{ "resourceType": "StructureDefinition", "id": "Sequence", "meta": { "lastUpdated": "2017-04-18T21:44:43.294+00:00" }, "text": { "status": "generated", "div": "
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\"SequenceΣIDomainResourceInformation about a biological sequence\r\n
+ Only 0 and 1 are valid for coordinateSystem
Elements defined in Ancestors: \r\n id, \r\n meta, \r\n implicitRules, \r\n language, \r\n text, \r\n contained, \r\n extension, \r\n modifierExtension
\".\"\".\"\".\"identifierΣ0..*IdentifierUnique ID for this particular sequence. This is a FHIR-defined id\r\n
\".\"\".\"\".\"typeΣ0..1codeaa | dna | rna\r\n
sequenceType (\r\n Example)\r\n
\".\"\".\"\".\"coordinateSystemΣ1..1integerBase number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
\".\"\".\"\".\"patientΣ0..1Reference(\r\n Patient)\r\n Who and/or what this is about
\".\"\".\"\".\"specimenΣ0..1Reference(\r\n Specimen)\r\n Specimen used for sequencing
\".\"\".\"\".\"deviceΣ0..1Reference(\r\n Device)\r\n The method for sequencing
\".\"\".\"\".\"performerΣ0..1Reference(\r\n Organization)\r\n Who should be responsible for test result
\".\"\".\"\".\"quantityΣ0..1QuantityThe number of copies of the seqeunce of interest. (RNASeq)
\".\"\".\"\".\"referenceSeqΣI0..1BackboneElementA sequence used as reference\r\n
+ Only +1 and -1 are valid for strand
+ GenomeBuild and chromosome must be both contained if either one of them is contained
+ Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
\".\"\".\"\".\"\".\"chromosomeΣ0..1CodeableConceptChromosome containing genetic finding\r\n
chromosome-human (\r\n Example)\r\n
\".\"\".\"\".\"\".\"genomeBuildΣ0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
\".\"\".\"\".\"\".\"referenceSeqIdΣ0..1CodeableConceptReference identifier\r\n
ENSEMBL (\r\n Example)\r\n
\".\"\".\"\".\"\".\"referenceSeqPointerΣ0..1Reference(\r\n Sequence)\r\n A Pointer to another Sequence entity as reference sequence
\".\"\".\"\".\"\".\"referenceSeqStringΣ0..1stringA string to represent reference sequence
\".\"\".\"\".\"\".\"strandΣ0..1integerDirectionality of DNA ( +1/-1)
\".\"\".\"\".\"\".\"windowStartΣ1..1integerStart position of the window on the reference sequence
\".\"\".\"\".\"\".\"windowEndΣ1..1integerEnd position of the window on the reference sequence
\".\"\".\"\".\"variantΣ0..*BackboneElementVariant in sequence\r\n
\".\"\".\"\".\"\".\"startΣ0..1integerStart position of the variant on the reference sequence
\".\"\".\"\".\"\".\"endΣ0..1integerEnd position of the variant on the reference sequence
\".\"\".\"\".\"\".\"observedAlleleΣ0..1stringAllele that was observed
\".\"\".\"\".\"\".\"referenceAlleleΣ0..1stringAllele in the reference sequence
\".\"\".\"\".\"\".\"cigarΣ0..1stringExtended CIGAR string for aligning the sequence with reference bases
\".\"\".\"\".\"\".\"variantPointerΣ0..1Reference(\r\n Observation)\r\n Pointer to observed variant information
\".\"\".\"\".\"observedSeqΣ0..1stringSequence that was observed
\".\"\".\"\".\"qualityΣ0..*BackboneElementAn set of value as quality of sequence\r\n
\".\"\".\"\".\"\".\"typeΣ1..1codeindel | snp | unknown\r\n
qualityType (\r\n Required)\r\n
\".\"\".\"\".\"\".\"standardSequenceΣ0..1CodeableConceptStandard sequence for comparison\r\n
FDA-StandardSequence (\r\n Example)\r\n
\".\"\".\"\".\"\".\"startΣ0..1integerStart position of the sequence
\".\"\".\"\".\"\".\"endΣ0..1integerEnd position of the sequence
\".\"\".\"\".\"\".\"scoreΣ0..1QuantityQuality score for the comparison
\".\"\".\"\".\"\".\"methodΣ0..1CodeableConceptMethod to get quality\r\n
FDA-Method (\r\n Example)\r\n
\".\"\".\"\".\"\".\"truthTPΣ0..1decimalTrue positives from the perspective of the truth data
\".\"\".\"\".\"\".\"queryTPΣ0..1decimalTrue positives from the perspective of the query data
\".\"\".\"\".\"\".\"truthFNΣ0..1decimalFalse negatives
\".\"\".\"\".\"\".\"queryFPΣ0..1decimalFalse positives
\".\"\".\"\".\"\".\"gtFPΣ0..1decimalFalse positives where the non-REF alleles in the Truth and Query Call Sets match
\".\"\".\"\".\"\".\"precisionΣ0..1decimalPrecision of comparison
\".\"\".\"\".\"\".\"recallΣ0..1decimalRecall of comparison
\".\"\".\"\".\"\".\"fScoreΣ0..1decimalF-score
\".\"\".\"\".\"readCoverageΣ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
\".\"\".\"\".\"repositoryΣ0..*BackboneElementExternal repository which contains detailed report related with observedSeq in this resource\r\n
\".\"\".\"\".\"\".\"typeΣ1..1codedirectlink | openapi | login | oauth | other\r\n
repositoryType (\r\n Required)\r\n
\".\"\".\"\".\"\".\"urlΣ0..1uriURI of the repository
\".\"\".\"\".\"\".\"nameΣ0..1stringRepository's name
\".\"\".\"\".\"\".\"datasetIdΣ0..1stringId of the dataset that used to call for dataset in repository
\".\"\".\"\".\"\".\"variantsetIdΣ0..1stringId of the variantset that used to call for variantset in repository
\".\"\".\"\".\"\".\"readsetIdΣ0..1stringId of the read
\".\"\".\"\".\"pointerΣ0..*Reference(\r\n Sequence)\r\n Pointer to next atomic sequence\r\n

\"doco\" Documentation for this format\r\n
