STU 3 Ballot
DiagnosticsThis page is part of the FHIR Specification (v1.6.0: STU 3 Ballot 4). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions 
StructureDefinition for sequence
{
"resourceType": "StructureDefinition",
"id": "Sequence",
"meta": {
"lastUpdated": "2016-08-11T17:02:54.322+10:00"
},
"text": {
"status": "generated",
"div": "<div>!-- Snipped for Brevity --></div>"
},
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger": 0
}
],
"url": "http://hl7.org/fhir/StructureDefinition/Sequence",
"name": "Sequence",
"status": "draft",
"publisher": "Health Level Seven International (Clinical Genomics)",
"contact": [
{
"telecom": [
{
"system": "other",
"value": "http://hl7.org/fhir"
}
]
},
{
"telecom": [
{
"system": "other",
"value": "http://www.hl7.org/Special/committees/clingenomics/index.cfm"
}
]
}
],
"date": "2016-08-11T17:02:54+10:00",
"description": "Base StructureDefinition for Sequence Resource",
"fhirVersion": "1.6.0",
"mapping": [
{
"identity": "w5",
"uri": "http://hl7.org/fhir/w5",
"name": "W5 Mapping"
},
{
"identity": "rim",
"uri": "http://hl7.org/v3",
"name": "RIM Mapping"
}
],
"kind": "resource",
"abstract": false,
"type": "Sequence",
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/DomainResource",
"derivation": "specialization",
"snapshot": {
"element": [
{
"id": "Sequence",
"path": "Sequence",
"short": "Information about a biological sequence",
"definition": "Raw data describing a biological sequence.",
"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()",
"xpath": "not(parent::f:contained and f:contained)"
},
{
"key": "dom-1",
"severity": "error",
"human": "If the resource is contained in another resource, it SHALL NOT contain any narrative",
"expression": "contained.text.empty()",
"xpath": "not(parent::f:contained and f:text)"
},
{
"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()",
"xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))"
},
{
"key": "dom-3",
"severity": "error",
"human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource",
"expression": "contained.where(('#'+id in %resource.descendants().reference).not()).empty()",
"xpath": "not(exists(for $id in f:contained/*/@id return $id[not(ancestor::f:contained/parent::*/descendant::f:reference/@value=concat('#', $id))]))"
}
],
"mapping": [
{
"identity": "rim",
"map": "Entity. Role, or Act"
},
{
"identity": "w5",
"map": "clinical.diagnostics"
}
]
},
{
"id": "Sequence.id",
"path": "Sequence.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.",
"comments": "The only time that a resource does not have an id is when it is being submitted to the server using a create operation.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.id",
"min": 0,
"max": "*"
},
"type": [
{
"code": "id"
}
],
"isSummary": true
},
{
"id": "Sequence.meta",
"path": "Sequence.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 may not always be associated with version changes to the resource.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.meta",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Meta"
}
],
"isSummary": true
},
{
"id": "Sequence.implicitRules",
"path": "Sequence.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.",
"comments": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element as much as possible.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.implicitRules",
"min": 0,
"max": "*"
},
"type": [
{
"code": "uri"
}
],
"isModifier": true,
"isSummary": true
},
{
"id": "Sequence.language",
"path": "Sequence.language",
"short": "Language of the resource content",
"definition": "The base language in which the resource is written.",
"comments": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).",
"min": 0,
"max": "1",
"base": {
"path": "Resource.language",
"min": 0,
"max": "*"
},
"type": [
{
"code": "code"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet",
"valueReference": {
"reference": "http://hl7.org/fhir/ValueSet/all-languages"
}
}
],
"strength": "extensible",
"description": "A human language.",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/languages"
}
}
},
{
"id": "Sequence.text",
"path": "Sequence.text",
"short": "Text summary of the resource, for human interpretation",
"definition": "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.",
"comments": "Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded in formation is added later.",
"alias": [
"narrative",
"html",
"xhtml",
"display"
],
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.text",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Narrative"
}
],
"condition": [
"dom-1"
],
"mapping": [
{
"identity": "rim",
"map": "Act.text?"
