DiagnosticsClinical Genomics  Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: Patient |
This is a representation of the json schema for MolecularSequence, which is just a part of the full JSON Schema.
{
"$schema": "http://json-schema.org/draft-06/schema#",
"id": "http://hl7.org/fhir/json-schema/MolecularSequence",
"$ref": "#/definitions/MolecularSequence",
"description": "see http://hl7.org/fhir/json.html#schema for information about the FHIR Json Schemas",
"definitions": {
"MolecularSequence": {
"description": "Raw data describing a biological sequence.",
"properties": {
"resourceType": {
"description": "This is a MolecularSequence resource",
"const": "MolecularSequence"
},
"id": {
"description": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.",
"$ref": "id.schema.json#/definitions/id"
},
"meta": {
"description": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.",
"$ref": "Meta.schema.json#/definitions/Meta"
},
"implicitRules": {
"description": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.",
"$ref": "#/definitions/uri"
},
"_implicitRules": {
"description": "Extensions for implicitRules",
"$ref": "Element.schema.json#/definitions/Element"
},
"language": {
"description": "The base language in which the resource is written.",
"$ref": "#/definitions/code"
},
"_language": {
"description": "Extensions for language",
"$ref": "Element.schema.json#/definitions/Element"
},
"text": {
"description": "A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.",
"$ref": "Narrative.schema.json#/definitions/Narrative"
},
"contained": {
"description": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.",
"items": {
"$ref": "ResourceList.schema.json#/definitions/ResourceList"
},
"type": "array"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"identifier": {
"description": "A unique identifier for this particular sequence instance. This is a FHIR-defined id.",
"items": {
"$ref": "Identifier.schema.json#/definitions/Identifier"
},
"type": "array"
},
"type": {
"description": "Amino Acid Sequence/ DNA Sequence / RNA Sequence.",
"enum": [
"aa",
"dna",
"rna"
]
},
"_type": {
"description": "Extensions for type",
"$ref": "Element.schema.json#/definitions/Element"
},
"coordinateSystem": {
"description": "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).",
"$ref": "#/definitions/integer"
},
"_coordinateSystem": {
"description": "Extensions for coordinateSystem",
"$ref": "Element.schema.json#/definitions/Element"
},
"patient": {
"description": "The patient whose sequencing results are described by this resource.",
"$ref": "Reference.schema.json#/definitions/Reference"
},
"specimen": {
"description": "Specimen used for sequencing.",
"$ref": "Reference.schema.json#/definitions/Reference"
},
"device": {
"description": "The method for sequencing, for example, chip information.",
"$ref": "Reference.schema.json#/definitions/Reference"
},
"performer": {
"description": "The organization or lab that should be responsible for this result.",
"$ref": "Reference.schema.json#/definitions/Reference"
},
"quantity": {
"description": "The number of copies of the sequence of interest. (RNASeq).",
"$ref": "Quantity.schema.json#/definitions/Quantity"
},
"referenceSeq": {
"description": "A sequence that is used as a reference to describe variants that are present in a sequence analyzed.",
"$ref": "#/definitions/MolecularSequence_ReferenceSeq"
},
"variant": {
"description": "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.",
"items": {
"$ref": "#/definitions/MolecularSequence_Variant"
},
"type": "array"
},
"observedSeq": {
"description": "Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.",
"$ref": "#/definitions/string"
},
"_observedSeq": {
"description": "Extensions for observedSeq",
"$ref": "Element.schema.json#/definitions/Element"
},
"quality": {
"description": "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).",
"items": {
"$ref": "#/definitions/MolecularSequence_Quality"
},
"type": "array"
},
"readCoverage": {
"description": "Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.",
"$ref": "#/definitions/integer"
},
"_readCoverage": {
"description": "Extensions for readCoverage",
"$ref": "Element.schema.json#/definitions/Element"
},
"repository": {
"description": "Configurations of the external repository. The repository shall store target\u0027s observedSeq or records related with target\u0027s observedSeq.",
"items": {
"$ref": "#/definitions/MolecularSequence_Repository"
},
"type": "array"
},
"pointer": {
"description": "Pointer to next atomic sequence which at most contains one variant.",
"items": {
"$ref": "Reference.schema.json#/definitions/Reference"
},
"type": "array"
},
"structureVariant": {
"description": "Information about chromosome structure variation.",
"items": {
"$ref": "#/definitions/MolecularSequence_StructureVariant"
},
"type": "array"
}
},
"additionalProperties": false,
"required": [
"resourceType"
]
},
"MolecularSequence_ReferenceSeq": {
