Connectathon 11 Snapshot
This page is part of the FHIR Specification (v1.2.0: STU 3 Draft). 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": "2015-12-11T17:38:40.294+11:00"
},
"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": "2015-12-11T17:38:40+11:00",
"description": "Base StructureDefinition for Sequence Resource",
"fhirVersion": "1.2.0",
"mapping": [
{
"identity": "w5",
"uri": "http://hl7.org/fhir/w5",
"name": "W5 Mapping"
},
{
"identity": "rim",
"uri": "http://hl7.org/v3",
"name": "RIM"
}
],
"kind": "resource",
"abstract": false,
"base": "http://hl7.org/fhir/StructureDefinition/DomainResource",
"snapshot": {
"element": [
{
"path": "Sequence",
"short": "A Sequence",
"definition": "Variation and Sequence data.",
"min": 0,
"max": "*",
"type": [
{
"code": "DomainResource"
}
],
"isSummary": true,
"mapping": [
{
"identity": "w5",
"map": "clinical.diagnostics"
}
]
},
{
"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. Bundles always have an id, though it is usually a generated UUID.",
"min": 0,
"max": "1",
"type": [
{
"code": "id"
}
],
"isSummary": true
},
{
"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",
"type": [
{
"code": "Meta"
}
],
"isSummary": true
},
{
"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",
"type": [
{
"code": "uri"
}
],
"isModifier": true,
"isSummary": true
},
{
"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",
"type": [
{
"code": "code"
}
],
"binding": {
"strength": "required",
"description": "A human language.",
"valueSetUri": "http://tools.ietf.org/html/bcp47"
}
},
{
"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.",
"alias": [
"narrative",
"html",
"xhtml",
"display"
],
"min": 0,
"max": "1",
"type": [
{
"code": "Narrative"
}
],
"condition": [
"dom-1"
],
"mapping": [
{
"identity": "rim",
"map": "Act.text?"
}
]
},
{
"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": "*",
"type": [
{
"code": "Resource"
}
],
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"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": "*",
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"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": "*",
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"path": "Sequence.type",
"short": "AA | DNA | RNA",
"definition": "Amino acid / cDNA transcript / RNA variation.",
"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"
}
}
},
{
"path": "Sequence.variationID",
"short": "Identifier for variant and ClinVar, dbSNP or COSMIC identifier should be used",
"definition": "Identifier for variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC).",
"min": 0,
"max": "*",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Variant ID",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-variationID"
}
}
},
{
"path": "Sequence.referenceSeq",
"short": "Reference identifier. It must match the type in the Sequence.type field",
"definition": "Reference identifier for cDNA transcript/protein, with version, from NCBI's RefSeq or ENSEMBL. This reference sequence identifier must match the type in the Sequence.type field.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Reference identifier",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-referenceSeq"
}
}
},
{
"path": "Sequence.quantity",
"short": "Quantity of the sequence",
"definition": "Quantity of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate",
"short": "The coordinate of the variant",
"definition": "The coordinate of the variant.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"definition": "unique id for the element within a resource (for internal references).",
"min": 0,
"max": "1",
"type": [
{
"code": "id"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"path": "Sequence.coordinate.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": "*",
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"path": "Sequence.coordinate.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": "*",
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"path": "Sequence.coordinate.chromosome",
"short": "The chromosome containing the genetic finding",
"definition": "The chromosome containing the genetic finding. The value set will be 1-22, X, Y when the species is human without chromosome abnormality. Otherwise, NCBI-Gene code system should be used.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate.start",
"short": "0-based start position (inclusive) of the sequence",
"definition": "Inclusive 0-based nucleotide position for start of genomic finding on the positive (+) genomics strand.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate.end",
"short": "0-based end position (exclusive) of the sequence",
"definition": "Exclusive 0-based nucleotide position for end of genomic finding on the positive (+) genomic strand.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate.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": "CodeableConcept"
}
],
"isSummary": true
},
{
"path": "Sequence.species",
"short": "Supporting tests of human, viruses, and bacteria",
"definition": "The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteria.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"path": "Sequence.observedAllele",
"short": "Nucleotide(s)/amino acids from start position of sequence to stop position of observed sequence",
"definition": "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
},
{
"path": "Sequence.referenceAllele",
"short": "Nucleotide(s)/amino acids from start position of sequence to stop position of reference sequence",
"definition": "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
},
{
"path": "Sequence.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
},
{
"path": "Sequence.quality",
"short": "Sequence Quality",
"definition": "Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"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).",
