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Molecularsequence.profile.json

Clinical Genomics Work GroupMaturity Level: N/ABallot Status: InformativeCompartments: Patient

Raw JSON (каноническая форма + also see JSON Format Specification)

StructureDefinition for molecularsequence

{
  "resourceType" : "StructureDefinition",
  "id" : "MolecularSequence",
  "meta" : {
    "lastUpdated" : "2019-05-17T12:34:53.932+00:00"
  },
  "text" : {
    "status" : "generated",
    "div" : "<div>!-- Snipped for Brevity --></div>"
  },
  "extension" : [{
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
    "valueCode" : "trial-use"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
    "valueInteger" : 1
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category",
    "valueCode" : "patient"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
    "valueCode" : "cg"
  }],
  "url" : "http://hl7.org/fhir/StructureDefinition/MolecularSequence",
  "version" : "3.6.0",
  "name" : "MolecularSequence",
  "status" : "draft",
  "date" : "2019-05-17T12:34:53+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" : "Raw data describing a biological sequence.",
  "fhirVersion" : "3.6.0",
  "mapping" : [{
    "identity" : "w5",
    "uri" : "http://hl7.org/fhir/fivews",
    "name" : "FiveWs Pattern"
  },
  {
    "identity" : "rim",
    "uri" : "http://hl7.org/v3",
    "name" : "RIM Mapping"
  }],
  "kind" : "resource",
  "abstract" : false,
  "type" : "MolecularSequence",
  "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/DomainResource",
  "derivation" : "specialization",
  "snapshot" : {
    "element" : [{
      "id" : "MolecularSequence",
      "path" : "MolecularSequence",
      "short" : "Information about a biological sequence",
      "definition" : "Raw data describing a biological sequence.",
      "min" : 0,
      "max" : "*",
      "base" : {
        "path" : "MolecularSequence",
        "min" : 0,
        "max" : "*"
      },
      "constraint" : [{
        "key" : "dom-2",
        "severity" : "error",
        "human" : "Если ресурс встроен в другой ресурс, он НЕ ДОЛЖЕН содержать описательной части",
        "expression" : "contained.contained.empty()",
        "xpath" : "not(parent::f:contained and f:contained)",
        "source" : "DomainResource"
      },
      {
        "key" : "dom-4",
        "severity" : "error",
        "human" : "Если ресурс встроен в другой ресурс, он НЕ ДОЛЖЕН иметь meta.versionId или 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" : "Если ресурс встроен в другой ресурс, где-то в родительском ресурсе на него ДОЛЖНА БЫТЬ дана ссылка or SHALL refer to the containing resource",
        "expression" : "contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()",
        "xpath" : "not(exists(for $contained in f:contained return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))",
        "source" : "DomainResource"
      },
      {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice",
          "valueBoolean" : true
        },
        {
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation",
          "valueMarkdown" : "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time."
        }],
        "key" : "dom-6",
        "severity" : "warning",
        "human" : "A resource should have narrative for robust management",
        "expression" : "text.div.exists()",
        "xpath" : "exists(f:text/h:div)",
        "source" : "DomainResource"
      },
      {
        "key" : "dom-5",
        "severity" : "error",
        "human" : "If a resource is contained in another resource, it SHALL NOT have a security label",
        "expression" : "contained.meta.security.empty()",
        "xpath" : "not(exists(f:contained/*/f:meta/f:security))",
        "source" : "DomainResource"
      },
      {
        "key" : "msq-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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "Entity. Role, or Act"
      }]
    },
    {
      "id" : "MolecularSequence.id",
      "path" : "MolecularSequence.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"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.meta",
      "path" : "MolecularSequence.meta",
      "short" : "Метаданные ресурса",
      "definition" : "Метаданные ресурса. Это такая информация, которая поддерживается инфраструктурой. Изменения этой информации не всегда можно ассоциировать с версионными изменениями ресурса.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Resource.meta",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Meta"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.implicitRules",
      "path" : "MolecularSequence.implicitRules",
      "short" : "Свод правил, в соответствии с которыми создавалось это содержимое",
      "definition" : "Ссылка на свод правил, которым следовали при создании этого ресурса и которые необходимо понимать при обработке этого содержимого. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.",
      "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. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Resource.implicitRules",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "uri"
      }],
      "isModifier" : true,
      "isModifierReason" : "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation",
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.language",
      "path" : "MolecularSequence.language",
      "short" : "Язык содержимого ресурса",
      "definition" : "Основной язык, на котором написан ресурс.",
      "comment" : "Язык указывается для поддержки предварительной обработки текстов и доступности для понимания (например при преобразовании текста в речь используется языковой тег). HTML-тег language в описательной части применяется к этой описательной части. Языковой тег ресурса может использоваться для указания языков других представлений, генерируемых из данных ресурса\n\nНе все содержание ресурса должно быть на указанном основном языке. Resource.language нельзя автоматически принимать за язык описательной части. Если язык указан, его также следует указать в элементе div в HTML (информацию о связи между xml:lang и HTML-атрибутом lang см. в правилах HTML5).",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Resource.language",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "code"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet",
          "valueCanonical" : "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" : "preferred",
        "description" : "Естественный язык.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/languages"
      }
    },
    {
      "id" : "MolecularSequence.text",
      "path" : "MolecularSequence.text",
      "short" : "Краткое текстовое изложение ресурса для интерпретации человеком",
      "definition" : "Человекочитаемая описательная часть, содержащая краткое изложение ресурса, которая может использоваться для представления содержимого ресурса человеку. От описательной части не требуется кодировать все структурированные данные, но она должна содержать достаточно сведений, чтобы простое её прочтение человеком было \"клинически безопасным\". Определения ресурсов могут описывать, какое содержимое должно быть представлено в описательной части для обеспечения клинической безопасной.",
