId": "Sequence.quality.truthFN.value", "text": "False negatives", "type": "decimal", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "decimal" } ], "linkId": "Sequence.quality.queryFP", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.", "type": "display" }, { "linkId": "Sequence.quality.queryFP.value", "text": "False positives", "type": "decimal", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "decimal" } ], "linkId": "Sequence.quality.gtFP", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).", "type": "display" }, { "linkId": "Sequence.quality.gtFP.value", "text": "False positives where the non-REF alleles in the Truth and Query Call Sets match", "type": "decimal", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "decimal" } ], "linkId": "Sequence.quality.precision", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "QUERY.TP / (QUERY.TP + QUERY.FP).", "type": "display" }, { "linkId": "Sequence.quality.precision.value", "text": "Precision of comparison", "type": "decimal", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "decimal" } ], "linkId": "Sequence.quality.recall", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).", "type": "display" }, { "linkId": "Sequence.quality.recall.value", "text": "Recall of comparison", "type": "decimal", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "decimal" } ], "linkId": "Sequence.quality.fScore", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).", "type": "display" }, { "linkId": "Sequence.quality.fScore.value", "text": "F-score", "type": "decimal", "required": false, "repeats": false } ] } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "integer" } ], "linkId": "Sequence.readCoverage", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.", "type": "display" }, { "linkId": "Sequence.readCoverage.value", "text": "Average number of reads representing a given nucleotide in the reconstructed sequence", "type": "integer", "required": false, "repeats": false } ] }, { "linkId": "Sequence.repository", "text": "External repository which contains detailed report related with observedSeq in this resource", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.repository.id", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", "type": "display" }, { "linkId": "Sequence.repository.id.value", "text": "xml:id (or equivalent in JSON)", "type": "string", "required": false, "repeats": false } ] }, { "linkId": "Sequence.repository.extension", "text": "Additional Content defined by implementations", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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.", "type": "display" } ] }, { "linkId": "Sequence.repository.modifierExtension", "text": "Extensions that cannot be ignored", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "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 that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. 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.", "type": "display" } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-minOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "code" } ], "linkId": "Sequence.repository.type", "type": "group", "required": true, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.", "type": "display" }, { "linkId": "Sequence.repository.type.value", "text": "type", "type": "choice", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "uri" } ], "linkId": "Sequence.repository.url", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "URI of an external repository which contains further details about the genetics data.", "type": "display" }, { "linkId": "Sequence.repository.url.value", "text": "URI of the repository", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.repository.name", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "URI of an external repository which contains further details about the genetics data.", "type": "display" }, { "linkId": "Sequence.repository.name.value", "text": "Repository's name", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.repository.datasetId", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository.", "type": "display" }, { "linkId": "Sequence.repository.datasetId.value", "text": "Id of the dataset that used to call for dataset in repository", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.repository.variantsetId", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository.", "type": "display" }, { "linkId": "Sequence.repository.variantsetId.value", "text": "Id of the variantset that used to call for variantset in repository", "type": "string", "required": false, "repeats": false } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "string" } ], "linkId": "Sequence.repository.readsetId", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Id of the read in this external repository.", "type": "display" }, { "linkId": "Sequence.repository.readsetId.value", "text": "Id of the read", "type": "string", "required": false, "repeats": false } ] } ] }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType", "valueString": "Reference" } ], "linkId": "Sequence.pointer", "type": "group", "required": false, "repeats": true, "item": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "flyover", "display": "Fly-over" } ] } } ], "text": "Pointer to next atomic sequence which at most contains one variant.", "type": "display" }, { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-allowedResource", "valueCode": "Sequence" }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-referenceFilter", "valueString": "subject=$subj&patient=$subj&encounter=$encounter" } ], "linkId": "Sequence.pointer.value", "text": "Pointer to next atomic sequence", "type": "reference", "required": false, "repeats": false } ] } ] } ] }
Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.