"min": 0,
"max": "1",
"type": [
{
"code": "id"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"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": "*",
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"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": "*",
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"path": "Sequence.quality.start",
"short": "0-based start position (inclusive) of the sequence",
"definition": "0-based start position (inclusive) of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"path": "Sequence.quality.end",
"short": "0-based end position (exclusive) of the sequence",
"definition": "0-based end position (exclusive) of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"path": "Sequence.quality.score",
"short": "Quality score",
"definition": "Quality score.",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"path": "Sequence.quality.platform",
"short": "Platform",
"definition": "Platform.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"path": "Sequence.allelicState",
"short": "The level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous",
"definition": "The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "LOINC answer list for AllelicState",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/LOINC-53034-5-answerlist"
}
}
},
{
"path": "Sequence.allelicFrequency",
"short": "Allele frequencies",
"definition": "Allele frequencies.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"path": "Sequence.copyNumberEvent",
"short": "Copy Number Event: Values: amplificaiton / deletion / LOH",
"definition": "Values: amplificaiton / deletion / LOH.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"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
},
{
"path": "Sequence.chip",
"short": "Information of chip",
"definition": "Information of chip.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"path": "Sequence.chip.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"definition": "unique id for the element within a resource (for internal references).",
"min": 0,
"max": "1",
"type": [
{
"code": "id"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"path": "Sequence.chip.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": "*",
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"path": "Sequence.chip.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": "*",
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"path": "Sequence.chip.chipId",
"short": "Chip id",
"definition": "Chip id.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.chip.manufacturerId",
"short": "Chip manufacturer id",
"definition": "Chip manufacturer id.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.chip.version",
"short": "Chip version",
"definition": "Chip version.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.repository",
"short": "External repository",
"definition": "External repository.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"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).",
"min": 0,
"max": "1",
"type": [
{
"code": "id"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"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": "*",
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"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": "*",
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"path": "Sequence.repository.url",
"short": "URI of the repository",
"definition": "URI of a GA4GH repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"type": [
{
"code": "uri"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.name",
"short": "Name of the repository",
"definition": "URI of a GA4GH repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.structure",
"short": "URI of the page containing information about the structure of the repository",
"definition": "URI of the page containing information about the structure of the repository.",
"min": 0,
"max": "1",
"type": [
{
"code": "uri"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.variantId",
"short": "Id of a GA4GH variant",
"definition": "Id of the GA4GH call set that matches identity of patient. A CallSet in GA4GH represents an individual.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.readGroupSetId",
"short": "Id of a GA4GH read group",
"definition": "Id of the GA4GH read group from which details about the sequence can be found. A read group in GA4GH represents a set of DNA reads processed the same way by the sequencer.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
}
]
},
"differential": {
"element": [
{
"path": "Sequence",
"short": "A Sequence",
"definition": "Variation and Sequence data.",
"min": 0,
"max": "*",
"type": [
{
"code": "DomainResource"
}
],
"isSummary": true,
"mapping": [
{
"identity": "w5",
"map": "clinical.diagnostics"
}
]
},
{
"path": "Sequence.type",
"short": "AA | DNA | RNA",
"definition": "Amino acid / cDNA transcript / RNA variation.",
"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"
}
}
},
{
"path": "Sequence.variationID",
"short": "Identifier for variant and ClinVar, dbSNP or COSMIC identifier should be used",
"definition": "Identifier for variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC).",
"min": 0,
"max": "*",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Variant ID",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-variationID"
}
}
},
{
"path": "Sequence.referenceSeq",
"short": "Reference identifier. It must match the type in the Sequence.type field",
"definition": "Reference identifier for cDNA transcript/protein, with version, from NCBI's RefSeq or ENSEMBL. This reference sequence identifier must match the type in the Sequence.type field.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "Reference identifier",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-referenceSeq"
}
}
},
{