}
]
},
{
"id": "Sequence.contained",
"path": "Sequence.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, and nor can they have their own independent transaction scope.",
"comments": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again.",
"alias": [
"inline resources",
"anonymous resources",
"contained resources"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.contained",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Resource"
}
],
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.extension",
"path": "Sequence.extension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.modifierExtension",
"path": "Sequence.modifierExtension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.identifier",
"path": "Sequence.identifier",
"short": "Unique ID for this particular sequence",
"definition": "A unique identifier for this particular sequence instance.",
"requirements": "Allows sequences to be distinguished and referenced.",
"min": 0,
"max": "*",
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "w5",
"map": "id"
}
]
},
{
"id": "Sequence.type",
"path": "Sequence.type",
"short": "AA | DNA | RNA",
"definition": "Amino acid / cDNA transcript / RNA variant.",
"min": 1,
"max": "1",
"type": [
{
"code": "code"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Type if a sequence -- DNA, RNA, or amino acid sequence",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-type"
}
}
},
{
"id": "Sequence.coordinateSystem",
"path": "Sequence.coordinateSystem",
"short": "Numbering used for sequence (0-based or 1-based)",
"definition": "Whether the sequence is numbered starting at 0 (0-based numbering or coordinates) or starting at 1 (1-based numbering). Values are \"0\" for 0-based numbering and \"1\" for one-based.",
"min": 1,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.patient",
"path": "Sequence.patient",
"short": "Who and/or what this is about",
"definition": "The patient whose sequencing results are described by this resource.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Patient"
}
],
"isSummary": true
},
{
"id": "Sequence.specimen",
"path": "Sequence.specimen",
"short": "Specimen used for sequencing",
"definition": "Specimen used for sequencing.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Specimen"
}
],
"isSummary": true
},
{
"id": "Sequence.device",
"path": "Sequence.device",
"short": "The method for sequencing",
"definition": "The method for sequencing, for example, chip information.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Device"
}
],
"isSummary": true
},
{
"id": "Sequence.quantity",
"path": "Sequence.quantity",
"short": "Quantity of the sequence",
"definition": "Quantity of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq",
"path": "Sequence.referenceSeq",
"short": "Reference sequence",
"definition": "A reference sequence is a sequence that is used to represent an allele or variant.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.id",
"path": "Sequence.referenceSeq.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": "*"
},
"type": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.referenceSeq.extension",
"path": "Sequence.referenceSeq.extension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.referenceSeq.modifierExtension",
"path": "Sequence.referenceSeq.modifierExtension",
"short": "Extensions that cannot be ignored",
"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 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.referenceSeq.chromosome",
"path": "Sequence.referenceSeq.chromosome",
"short": "Chromosome containing genetic finding",
"definition": "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)).",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Chromosome number for human",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/chromosome-human"
}
}
},
{
"id": "Sequence.referenceSeq.genomeBuild",
"path": "Sequence.referenceSeq.genomeBuild",
"short": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.referenceSeqId",
"path": "Sequence.referenceSeq.referenceSeqId",
"short": "Reference identifier",
"definition": "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.",
"min": 1,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Reference identifier",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-referenceSeq"
}
}
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer",
"path": "Sequence.referenceSeq.referenceSeqPointer",
"short": "A Pointer to another Sequence entity as refence sequence",
"definition": "A Pointer to another Sequence entity as refence sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.referenceSeqString",
"path": "Sequence.referenceSeq.referenceSeqString",
"short": "A Reference Sequence string",
"definition": "A Reference Sequence string.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.strand",
"path": "Sequence.referenceSeq.strand",
"short": "Strand of DNA",
"definition": "Strand of DNA. Available values are \"1\" for the plus strand and \"-1\" for the minus strand.",
"min": 1,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.windowStart",
"path": "Sequence.referenceSeq.windowStart",
"short": "Start position (inclusive) of the window on the reference sequence",
"definition": "Start position (inclusive) of the window on the reference sequence.",
"min": 1,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.windowEnd",
"path": "Sequence.referenceSeq.windowEnd",
"short": "End position (exclusive) of the window on the reference sequence",
"definition": "End position (exclusive) of the window on the reference sequence.",
"min": 1,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant",
"path": "Sequence.variant",
"short": "Sequence variant",
"definition": "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)).",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.id",