      "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 information is added later.",
      "alias" : ["narrative",
      "html",
      "xhtml",
      "display"],
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "DomainResource.text",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Narrative"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "Act.text?"
      }]
    },
    {
      "id" : "MolecularSequence.contained",
      "path" : "MolecularSequence.contained",
      "short" : "Вложенные, встроенные инлайн ресурсы",
      "definition" : "Эти ресурсы не обладают независимым существованием вне ресурса, который их содержит - их нельзя идентифицировать независимо, и они не могут иметь своей собственной независимой транзакционной области действия.",
      "comment" : "Этого не следует делать, когда содержимое может быть идентифицировано должным образом, поскольку, потеряв идентификацию, будет чрезвычайно сложно (и контекстно-зависимо) снова восстановить её. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.",
      "alias" : ["inline resources",
      "anonymous resources",
      "contained resources"],
      "min" : 0,
      "max" : "*",
      "base" : {
        "path" : "DomainResource.contained",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Resource"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "MolecularSequence.extension",
      "path" : "MolecularSequence.extension",
      "short" : "Дополнительное содержимое, определенное реализаторами",
      "definition" : "Может использоваться для представления дополнительной информации, не являющейся частью базового определения ресурса. Чтобы сделать использование расширений надежным и управляемым, существует строгий набор управления применительно к определению и использованию расширений. Хотя каждому реализатору разрешается определять расширения, имеется набор требований, которые должны выполняться в рамках определения расширения.",
      "comment" : "Не должно быть никаких предрассудков по использованию расширений любыми приложениями, проектами или стандартами - вне зависимости от учреждения или юрисдикции, которые используют или задают расширение. Именно использование расширений позволяет спецификации FHIR сохранять простоту для всех.",
      "alias" : ["extensions",
      "user content"],
      "min" : 0,
      "max" : "*",
      "base" : {
        "path" : "DomainResource.extension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "MolecularSequence.modifierExtension",
      "path" : "MolecularSequence.modifierExtension",
      "short" : "Расширения, которые нельзя игнорировать",
      "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. 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).",
      "comment" : "Не должно быть никаких предрассудков по использованию расширений любыми приложениями, проектами или стандартами - вне зависимости от учреждения или юрисдикции, которые используют или задают расширение. Именно использование расширений позволяет спецификации FHIR сохранять простоту для всех.",
      "alias" : ["extensions",
      "user content"],
      "min" : 0,
      "max" : "*",
      "base" : {
        "path" : "DomainResource.modifierExtension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : true,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them",
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "MolecularSequence.identifier",
      "path" : "MolecularSequence.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" : "*",
      "base" : {
        "path" : "MolecularSequence.identifier",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Identifier"
      }],
      "isModifier" : false,
      "isSummary" : true,
      "mapping" : [{
        "identity" : "w5",
        "map" : "FiveWs.identifier"
      }]
    },
    {
      "id" : "MolecularSequence.type",
      "path" : "MolecularSequence.type",
      "short" : "aa | dna | rna",
      "definition" : "Amino Acid Sequence/ DNA Sequence / RNA Sequence.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.type",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "code"
      }],
      "isModifier" : false,
      "isSummary" : true,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "sequenceType"
        }],
        "strength" : "required",
        "description" : "Type if a sequence -- DNA, RNA, or amino acid sequence.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/sequence-type"
      }
    },
    {
      "id" : "MolecularSequence.coordinateSystem",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.coordinateSystem",
        "min" : 1,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.patient",
      "path" : "MolecularSequence.patient",
      "short" : "Who and/or what this is about",
      "definition" : "The patient whose sequencing results are described by this resource.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.patient",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/StructureDefinition/Patient"]
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.specimen",
      "path" : "MolecularSequence.specimen",
      "short" : "Specimen used for sequencing",
      "definition" : "Specimen used for sequencing.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.specimen",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/StructureDefinition/Specimen"]
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.device",
      "path" : "MolecularSequence.device",
      "short" : "The method for sequencing",
      "definition" : "The method for sequencing, for example, chip information.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.device",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/StructureDefinition/Device"]
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.performer",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.performer",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/StructureDefinition/Organization"]
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quantity",
      "path" : "MolecularSequence.quantity",
      "short" : "The number of copies of the sequence of interest.  (RNASeq)",
      "definition" : "The number of copies of the sequence of interest. (RNASeq).",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.quantity",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Quantity"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.referenceSeq",
        "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() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      },
      {
        "key" : "msq-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"
      },
      {
        "key" : "msq-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)))"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.id",