" }, "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm", "valueInteger": 1 }, { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg", "valueCode": "cg" } ], "url": "http://hl7.org/fhir/StructureDefinition/Sequence", "name": "Sequence", "status": "draft", "date": "2017-04-18T21:44:43+00:00", "publisher": "Health Level Seven International (Clinical Genomics)", "contact": [ { "telecom": [ { "system": "url", "value": "http://hl7.org/fhir" } ] }, { "telecom": [ { "system": "url", "value": "http://www.hl7.org/Special/committees/clingenomics/index.cfm" } ] } ], "description": "Base StructureDefinition for Sequence Resource", "fhirVersion": "3.0.1", "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)", "source": "DomainResource" }, { "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)", "source": "DomainResource" }, { "key": "dom-4", "severity": "error", "human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated", "expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()", "xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))", "source": "DomainResource" }, { "key": "dom-3", "severity": "error", "human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource", "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))]))", "source": "DomainResource" }, { "key": "seq-3", "severity": "error", "human": "Only 0 and 1 are valid for coordinateSystem", "expression": "coordinateSystem = 1 or coordinateSystem = 0", "xpath": "count(f:coordinateSystem[@value=0 and @value=1]) = 1" } ], "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.", "comment": "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": "1" }, "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": "1" }, "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.", "comment": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. \n\nThis element is labelled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation.", "min": 0, "max": "1", "base": { "path": "Resource.implicitRules", "min": 0, "max": "1" }, "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.", "comment": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).", "min": 0, "max": "1", "base": { "path": "Resource.language", "min": 0, "max": "1" }, "type": [ { "code": "code" } ], "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet", "valueReference": { "reference": "http://hl7.org/fhir/ValueSet/all-languages" } }, { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "Language" }, { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding", "valueBoolean": true } ], "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.", "comment": "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": "1" }, "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.", "comment": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again.", "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "DomainResource.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "DomainResource.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. This is a FHIR-defined id", "definition": "A unique identifier for this particular sequence instance. This is a FHIR-defined id.", "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 Sequence/ DNA Sequence / RNA Sequence.", "min": 0, "max": "1", "type": [ { "code": "code" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "sequenceType" } ], "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": "Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)", "definition": "Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).", "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", "targetProfile": "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", "targetProfile": "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", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Device" } ], "isSummary": true }, { "id": "Sequence.performer", "path": "Sequence.performer", "short": "Who should be responsible for test result", "definition": "The organization or lab that should be responsible for this result.", "min": 0, "max": "1", "type": [ { "code": "Reference", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Organization" } ], "isSummary": true }, { "id": "Sequence.quantity", "path": "Sequence.quantity", "short": "The number of copies of the seqeunce of interest. (RNASeq)", "definition": "The number of copies of the seqeunce of interest. (RNASeq).", "min": 0, "max": "1", "type": [ { "code": "Quantity" } ], "isSummary": true }, { "id": "Sequence.referenceSeq", "path": "Sequence.referenceSeq", "short": "A sequence used as reference", "definition": "A sequence that is used as a reference to describe variants that are present in a sequence analyzed.", "min": 0, "max": "1", "type": [ { "code": "BackboneElement" } ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() | (children().count() > id.count())", "xpath": "@value|f:*|h:div", "source": "Element" }, { "key": "seq-4", "severity": "error", "human": "Only +1 and -1 are valid for strand", "expression": "strand.empty() or strand = 1 or strand = -1", "xpath": "not(exists(f:strand)) or count(f:strand[@value=-1 and @value=1]) = 1" }, { "key": "seq-5", "severity": "error", "human": "GenomeBuild and chromosome must be both contained if either one of them is contained", "expression": "(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())", "xpath": "(exists(f:chromosome) and exists(f:genomeBuild)) or (not(exists(f:chromosome)) and not(exists(f:genomeBuild)))" }, { "key": "seq-6", "severity": "error", "human": "Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;", "expression": "(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1", "xpath": "count(f:genomeBuild)+count(f:referenceSeqId)+count(f:referenceSeqPointer)+count(f:referenceSeqString)=1" } ], "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": "1" }, "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content", "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": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "chromosome-human" } ], "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": 0, "max": "1", "type": [ { "code": "CodeableConcept" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "sequenceReference" } ], "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 reference sequence", "definition": "A Pointer to another Sequence entity as reference sequence.", "min": 0, "max": "1", "type": [ { "code": "Reference", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Sequence" } ], "isSummary": true }, { "id": "Sequence.referenceSeq.referenceSeqString", "path": "Sequence.referenceSeq.referenceSeqString", "short": "A string to represent reference sequence", "definition": "A string