"path": "Sequence.variant.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": "*"
},
"type": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.variant.extension",
"path": "Sequence.variant.extension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.variant.modifierExtension",
"path": "Sequence.variant.modifierExtension",
"short": "Extensions that cannot be ignored",
"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 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.variant.start",
"path": "Sequence.variant.start",
"short": "Start position (inclusive) of the variant on the reference sequence",
"definition": "Start position (inclusive) of the variant on the reference sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.end",
"path": "Sequence.variant.end",
"short": "End position (exclusive) of the variant on the reference sequence",
"definition": "End position (exclusive) of the variant on the reference sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.observedAllele",
"path": "Sequence.variant.observedAllele",
"short": "Allele that was observed",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.referenceAllele",
"path": "Sequence.variant.referenceAllele",
"short": "Allele of reference sequence",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.cigar",
"path": "Sequence.variant.cigar",
"short": "Extended CIGAR string for aligning the sequence with reference bases",
"definition": "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).",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.variantPointer",
"path": "Sequence.variant.variantPointer",
"short": "Pointer to observed variant information",
"definition": "A pointer to an Observation containing variant information.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Observation"
}
],
"isSummary": true
},
{
"id": "Sequence.observedSeq",
"path": "Sequence.observedSeq",
"short": "Observed sequence",
"definition": "Sequence that was observed.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.quality",
"path": "Sequence.quality",
"short": "Sequence quality",
"definition": "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)).",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.id",
"path": "Sequence.quality.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": "*"
},
"type": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.quality.extension",
"path": "Sequence.quality.extension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.quality.modifierExtension",
"path": "Sequence.quality.modifierExtension",
"short": "Extensions that cannot be ignored",
"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 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.quality.standardSequence",
"path": "Sequence.quality.standardSequence",
"short": "Standard sequence for comparison",
"definition": "Gold standard sequence used for comparing against.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.start",
"path": "Sequence.quality.start",
"short": "Start position (inclusive) of the sequence",
"definition": "Start position (inclusive) of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.end",
"path": "Sequence.quality.end",
"short": "End position (exclusive) of the sequence",
"definition": "End position (exclusive) of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.score",
"path": "Sequence.quality.score",
"short": "Quality score",
"definition": "The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.method",
"path": "Sequence.quality.method",
"short": "Method for quality",
"definition": "Method for quality.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.truthTP",
"path": "Sequence.quality.truthTP",
"short": "True positives from the perspective of the truth data",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.queryTP",
"path": "Sequence.quality.queryTP",
"short": "True positives from the perspective of the query data",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.truthFN",
"path": "Sequence.quality.truthFN",
"short": "False negatives",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.queryFP",
"path": "Sequence.quality.queryFP",
"short": "False positives",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.gtFP",
"path": "Sequence.quality.gtFP",
"short": "False positives where the non-REF alleles in the Truth and Query Call Sets match",
"definition": "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).",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.precision",
"path": "Sequence.quality.precision",
"short": "Precision",
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.recall",
"path": "Sequence.quality.recall",
"short": "Recall",
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.fScore",
"path": "Sequence.quality.fScore",
"short": "F-score",
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.readCoverage",
"path": "Sequence.readCoverage",
"short": "Average number of reads representing a given nucleotide in the reconstructed sequence",
"definition": "Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.repository",
"path": "Sequence.repository",
"short": "External repository",
"definition": "Configurations of the external repository.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.id",
"path": "Sequence.repository.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": "*"
},
"type": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.repository.extension",
"path": "Sequence.repository.extension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.repository.modifierExtension",
"path": "Sequence.repository.modifierExtension",
"short": "Extensions that cannot be ignored",
"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 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.repository.url",