      "path" : "MolecularSequence.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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.referenceSeq.extension",
      "path" : "MolecularSequence.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. 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.",
      "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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.referenceSeq.modifierExtension",
      "path" : "MolecularSequence.referenceSeq.modifierExtension",
      "short" : "Extensions that cannot be ignored even if unrecognized",
      "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 in which it is contained. 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).",
      "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,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
      "isSummary" : true,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "MolecularSequence.referenceSeq.chromosome",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.chromosome",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isModifier" : false,
      "isSummary" : true,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "chromosome-human"
        }],
        "strength" : "example",
        "description" : "Chromosome number for human.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/chromosome-human"
      }
    },
    {
      "id" : "MolecularSequence.referenceSeq.genomeBuild",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.genomeBuild",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.orientation",
      "path" : "MolecularSequence.referenceSeq.orientation",
      "short" : "sense | antisense",
      "definition" : "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.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.orientation",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "code"
      }],
      "isModifier" : false,
      "isSummary" : true,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "orientationType"
        }],
        "strength" : "required",
        "description" : "Type for orientation.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/orientation-type"
      }
    },
    {
      "id" : "MolecularSequence.referenceSeq.referenceSeqId",
      "path" : "MolecularSequence.referenceSeq.referenceSeqId",
      "short" : "Reference identifier",
      "definition" : "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.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.referenceSeqId",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isModifier" : false,
      "isSummary" : true,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "sequenceReference"
        }],
        "strength" : "example",
        "description" : "Reference identifier.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/sequence-referenceSeq"
      }
    },
    {
      "id" : "MolecularSequence.referenceSeq.referenceSeqPointer",
      "path" : "MolecularSequence.referenceSeq.referenceSeqPointer",
      "short" : "A pointer to another MolecularSequence entity as reference sequence",
      "definition" : "A pointer to another MolecularSequence entity as reference sequence.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.referenceSeqPointer",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/StructureDefinition/MolecularSequence"]
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.referenceSeqString",
      "path" : "MolecularSequence.referenceSeq.referenceSeqString",
      "short" : "A string to represent reference sequence",
      "definition" : "A string like \"ACGT\".",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.referenceSeqString",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.strand",
      "path" : "MolecularSequence.referenceSeq.strand",
      "short" : "watson | crick",
      "definition" : "An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.strand",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "code"
      }],
      "isModifier" : false,
      "isSummary" : true,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "strandType"
        }],
        "strength" : "required",
        "description" : "Type for strand.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/strand-type"
      }
    },
    {
      "id" : "MolecularSequence.referenceSeq.windowStart",
      "path" : "MolecularSequence.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" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.windowStart",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.windowEnd",
      "path" : "MolecularSequence.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 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",
      "base" : {
        "path" : "MolecularSequence.referenceSeq.windowEnd",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.variant",
      "path" : "MolecularSequence.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" : "*",
      "base" : {
        "path" : "MolecularSequence.variant",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "BackboneElement"
      }],
      "constraint" : [{
        "key" : "ele-1",
        "severity" : "error",
        "human" : "All FHIR elements must have a @value or children",
        "expression" : "hasValue() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.variant.id",
      "path" : "MolecularSequence.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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.variant.extension",
      "path" : "MolecularSequence.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. 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.",
      "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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.variant.modifierExtension",
      "path" : "MolecularSequence.variant.modifierExtension",
      "short" : "Extensions that cannot be ignored even if unrecognized",
      "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 in which it is contained. 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).",
      "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,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
      "isSummary" : true,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "MolecularSequence.variant.start",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.variant.start",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.variant.end",
      "path" : "MolecularSequence.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 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",
      "base" : {
        "path" : "MolecularSequence.variant.end",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.variant.observedAllele",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.variant.observedAllele",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.variant.referenceAllele",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.variant.referenceAllele",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.variant.cigar",
      "path" : "MolecularSequence.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",