"path": "Sequence.quantity",
"short": "Quantity of the sequence",
"definition": "Quantity of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate",
"short": "The coordinate of the variant",
"definition": "The coordinate of the variant.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate.chromosome",
"short": "The chromosome containing the genetic finding",
"definition": "The chromosome containing the genetic finding. The value set will be 1-22, X, Y when the species is human without chromosome abnormality. Otherwise, NCBI-Gene code system should be used.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate.start",
"short": "0-based start position (inclusive) of the sequence",
"definition": "Inclusive 0-based nucleotide position for start of genomic finding on the positive (+) genomics strand.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate.end",
"short": "0-based end position (exclusive) of the sequence",
"definition": "Exclusive 0-based nucleotide position for end of genomic finding on the positive (+) genomic strand.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"path": "Sequence.coordinate.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": "CodeableConcept"
}
],
"isSummary": true
},
{
"path": "Sequence.species",
"short": "Supporting tests of human, viruses, and bacteria",
"definition": "The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteria.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"path": "Sequence.observedAllele",
"short": "Nucleotide(s)/amino acids from start position of sequence to stop position of observed sequence",
"definition": "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
},
{
"path": "Sequence.referenceAllele",
"short": "Nucleotide(s)/amino acids from start position of sequence to stop position of reference sequence",
"definition": "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
},
{
"path": "Sequence.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
},
{
"path": "Sequence.quality",
"short": "Sequence Quality",
"definition": "Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processing.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"path": "Sequence.quality.start",
"short": "0-based start position (inclusive) of the sequence",
"definition": "0-based start position (inclusive) of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"path": "Sequence.quality.end",
"short": "0-based end position (exclusive) of the sequence",
"definition": "0-based end position (exclusive) of the sequence.",
"min": 0,
"max": "1",
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"path": "Sequence.quality.score",
"short": "Quality score",
"definition": "Quality score.",
"min": 0,
"max": "1",
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"path": "Sequence.quality.platform",
"short": "Platform",
"definition": "Platform.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"path": "Sequence.allelicState",
"short": "The level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous",
"definition": "The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"strength": "example",
"description": "LOINC answer list for AllelicState",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/LOINC-53034-5-answerlist"
}
}
},
{
"path": "Sequence.allelicFrequency",
"short": "Allele frequencies",
"definition": "Allele frequencies.",
"min": 0,
"max": "1",
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"path": "Sequence.copyNumberEvent",
"short": "Copy Number Event: Values: amplificaiton / deletion / LOH",
"definition": "Values: amplificaiton / deletion / LOH.",
"min": 0,
"max": "1",
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true
},
{
"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
},
{
"path": "Sequence.chip",
"short": "Information of chip",
"definition": "Information of chip.",
"min": 0,
"max": "1",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"path": "Sequence.chip.chipId",
"short": "Chip id",
"definition": "Chip id.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.chip.manufacturerId",
"short": "Chip manufacturer id",
"definition": "Chip manufacturer id.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.chip.version",
"short": "Chip version",
"definition": "Chip version.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.repository",
"short": "External repository",
"definition": "External repository.",
"min": 0,
"max": "*",
"type": [
{
"code": "BackboneElement"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.url",
"short": "URI of the repository",
"definition": "URI of a GA4GH repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"type": [
{
"code": "uri"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.name",
"short": "Name of the repository",
"definition": "URI of a GA4GH repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.structure",
"short": "URI of the page containing information about the structure of the repository",
"definition": "URI of the page containing information about the structure of the repository.",
"min": 0,
"max": "1",
"type": [
{
"code": "uri"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.variantId",
"short": "Id of a GA4GH variant",
"definition": "Id of the GA4GH call set that matches identity of patient. A CallSet in GA4GH represents an individual.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"path": "Sequence.repository.readGroupSetId",
"short": "Id of a GA4GH read group",
"definition": "Id of the GA4GH read group from which details about the sequence can be found. A read group in GA4GH represents a set of DNA reads processed the same way by the sequencer.",
"min": 0,
"max": "1",
"type": [
{
"code": "string"
}
],
"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 DSTU2 (v1.2.0-7447) generated on Fri, Dec 11, 2015 17:42+1100.
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