"path": "Sequence.repository.url",
"short": "URI of the repository",
"definition": "URI of an external repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"type": [
{
"code": "uri"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.name",
"path": "Sequence.repository.name",
"short": "Name of the repository",
"definition": "URI of an external repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.variantId",
"path": "Sequence.repository.variantId",
"short": "Id of the variant",
"definition": "Id of the variant in this external repository.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.readId",
"path": "Sequence.repository.readId",
"short": "Id of the read",
"definition": "Id of the read in this external repository.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.pointer",
"path": "Sequence.pointer",
"short": "Pointer to next atomic sequence",
"definition": "Pointer to next atomic sequence which at most contains one variant.",
"min": 0,
"max": "*",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant",
"path": "Sequence.structureVariant",
"definition": "Structural variant.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.id",
"path": "Sequence.structureVariant.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": "*"
},
"type": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.structureVariant.extension",
"path": "Sequence.structureVariant.extension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.structureVariant.modifierExtension",
"path": "Sequence.structureVariant.modifierExtension",
"short": "Extensions that cannot be ignored",
"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 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.structureVariant.precisionOfBoundaries",
"path": "Sequence.structureVariant.precisionOfBoundaries",
"short": "Precision of boundaries",
"definition": "Precision of boundaries.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.reportedaCGHRatio",
"path": "Sequence.structureVariant.reportedaCGHRatio",
"short": "Structural Variant reported aCGH ratio",
"definition": "Structural Variant reported aCGH ratio.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.length",
"path": "Sequence.structureVariant.length",
"short": "Structural Variant Length",
"definition": "Structural Variant Length.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.outer",
"path": "Sequence.structureVariant.outer",
"definition": "Structural variant outer.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.outer.id",
"path": "Sequence.structureVariant.outer.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": "*"
},
"type": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.structureVariant.outer.extension",
"path": "Sequence.structureVariant.outer.extension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.structureVariant.outer.modifierExtension",
"path": "Sequence.structureVariant.outer.modifierExtension",
"short": "Extensions that cannot be ignored",
"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 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.structureVariant.outer.start",
"path": "Sequence.structureVariant.outer.start",
"short": "Structural Variant Outer Start-End",
"definition": "Structural Variant Outer Start-End.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.outer.end",
"path": "Sequence.structureVariant.outer.end",
"short": "Structural Variant Outer Start-End",
"definition": "Structural Variant Outer Start-End.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.inner",
"path": "Sequence.structureVariant.inner",
"definition": "Structural variant inner.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.inner.id",
"path": "Sequence.structureVariant.inner.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": "*"
},
"type": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.structureVariant.inner.extension",
"path": "Sequence.structureVariant.inner.extension",
"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. 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.structureVariant.inner.modifierExtension",
"path": "Sequence.structureVariant.inner.modifierExtension",
"short": "Extensions that cannot be ignored",
"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 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.",
"comments": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.structureVariant.inner.start",
"path": "Sequence.structureVariant.inner.start",
"short": "Structural Variant Inner Start-End",
"definition": "Structural Variant Inner Start-End.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.inner.end",
"path": "Sequence.structureVariant.inner.end",
"short": "Structural Variant Inner Start-End",
"definition": "Structural Variant Inner Start-End.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
}
]
},
"differential": {
"element": [
{
"id": "Sequence",
"path": "Sequence",
"short": "Information about a biological sequence",
"definition": "Raw data describing a biological sequence.",
"min": 0,
"max": "*",
"mapping": [
{
"identity": "w5",
"map": "clinical.diagnostics"
}
]
},
{
"id": "Sequence.identifier",
"path": "Sequence.identifier",
"short": "Unique ID for this particular sequence",
"definition": "A unique identifier for this particular sequence instance.",
"requirements": "Allows sequences to be distinguished and referenced.",
"min": 0,
"max": "*",
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "w5",
"map": "id"
}
]
},
{
"id": "Sequence.type",
"path": "Sequence.type",
"short": "AA | DNA | RNA",
"definition": "Amino acid / cDNA transcript / RNA variant.",
"min": 1,
"max": "1",
"type": [
{