      "base" : {
        "path" : "MolecularSequence.variant.cigar",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.variant.variantPointer",
      "path" : "MolecularSequence.variant.variantPointer",
      "short" : "Pointer to observed variant information",
      "definition" : "A pointer to an Observation containing variant information.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.variant.variantPointer",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/StructureDefinition/Observation"]
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.observedSeq",
      "path" : "MolecularSequence.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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.observedSeq",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality",
      "path" : "MolecularSequence.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" : "*",
      "base" : {
        "path" : "MolecularSequence.quality",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "BackboneElement"
      }],
      "constraint" : [{
        "key" : "ele-1",
        "severity" : "error",
        "human" : "All FHIR elements must have a @value or children",
        "expression" : "hasValue() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.id",
      "path" : "MolecularSequence.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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.quality.extension",
      "path" : "MolecularSequence.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. 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.",
      "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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.quality.modifierExtension",
      "path" : "MolecularSequence.quality.modifierExtension",
      "short" : "Extensions that cannot be ignored even if unrecognized",
      "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 in which it is contained. 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).",
      "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,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
      "isSummary" : true,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "MolecularSequence.quality.type",
      "path" : "MolecularSequence.quality.type",
      "short" : "indel | snp | unknown",
      "definition" : "INDEL / SNP / Undefined variant.",
      "min" : 1,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.quality.type",
        "min" : 1,
        "max" : "1"
      },
      "type" : [{
        "code" : "code"
      }],
      "isModifier" : false,
      "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"
      }
    },
    {
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.standardSequence",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.start",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.end",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.score",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "Quantity"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.method",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.truthTP",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.queryTP",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.truthFN",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.queryFP",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.gtFP",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.precision",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.recall",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.fScore",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.quality.roc",
        "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() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality.roc.id",
      "path" : "MolecularSequence.quality.roc.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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.quality.roc.extension",
      "path" : "MolecularSequence.quality.roc.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. 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.",
      "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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.quality.roc.modifierExtension",
      "path" : "MolecularSequence.quality.roc.modifierExtension",
      "short" : "Extensions that cannot be ignored even if unrecognized",
      "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 in which it is contained. 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).",
      "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,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
      "isSummary" : true,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.quality.roc.score",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.quality.roc.numTP",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.quality.roc.numFP",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.quality.roc.numFN",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.quality.roc.precision",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.quality.roc.sensitivity",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.quality.roc.fMeasure",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "decimal"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.readCoverage",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.repository",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "BackboneElement"
      }],
      "constraint" : [{
        "key" : "ele-1",
        "severity" : "error",
        "human" : "All FHIR elements must have a @value or children",
        "expression" : "hasValue() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.repository.id",
      "path" : "MolecularSequence.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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.repository.extension",
      "path" : "MolecularSequence.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. 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.",
      "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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.repository.modifierExtension",
      "path" : "MolecularSequence.repository.modifierExtension",
      "short" : "Extensions that cannot be ignored even if unrecognized",
      "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 in which it is contained. 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).",
      "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,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
      "isSummary" : true,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "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",
      "base" : {
        "path" : "MolecularSequence.repository.type",
        "min" : 1,
        "max" : "1"
      },
      "type" : [{
        "code" : "code"
      }],
      "isModifier" : false,
      "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"
      }
    },
    {
      "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",