"description": "Raw data describing a biological sequence.",
"properties": {
"id": {
"description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"$ref": "string.schema.json#/definitions/string"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"chromosome": {
"description": "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)).",
"$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
},
"genomeBuild": {
"description": "The Genome Build used for reference, following GRCh build versions e.g. \u0027GRCh 37\u0027. Version number must be included if a versioned release of a primary build was used.",
"$ref": "#/definitions/string"
},
"_genomeBuild": {
"description": "Extensions for genomeBuild",
"$ref": "Element.schema.json#/definitions/Element"
},
"orientation": {
"description": "A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the \"sense\" strand, and the opposite complementary strand is the \"antisense\" strand.",
"enum": [
"sense",
"antisense"
]
},
"_orientation": {
"description": "Extensions for orientation",
"$ref": "Element.schema.json#/definitions/Element"
},
"referenceSeqId": {
"description": "Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.",
"$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
},
"referenceSeqPointer": {
"description": "A pointer to another MolecularSequence entity as reference sequence.",
"$ref": "Reference.schema.json#/definitions/Reference"
},
"referenceSeqString": {
"description": "A string like \"ACGT\".",
"$ref": "#/definitions/string"
},
"_referenceSeqString": {
"description": "Extensions for referenceSeqString",
"$ref": "Element.schema.json#/definitions/Element"
},
"strand": {
"description": "An absolute reference to a strand. The Watson strand is the strand whose 5\u0027-end is on the short arm of the chromosome, and the Crick strand as the one whose 5\u0027-end is on the long arm.",
"enum": [
"watson",
"crick"
]
},
"_strand": {
"description": "Extensions for strand",
"$ref": "Element.schema.json#/definitions/Element"
},
"windowStart": {
"description": "Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"$ref": "#/definitions/integer"
},
"_windowStart": {
"description": "Extensions for windowStart",
"$ref": "Element.schema.json#/definitions/Element"
},
"windowEnd": {
"description": "End position of the window on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"$ref": "#/definitions/integer"
},
"_windowEnd": {
"description": "Extensions for windowEnd",
"$ref": "Element.schema.json#/definitions/Element"
}
},
"additionalProperties": false
},
"MolecularSequence_Variant": {
"description": "Raw data describing a biological sequence.",
"properties": {
"id": {
"description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"$ref": "string.schema.json#/definitions/string"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"start": {
"description": "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.",
"$ref": "#/definitions/integer"
},
"_start": {
"description": "Extensions for start",
"$ref": "Element.schema.json#/definitions/Element"
},
"end": {
"description": "End position of the variant on the reference sequence. If the coordinate system is 0-based then end 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.",
"$ref": "#/definitions/integer"
},
"_end": {
"description": "Extensions for end",
"$ref": "Element.schema.json#/definitions/Element"
},
"observedAllele": {
"description": "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.",
"$ref": "#/definitions/string"
},
"_observedAllele": {
"description": "Extensions for observedAllele",
"$ref": "Element.schema.json#/definitions/Element"
},
"referenceAllele": {
"description": "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.",
"$ref": "#/definitions/string"
},
"_referenceAllele": {
"description": "Extensions for referenceAllele",
"$ref": "Element.schema.json#/definitions/Element"
},
"cigar": {
"description": "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).",
"$ref": "#/definitions/string"
},
"_cigar": {
"description": "Extensions for cigar",
"$ref": "Element.schema.json#/definitions/Element"
},
"variantPointer": {
"description": "A pointer to an Observation containing variant information.",
"$ref": "Reference.schema.json#/definitions/Reference"
}
},
"additionalProperties": false
},
"MolecularSequence_Quality": {
"description": "Raw data describing a biological sequence.",
"properties": {
"id": {
"description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"$ref": "string.schema.json#/definitions/string"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"type": {
"description": "INDEL / SNP / Undefined variant.",
"enum": [
"indel",
"snp",
"unknown"
]
},
"_type": {
"description": "Extensions for type",
"$ref": "Element.schema.json#/definitions/Element"
},
"standardSequence": {
"description": "Gold standard sequence used for comparing against.",
"$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
},
"start": {
