### ----------------------------------------------------
### -- FHIR
### -- Licenses: Artistic-2.0
### -- Authors: Hugh Simpson
### -- File: t/resources/structureDefinition/MolecularSequence.json
### ----------------------------------------------------
### -- Chunk 16 of 16
001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "BackboneElement"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.type",
      "path" : "MolecularSequence.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.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/quality-type|4.0.0"
      }
    },
    {
      "id" : "MolecularSequence.quality.standardSequence",
      "path" : "MolecularSequence.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.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence"
      }
    },
    {
      "id" : "MolecularSequence.quality.start",
      "path" : "MolecularSequence.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" : "MolecularSequence.quality.end",
      "path" : "MolecularSequence.quality.end",
      "short" : "End position of the sequence",
      "definition" : "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.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.score",
      "path" : "MolecularSequence.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" : "MolecularSequence.quality.method",
      "path" : "MolecularSequence.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.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/sequence-quality-method"
      }
    },
    {
      "id" : "MolecularSequence.quality.truthTP",
      "path" : "MolecularSequence.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" : "MolecularSequence.quality.queryTP",
      "path" : "MolecularSequence.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" : "MolecularSequence.quality.truthFN",
      "path" : "MolecularSequence.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" : "MolecularSequence.quality.queryFP",
      "path" : "MolecularSequence.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" : "MolecularSequence.quality.gtFP",
      "path" : "MolecularSequence.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" : "MolecularSequence.quality.precision",
      "path" : "MolecularSequence.quality.precision",
      "short" : "Precision of comparison",
      "definition" : "QUERY.TP / (QUERY.TP + QUERY.FP).",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "decimal"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.recall",
      "path" : "MolecularSequence.quality.recall",
      "short" : "Recall of comparison",
      "definition" : "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "decimal"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.fScore",
      "path" : "MolecularSequence.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" : "MolecularSequence.quality.roc",
      "path" : "MolecularSequence.quality.roc",
      "short" : "Receiver Operator Characteristic (ROC) Curve",
      "definition" : "Receiver Operator Characteristic (ROC) Curve  to give sensitivity/specificity tradeoff.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "BackboneElement"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.roc.score",
      "path" : "MolecularSequence.quality.roc.score",
      "short" : "Genotype quality score",
      "definition" : "Invidual data point representing the GQ (genotype quality) score threshold.",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.roc.numTP",
      "path" : "MolecularSequence.quality.roc.numTP",
      "short" : "Roc score true positive numbers",
      "definition" : "The number of true positives if the GQ score threshold was set to \"score\" field value.",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.roc.numFP",
      "path" : "MolecularSequence.quality.roc.numFP",
      "short" : "Roc score false positive numbers",
      "definition" : "The number of false positives if the GQ score threshold was set to \"score\" field value.",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.roc.numFN",
      "path" : "MolecularSequence.quality.roc.numFN",
      "short" : "Roc score false negative numbers",
      "definition" : "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.roc.precision",
      "path" : "MolecularSequence.quality.roc.precision",
      "short" : "Precision of the GQ score",
      "definition" : "Calculated precision if the GQ score threshold was set to \"score\" field value.",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "decimal"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.roc.sensitivity",
      "path" : "MolecularSequence.quality.roc.sensitivity",
      "short" : "Sensitivity of the GQ score",
      "definition" : "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "decimal"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.roc.fMeasure",
      "path" : "MolecularSequence.quality.roc.fMeasure",
      "short" : "FScore of the GQ score",
      "definition" : "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "decimal"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.readCoverage",
      "path" : "MolecularSequence.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" : "MolecularSequence.repository",
      "path" : "MolecularSequence.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" : "MolecularSequence.repository.type",
      "path" : "MolecularSequence.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.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/repository-type|4.0.0"
      }
    },
    {
      "id" : "MolecularSequence.repository.url",
      "path" : "MolecularSequence.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" : "MolecularSequence.repository.name",
      "path" : "MolecularSequence.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" : "MolecularSequence.repository.datasetId",
      "path" : "MolecularSequence.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" : "MolecularSequence.repository.variantsetId",
      "path" : "MolecularSequence.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" : "MolecularSequence.repository.readsetId",
      "path" : "MolecularSequence.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" : "MolecularSequence.pointer",
      "path" : "MolecularSequence.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/MolecularSequence"]
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant",
      "path" : "MolecularSequence.structureVariant",
      "short" : "Structural variant",
      "definition" : "Information about chromosome structure variation.",
      "min" : 0,
      "max" : "*",
      "type" : [{
        "code" : "BackboneElement"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.variantType",
      "path" : "MolecularSequence.structureVariant.variantType",
      "short" : "Structural variant change type",
      "definition" : "Information about chromosome structure variation DNA change type.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isSummary" : true,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "LOINC LL379-9 answerlist"
        }],
        "strength" : "required",
        "description" : "DNA change type.",
        "valueSet" : "http://loinc.org/vs/LL379-9|4.0.0"
      }
    },
    {
      "id" : "MolecularSequence.structureVariant.exact",
      "path" : "MolecularSequence.structureVariant.exact",
      "short" : "Does the structural variant have base pair resolution breakpoints?",
      "definition" : "Used to indicate if the outer and inner start-end values have the same meaning.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "boolean"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.length",
      "path" : "MolecularSequence.structureVariant.length",
      "short" : "Structural variant length",
      "definition" : "Length of the variant chromosome.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.outer",
      "path" : "MolecularSequence.structureVariant.outer",
      "short" : "Structural variant outer",
      "definition" : "Structural variant outer.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "BackboneElement"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.outer.start",
      "path" : "MolecularSequence.structureVariant.outer.start",
      "short" : "Structural variant outer start",
      "definition" : "Structural variant outer start. 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" : "MolecularSequence.structureVariant.outer.end",
      "path" : "MolecularSequence.structureVariant.outer.end",
      "short" : "Structural variant outer end",
      "definition" : "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.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.inner",
      "path" : "MolecularSequence.structureVariant.inner",
      "short" : "Structural variant inner",
      "definition" : "Structural variant inner.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "BackboneElement"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.inner.start",
      "path" : "MolecularSequence.structureVariant.inner.start",
      "short" : "Structural variant inner start",
      "definition" : "Structural variant inner start. 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" : "MolecularSequence.structureVariant.inner.end",
      "path" : "MolecularSequence.structureVariant.inner.end",
      "short" : "Structural variant inner end",
      "definition" : "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.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    }]
  }
}