"code": "code"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Type if a sequence -- DNA, RNA, or amino acid sequence",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-type"
}
}
},
{
"id": "Sequence.coordinateSystem",
"path": "Sequence.coordinateSystem",
"short": "Numbering used for sequence (0-based or 1-based)",
"definition": "Whether the sequence is numbered starting at 0 (0-based numbering or coordinates) or starting at 1 (1-based numbering). Values are \"0\" for 0-based numbering and \"1\" for one-based.",
"min": 1,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.patient",
"path": "Sequence.patient",
"short": "Who and/or what this is about",
"definition": "The patient whose sequencing results are described by this resource.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Patient"
}
],
"isSummary": true
},
{
"id": "Sequence.specimen",
"path": "Sequence.specimen",
"short": "Specimen used for sequencing",
"definition": "Specimen used for sequencing.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Specimen"
}
],
"isSummary": true
},
{
"id": "Sequence.device",
"path": "Sequence.device",
"short": "The method for sequencing",
"definition": "The method for sequencing, for example, chip information.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Device"
}
],
"isSummary": true
},
{
"id": "Sequence.quantity",
"path": "Sequence.quantity",
"short": "Quantity of the sequence",
"definition": "Quantity of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq",
"path": "Sequence.referenceSeq",
"short": "Reference sequence",
"definition": "A reference sequence is a sequence that is used to represent an allele or variant.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.chromosome",
"path": "Sequence.referenceSeq.chromosome",
"short": "Chromosome containing genetic finding",
"definition": "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)).",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Chromosome number for human",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/chromosome-human"
}
}
},
{
"id": "Sequence.referenceSeq.genomeBuild",
"path": "Sequence.referenceSeq.genomeBuild",
"short": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.referenceSeqId",
"path": "Sequence.referenceSeq.referenceSeqId",
"short": "Reference identifier",
"definition": "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.",
"min": 1,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Reference identifier",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-referenceSeq"
}
}
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer",
"path": "Sequence.referenceSeq.referenceSeqPointer",
"short": "A Pointer to another Sequence entity as refence sequence",
"definition": "A Pointer to another Sequence entity as refence sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.referenceSeqString",
"path": "Sequence.referenceSeq.referenceSeqString",
"short": "A Reference Sequence string",
"definition": "A Reference Sequence string.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.strand",
"path": "Sequence.referenceSeq.strand",
"short": "Strand of DNA",
"definition": "Strand of DNA. Available values are \"1\" for the plus strand and \"-1\" for the minus strand.",
"min": 1,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.windowStart",
"path": "Sequence.referenceSeq.windowStart",
"short": "Start position (inclusive) of the window on the reference sequence",
"definition": "Start position (inclusive) of the window on the reference sequence.",
"min": 1,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.windowEnd",
"path": "Sequence.referenceSeq.windowEnd",
"short": "End position (exclusive) of the window on the reference sequence",
"definition": "End position (exclusive) of the window on the reference sequence.",
"min": 1,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant",
"path": "Sequence.variant",
"short": "Sequence variant",
"definition": "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)).",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.start",
"path": "Sequence.variant.start",
"short": "Start position (inclusive) of the variant on the reference sequence",
"definition": "Start position (inclusive) of the variant on the reference sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.end",
"path": "Sequence.variant.end",
"short": "End position (exclusive) of the variant on the reference sequence",
"definition": "End position (exclusive) of the variant on the reference sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.observedAllele",
"path": "Sequence.variant.observedAllele",
"short": "Allele that was observed",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.referenceAllele",
"path": "Sequence.variant.referenceAllele",
"short": "Allele of reference sequence",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.cigar",
"path": "Sequence.variant.cigar",
"short": "Extended CIGAR string for aligning the sequence with reference bases",
"definition": "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).",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.variantPointer",
"path": "Sequence.variant.variantPointer",
"short": "Pointer to observed variant information",
"definition": "A pointer to an Observation containing variant information.",
"min": 0,
"max": "1",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Observation"
}
],
"isSummary": true
},
{
"id": "Sequence.observedSeq",
"path": "Sequence.observedSeq",
"short": "Observed sequence",
"definition": "Sequence that was observed.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.quality",
"path": "Sequence.quality",
"short": "Sequence quality",
"definition": "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)).",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.standardSequence",
"path": "Sequence.quality.standardSequence",