"description": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"$ref": "#/definitions/integer"
},
"_start": {
"description": "Extensions for start",
"$ref": "Element.schema.json#/definitions/Element"
},
"end": {
"description": "End position of the sequence. If the coordinate system is 0-based then end 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.",
"$ref": "#/definitions/integer"
},
"_end": {
"description": "Extensions for end",
"$ref": "Element.schema.json#/definitions/Element"
},
"score": {
"description": "The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).",
"$ref": "Quantity.schema.json#/definitions/Quantity"
},
"method": {
"description": "Which method is used to get sequence quality.",
"$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
},
"truthTP": {
"description": "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.",
"$ref": "#/definitions/decimal"
},
"_truthTP": {
"description": "Extensions for truthTP",
"$ref": "Element.schema.json#/definitions/Element"
},
"queryTP": {
"description": "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.",
"$ref": "#/definitions/decimal"
},
"_queryTP": {
"description": "Extensions for queryTP",
"$ref": "Element.schema.json#/definitions/Element"
},
"truthFN": {
"description": "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.",
"$ref": "#/definitions/decimal"
},
"_truthFN": {
"description": "Extensions for truthFN",
"$ref": "Element.schema.json#/definitions/Element"
},
"queryFP": {
"description": "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.",
"$ref": "#/definitions/decimal"
},
"_queryFP": {
"description": "Extensions for queryFP",
"$ref": "Element.schema.json#/definitions/Element"
},
"gtFP": {
"description": "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).",
"$ref": "#/definitions/decimal"
},
"_gtFP": {
"description": "Extensions for gtFP",
"$ref": "Element.schema.json#/definitions/Element"
},
"precision": {
"description": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"$ref": "#/definitions/decimal"
},
"_precision": {
"description": "Extensions for precision",
"$ref": "Element.schema.json#/definitions/Element"
},
"recall": {
"description": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"$ref": "#/definitions/decimal"
},
"_recall": {
"description": "Extensions for recall",
"$ref": "Element.schema.json#/definitions/Element"
},
"fScore": {
"description": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"$ref": "#/definitions/decimal"
},
"_fScore": {
"description": "Extensions for fScore",
"$ref": "Element.schema.json#/definitions/Element"
},
"roc": {
"description": "Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.",
"$ref": "#/definitions/MolecularSequence_Roc"
}
},
"additionalProperties": false
},
"MolecularSequence_Roc": {
"description": "Raw data describing a biological sequence.",
"properties": {
"id": {
"description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"$ref": "string.schema.json#/definitions/string"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"score": {
"description": "Invidual data point representing the GQ (genotype quality) score threshold.",
"items": {
"$ref": "#/definitions/integer"
},
"type": "array"
},
"_score": {
"description": "Extensions for score",
"items": {
"$ref": "Element.schema.json#/definitions/Element"
},
"type": "array"
},
"numTP": {
"description": "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"items": {
"$ref": "#/definitions/integer"
},
"type": "array"
},
"_numTP": {
"description": "Extensions for numTP",
"items": {
"$ref": "Element.schema.json#/definitions/Element"
},
"type": "array"
},
"numFP": {
"description": "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"items": {
"$ref": "#/definitions/integer"
},
"type": "array"
},
"_numFP": {
"description": "Extensions for numFP",
"items": {
"$ref": "Element.schema.json#/definitions/Element"
},
"type": "array"
},
"numFN": {
"description": "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"items": {
"$ref": "#/definitions/integer"
},
"type": "array"
},
"_numFN": {
"description": "Extensions for numFN",
"items": {
"$ref": "Element.schema.json#/definitions/Element"
},
"type": "array"
},
"precision": {
"description": "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"items": {
"$ref": "#/definitions/decimal"
},
"type": "array"
},
"_precision": {
"description": "Extensions for precision",
"items": {
"$ref": "Element.schema.json#/definitions/Element"
},
"type": "array"
},
"sensitivity": {
"description": "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"items": {
"$ref": "#/definitions/decimal"
},
"type": "array"
},
"_sensitivity": {
"description": "Extensions for sensitivity",
"items": {
"$ref": "Element.schema.json#/definitions/Element"
},
"type": "array"
},
"fMeasure": {
"description": "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"items": {
"$ref": "#/definitions/decimal"
},
"type": "array"
},
"_fMeasure": {
"description": "Extensions for fMeasure",
"items": {
"$ref": "Element.schema.json#/definitions/Element"