like \"ACGT\".", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.referenceSeq.strand", "path": "Sequence.referenceSeq.strand", "short": "Directionality of DNA ( +1/-1)", "definition": "Directionality of DNA sequence. Available values are \"1\" for the plus strand (5' to 3')/Watson/Sense/positive and \"-1\" for the minus strand(3' to 5')/Crick/Antisense/negative.", "min": 0, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.referenceSeq.windowStart", "path": "Sequence.referenceSeq.windowStart", "short": "Start position of the window on the reference sequence", "definition": "Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "min": 1, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.referenceSeq.windowEnd", "path": "Sequence.referenceSeq.windowEnd", "short": "End position of the window on the reference sequence", "definition": "End position of the window on the reference sequence. If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "min": 1, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.variant", "path": "Sequence.variant", "short": "Variant in sequence", "definition": "The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.", "min": 0, "max": "*", "type": [ { "code": "BackboneElement" } ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() | (children().count() > id.count())", "xpath": "@value|f:*|h:div", "source": "Element" } ], "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": "1" }, "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content", "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 of the variant on the reference sequence", "definition": "Start position of the variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "min": 0, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.variant.end", "path": "Sequence.variant.end", "short": "End position of the variant on the reference sequence", "definition": "End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "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. This will lay in the range between variant.start and variant.end.", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.variant.referenceAllele", "path": "Sequence.variant.referenceAllele", "short": "Allele in the 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. This will lay in the range between variant.start and variant.end.", "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", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Observation" } ], "isSummary": true }, { "id": "Sequence.observedSeq", "path": "Sequence.observedSeq", "short": "Sequence that was observed", "definition": "Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.quality", "path": "Sequence.quality", "short": "An set of value as quality of sequence", "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" } ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() | (children().count() > id.count())", "xpath": "@value|f:*|h:div", "source": "Element" } ], "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": "1" }, "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content", "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.type", "path": "Sequence.quality.type", "short": "indel | snp | unknown", "definition": "INDEL / SNP / Undefined variant.", "min": 1, "max": "1", "type": [ { "code": "code" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "qualityType" } ], "strength": "required", "description": "Type for quality report", "valueSetReference": { "reference": "http://hl7.org/fhir/ValueSet/quality-type" } } }, { "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, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "qualityStandardSequence" } ], "strength": "example", "description": "Reference identifier of the sequence that used to mark the quality of tested samples.", "valueSetReference": { "reference": "http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence" } } }, { "id": "Sequence.quality.start", "path": "Sequence.quality.start", "short": "Start position of the sequence", "definition": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "min": 0, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.quality.end", "path": "Sequence.quality.end", "short": "End position of the sequence", "definition": "End position of the sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "min": 0, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.quality.score", "path": "Sequence.quality.score", "short": "Quality score for the comparison", "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 to get quality", "definition": "Which method is used to get sequence quality.", "min": 0, "max": "1", "type": [ { "code": "CodeableConcept" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "qualityMethod" } ], "strength": "example", "description": "The method used to evaluate the numerical quality of the observed sequence.", "valueSetReference": { "reference": "http://hl7.org/fhir/ValueSet/sequence-quality-method" } } }, { "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 of comparison", "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 of comparison", "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 which contains detailed report related with observedSeq in this resource", "definition": "Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.", "min": 0, "max": "*", "type": [ { "code": "BackboneElement" } ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() | (children().count() > id.count())", "xpath": "@value|f:*|h:div", "source": "Element" } ], "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": "1" }, "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "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.