"short": "Standard sequence for comparison",
"definition": "Gold standard sequence used for comparing against.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.start",
"path": "Sequence.quality.start",
"short": "Start position (inclusive) of the sequence",
"definition": "Start position (inclusive) of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.end",
"path": "Sequence.quality.end",
"short": "End position (exclusive) of the sequence",
"definition": "End position (exclusive) of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.score",
"path": "Sequence.quality.score",
"short": "Quality score",
"definition": "The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.method",
"path": "Sequence.quality.method",
"short": "Method for quality",
"definition": "Method for quality.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.truthTP",
"path": "Sequence.quality.truthTP",
"short": "True positives from the perspective of the truth data",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.queryTP",
"path": "Sequence.quality.queryTP",
"short": "True positives from the perspective of the query data",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.truthFN",
"path": "Sequence.quality.truthFN",
"short": "False negatives",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.queryFP",
"path": "Sequence.quality.queryFP",
"short": "False positives",
"definition": "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.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.gtFP",
"path": "Sequence.quality.gtFP",
"short": "False positives where the non-REF alleles in the Truth and Query Call Sets match",
"definition": "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).",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.precision",
"path": "Sequence.quality.precision",
"short": "Precision",
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.recall",
"path": "Sequence.quality.recall",
"short": "Recall",
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.fScore",
"path": "Sequence.quality.fScore",
"short": "F-score",
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.readCoverage",
"path": "Sequence.readCoverage",
"short": "Average number of reads representing a given nucleotide in the reconstructed sequence",
"definition": "Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.repository",
"path": "Sequence.repository",
"short": "External repository",
"definition": "Configurations of the external repository.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.url",
"path": "Sequence.repository.url",
"short": "URI of the repository",
"definition": "URI of an external repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"type": [
{
"code": "uri"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.name",
"path": "Sequence.repository.name",
"short": "Name of the repository",
"definition": "URI of an external repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.variantId",
"path": "Sequence.repository.variantId",
"short": "Id of the variant",
"definition": "Id of the variant in this external repository.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.readId",
"path": "Sequence.repository.readId",
"short": "Id of the read",
"definition": "Id of the read in this external repository.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.pointer",
"path": "Sequence.pointer",
"short": "Pointer to next atomic sequence",
"definition": "Pointer to next atomic sequence which at most contains one variant.",
"min": 0,
"max": "*",
"type": [
{
"code": "Reference",
"profile": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant",
"path": "Sequence.structureVariant",
"definition": "Structural variant.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.precisionOfBoundaries",
"path": "Sequence.structureVariant.precisionOfBoundaries",
"short": "Precision of boundaries",
"definition": "Precision of boundaries.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.reportedaCGHRatio",
"path": "Sequence.structureVariant.reportedaCGHRatio",
"short": "Structural Variant reported aCGH ratio",
"definition": "Structural Variant reported aCGH ratio.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.length",
"path": "Sequence.structureVariant.length",
"short": "Structural Variant Length",
"definition": "Structural Variant Length.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.outer",
"path": "Sequence.structureVariant.outer",
"definition": "Structural variant outer.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.outer.start",
"path": "Sequence.structureVariant.outer.start",
"short": "Structural Variant Outer Start-End",
"definition": "Structural Variant Outer Start-End.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.outer.end",
"path": "Sequence.structureVariant.outer.end",
"short": "Structural Variant Outer Start-End",
"definition": "Structural Variant Outer Start-End.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.inner",
"path": "Sequence.structureVariant.inner",
"definition": "Structural variant inner.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.inner.start",
"path": "Sequence.structureVariant.inner.start",
"short": "Structural Variant Inner Start-End",
"definition": "Structural Variant Inner Start-End.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.structureVariant.inner.end",
"path": "Sequence.structureVariant.inner.end",
"short": "Structural Variant Inner Start-End",
"definition": "Structural Variant Inner Start-End.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
}
]
}
}
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.
© HL7.org 2011+. FHIR STU3 Ballot (v1.6.0-9663) generated on Thu, Aug 11, 2016 17:07+1000. QA Page
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