},
"type": "array"
}
},
"additionalProperties": false
},
"MolecularSequence_Repository": {
"description": "Raw data describing a biological sequence.",
"properties": {
"id": {
"description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"$ref": "string.schema.json#/definitions/string"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"type": {
"description": "Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.",
"enum": [
"directlink",
"openapi",
"login",
"oauth",
"other"
]
},
"_type": {
"description": "Extensions for type",
"$ref": "Element.schema.json#/definitions/Element"
},
"url": {
"description": "URI of an external repository which contains further details about the genetics data.",
"$ref": "#/definitions/uri"
},
"_url": {
"description": "Extensions for url",
"$ref": "Element.schema.json#/definitions/Element"
},
"name": {
"description": "URI of an external repository which contains further details about the genetics data.",
"$ref": "#/definitions/string"
},
"_name": {
"description": "Extensions for name",
"$ref": "Element.schema.json#/definitions/Element"
},
"datasetId": {
"description": "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.",
"$ref": "#/definitions/string"
},
"_datasetId": {
"description": "Extensions for datasetId",
"$ref": "Element.schema.json#/definitions/Element"
},
"variantsetId": {
"description": "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.",
"$ref": "#/definitions/string"
},
"_variantsetId": {
"description": "Extensions for variantsetId",
"$ref": "Element.schema.json#/definitions/Element"
},
"readsetId": {
"description": "Id of the read in this external repository.",
"$ref": "#/definitions/string"
},
"_readsetId": {
"description": "Extensions for readsetId",
"$ref": "Element.schema.json#/definitions/Element"
}
},
"additionalProperties": false
},
"MolecularSequence_StructureVariant": {
"description": "Raw data describing a biological sequence.",
"properties": {
"id": {
"description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"$ref": "string.schema.json#/definitions/string"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"variantType": {
"description": "Information about chromosome structure variation DNA change type.",
"$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
},
"exact": {
"description": "Used to indicate if the outer and inner start-end values have the same meaning.",
"$ref": "#/definitions/boolean"
},
"_exact": {
"description": "Extensions for exact",
"$ref": "Element.schema.json#/definitions/Element"
},
"length": {
"description": "Length of the variant chromosome.",
"$ref": "#/definitions/integer"
},
"_length": {
"description": "Extensions for length",
"$ref": "Element.schema.json#/definitions/Element"
},
"outer": {
"description": "Structural variant outer.",
"$ref": "#/definitions/MolecularSequence_Outer"
},
"inner": {
"description": "Structural variant inner.",
"$ref": "#/definitions/MolecularSequence_Inner"
}
},
"additionalProperties": false
},
"MolecularSequence_Outer": {
"description": "Raw data describing a biological sequence.",
"properties": {
"id": {
"description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"$ref": "string.schema.json#/definitions/string"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"start": {
"description": "Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"$ref": "#/definitions/integer"
},
"_start": {
"description": "Extensions for start",
"$ref": "Element.schema.json#/definitions/Element"
},
"end": {
"description": "Structural variant outer end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"$ref": "#/definitions/integer"
},
"_end": {
"description": "Extensions for end",
"$ref": "Element.schema.json#/definitions/Element"
}
},
"additionalProperties": false
},
"MolecularSequence_Inner": {
"description": "Raw data describing a biological sequence.",
"properties": {
"id": {
"description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"$ref": "string.schema.json#/definitions/string"
},
"extension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"modifierExtension": {
"description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"items": {
"$ref": "Extension.schema.json#/definitions/Extension"
},
"type": "array"
},
"start": {
"description": "Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"$ref": "#/definitions/integer"
},
"_start": {
"description": "Extensions for start",
"$ref": "Element.schema.json#/definitions/Element"
},
"end": {
"description": "Structural variant inner end. If the coordinate system is 0-based then end 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.",
"$ref": "#/definitions/integer"
},
"_end": {
"description": "Extensions for end",
"$ref": "Element.schema.json#/definitions/Element"
}
},
"additionalProperties": false
}
}
}
®© HL7.org 2011+. FHIR Release 4 (Technical Correction #1) (v4.0.1) generated on Thu, Jan 21, 2021 15:38+0000. QA Page
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