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content", "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.type", "path": "Sequence.repository.type", "short": "directlink | openapi | login | oauth | other", "definition": "Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.", "min": 1, "max": "1", "type": [ { "code": "code" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "repositoryType" } ], "strength": "required", "description": "Type for access of external URI", "valueSetReference": { "reference": "http://hl7.org/fhir/ValueSet/repository-type" } } }, { "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": "Repository's name", "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.datasetId", "path": "Sequence.repository.datasetId", "short": "Id of the dataset that used to call for dataset in repository", "definition": "Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository.", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.repository.variantsetId", "path": "Sequence.repository.variantsetId", "short": "Id of the variantset that used to call for variantset in repository", "definition": "Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository.", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.repository.readsetId", "path": "Sequence.repository.readsetId", "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", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Sequence" } ], "isSummary": true } ] }, "differential": { "element": [ { "id": "Sequence", "path": "Sequence", "short": "Information about a biological sequence", "definition": "Raw data describing a biological sequence.", "min": 0, "max": "*", "constraint": [ { "key": "seq-3", "severity": "error", "human": "Only 0 and 1 are valid for coordinateSystem", "expression": "coordinateSystem = 1 or coordinateSystem = 0", "xpath": "count(f:coordinateSystem[@value=0 and @value=1]) = 1" } ], "mapping": [ { "identity": "w5", "map": "clinical.diagnostics" } ] }, { "id": "Sequence.identifier", "path": "Sequence.identifier", "short": "Unique ID for this particular sequence. This is a FHIR-defined id", "definition": "A unique identifier for this particular sequence instance. This is a FHIR-defined id.", "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 Sequence/ DNA Sequence / RNA Sequence.", "min": 0, "max": "1", "type": [ { "code": "code" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "sequenceType" } ], "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": "Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)", "definition": "Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).", "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", "targetProfile": "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", "targetProfile": "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", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Device" } ], "isSummary": true }, { "id": "Sequence.performer", "path": "Sequence.performer", "short": "Who should be responsible for test result", "definition": "The organization or lab that should be responsible for this result.", "min": 0, "max": "1", "type": [ { "code": "Reference", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Organization" } ], "isSummary": true }, { "id": "Sequence.quantity", "path": "Sequence.quantity", "short": "The number of copies of the seqeunce of interest. (RNASeq)", "definition": "The number of copies of the seqeunce of interest. (RNASeq).", "min": 0, "max": "1", "type": [ { "code": "Quantity" } ], "isSummary": true }, { "id": "Sequence.referenceSeq", "path": "Sequence.referenceSeq", "short": "A sequence used as reference", "definition": "A sequence that is used as a reference to describe variants that are present in a sequence analyzed.", "min": 0, "max": "1", "type": [ { "code": "BackboneElement" } ], "constraint": [ { "key": "seq-4", "severity": "error", "human": "Only +1 and -1 are valid for strand", "expression": "strand.empty() or strand = 1 or strand = -1", "xpath": "not(exists(f:strand)) or count(f:strand[@value=-1 and @value=1]) = 1" }, { "key": "seq-5", "severity": "error", "human": "GenomeBuild and chromosome must be both contained if either one of them is contained", "expression": "(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())", "xpath": "(exists(f:chromosome) and exists(f:genomeBuild)) or (not(exists(f:chromosome)) and not(exists(f:genomeBuild)))" }, { "key": "seq-6", "severity": "error", "human": "Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;", "expression": "(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1", "xpath": "count(f:genomeBuild)+count(f:referenceSeqId)+count(f:referenceSeqPointer)+count(f:referenceSeqString)=1" } ], "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": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "chromosome-human" } ], "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": 0, "max": "1", "type": [ { "code": "CodeableConcept" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "sequenceReference" } ], "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 reference sequence", "definition": "A Pointer to another Sequence entity as reference sequence.", "min": 0, "max": "1", "type": [ { "code": "Reference", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Sequence" } ], "isSummary": true }, { "id": "Sequence.referenceSeq.referenceSeqString", "path": "Sequence.referenceSeq.referenceSeqString", "short": "A string to represent reference sequence", "definition": "A string like \"ACGT\".", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.referenceSeq.strand", "path": "Sequence.referenceSeq.strand", "short": "Directionality of DNA ( +1/-1)", "definition": "Directionality of DNA sequence. Available values are \"1\" for the plus strand (5' to 3')/Watson/Sense/positive and \"-1\" for the minus strand(3' to 5')/Crick/Antisense/negative.", "min": 0, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.referenceSeq.windowStart", "path": "Sequence.referenceSeq.windowStart", "short": "Start position of the window on the reference sequence", "definition": "Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "min": 1, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.referenceSeq.windowEnd", "path": "Sequence.referenceSeq.windowEnd", "short": "End position of the window on the reference sequence", "definition": "End position of the window on the reference sequence. If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "min": 1, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.variant", "path": "Sequence.variant", "short": "Variant in sequence", "definition": "The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.", "min": 0, "max": "*", "type": [ { "code": "BackboneElement" } ], "isSummary": true }, { "id": "Sequence.variant.start", "path": "Sequence.variant.start", "short": "Start position of the variant on the reference sequence", "definition": "Start position of the variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "min": 0, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.variant.end", "path": "Sequence.variant.end", "short": "End position of the variant on the reference sequence", "definition": "End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "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. This will lay in the range between variant.start and variant.end.", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.variant.referenceAllele", "path": "Sequence.variant.referenceAllele", "short": "Allele in the 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. This will lay in the range between variant.start and variant.end.", "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", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Observation" } ], "isSummary": true }, { "id": "Sequence.observedSeq", "path": "Sequence.observedSeq", "short": "Sequence that was observed", "definition": "Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.quality", "path": "Sequence.quality", "short": "An set of value as quality of sequence", "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.type", "path": "Sequence.quality.type", "short": "indel | snp | unknown", "definition": "INDEL / SNP / Undefined variant.", "min": 1, "max": "1", "type": [ { "code": "code" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "qualityType" } ], "strength": "required", "description": "Type for quality report", "valueSetReference": { "reference": "http://hl7.org/fhir/ValueSet/quality-type" } } }, { "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, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "qualityStandardSequence" } ], "strength": "example", "description": "Reference identifier of the sequence that used to mark the quality of tested samples.", "valueSetReference": { "reference": "http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence" } } }, { "id": "Sequence.quality.start", "path": "Sequence.quality.start", "short": "Start position of the sequence", "definition": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.", "min": 0, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.quality.end", "path": "Sequence.quality.end", "short": "End position of the sequence", "definition": "End position of the sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.", "min": 0, "max": "1", "type": [ { "code": "integer" } ], "isSummary": true }, { "id": "Sequence.quality.score", "path": "Sequence.quality.score", "short": "Quality score for the comparison", "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 to get quality", "definition": "Which method is used to get sequence quality.", "min": 0, "max": "1", "type": [ { "code": "CodeableConcept" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "qualityMethod" } ], "strength": "example", "description": "The method used to evaluate the numerical quality of the observed sequence.", "valueSetReference": { "reference": "http://hl7.org/fhir/ValueSet/sequence-quality-method" } } }, { "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 of comparison", "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 of comparison", "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 which contains detailed report related with observedSeq in this resource", "definition": "Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.", "min": 0, "max": "*", "type": [ { "code": "BackboneElement" } ], "isSummary": true }, { "id": "Sequence.repository.type", "path": "Sequence.repository.type", "short": "directlink | openapi | login | oauth | other", "definition": "Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.", "min": 1, "max": "1", "type": [ { "code": "code" } ], "isSummary": true, "binding": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "repositoryType" } ], "strength": "required", "description": "Type for access of external URI", "valueSetReference": { "reference": "http://hl7.org/fhir/ValueSet/repository-type" } } }, { "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": "Repository's name", "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.datasetId", "path": "Sequence.repository.datasetId", "short": "Id of the dataset that used to call for dataset in repository", "definition": "Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository.", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.repository.variantsetId", "path": "Sequence.repository.variantsetId", "short": "Id of the variantset that used to call for variantset in repository", "definition": "Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository.", "min": 0, "max": "1", "type": [ { "code": "string" } ], "isSummary": true }, { "id": "Sequence.repository.readsetId", "path": "Sequence.repository.readsetId", "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", "targetProfile": "http://hl7.org/fhir/StructureDefinition/Sequence" } ], "isSummary": true } ] } }