      "base" : {
        "path" : "MolecularSequence.repository.url",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "uri"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.repository.name",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.repository.datasetId",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.repository.variantsetId",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.repository.readsetId",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "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" : "*",
      "base" : {
        "path" : "MolecularSequence.pointer",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/StructureDefinition/MolecularSequence"]
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant",
      "path" : "MolecularSequence.structureVariant",
      "short" : "Structural variant",
      "definition" : "Information about chromosome structure variation.",
      "min" : 0,
      "max" : "*",
      "base" : {
        "path" : "MolecularSequence.structureVariant",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "BackboneElement"
      }],
      "constraint" : [{
        "key" : "ele-1",
        "severity" : "error",
        "human" : "All FHIR elements must have a @value or children",
        "expression" : "hasValue() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.id",
      "path" : "MolecularSequence.structureVariant.id",
      "representation" : ["xmlAttr"],
      "short" : "xml:id (or equivalent in JSON)",
      "definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.id",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.structureVariant.extension",
      "path" : "MolecularSequence.structureVariant.extension",
      "short" : "Additional content defined by implementations",
      "definition" : "May be used to represent additional information that is not part of the basic definition of the element. 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.",
      "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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.structureVariant.modifierExtension",
      "path" : "MolecularSequence.structureVariant.modifierExtension",
      "short" : "Extensions that cannot be ignored even if unrecognized",
      "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 in which it is contained. 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).",
      "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,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
      "isSummary" : true,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "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",
      "base" : {
        "path" : "MolecularSequence.structureVariant.variantType",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isModifier" : false,
      "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"
      }
    },
    {
      "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",
      "base" : {
        "path" : "MolecularSequence.structureVariant.exact",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "boolean"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.length",
      "path" : "MolecularSequence.structureVariant.length",
      "short" : "Structural Variant Length",
      "definition" : "Length of the variant chromosome.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.structureVariant.length",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.outer",
      "path" : "MolecularSequence.structureVariant.outer",
      "short" : "Structural variant outer",
      "definition" : "Structural variant outer.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.structureVariant.outer",
        "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() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.outer.id",
      "path" : "MolecularSequence.structureVariant.outer.id",
      "representation" : ["xmlAttr"],
      "short" : "xml:id (or equivalent in JSON)",
      "definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.id",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.structureVariant.outer.extension",
      "path" : "MolecularSequence.structureVariant.outer.extension",
      "short" : "Additional content defined by implementations",
      "definition" : "May be used to represent additional information that is not part of the basic definition of the element. 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.",
      "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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.structureVariant.outer.modifierExtension",
      "path" : "MolecularSequence.structureVariant.outer.modifierExtension",
      "short" : "Extensions that cannot be ignored even if unrecognized",
      "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 in which it is contained. 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).",
      "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,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
      "isSummary" : true,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "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",
      "base" : {
        "path" : "MolecularSequence.structureVariant.outer.start",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.structureVariant.outer.end",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.inner",
      "path" : "MolecularSequence.structureVariant.inner",
      "short" : "Structural variant inner",
      "definition" : "Structural variant inner.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "MolecularSequence.structureVariant.inner",
        "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() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      }],
      "isModifier" : false,
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.structureVariant.inner.id",
      "path" : "MolecularSequence.structureVariant.inner.id",
      "representation" : ["xmlAttr"],
      "short" : "xml:id (or equivalent in JSON)",
      "definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.id",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.structureVariant.inner.extension",
      "path" : "MolecularSequence.structureVariant.inner.extension",
      "short" : "Additional content defined by implementations",
      "definition" : "May be used to represent additional information that is not part of the basic definition of the element. 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.",
      "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"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "MolecularSequence.structureVariant.inner.modifierExtension",
      "path" : "MolecularSequence.structureVariant.inner.modifierExtension",
      "short" : "Extensions that cannot be ignored even if unrecognized",
      "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 in which it is contained. 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).",
      "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,
      "isModifierReason" : "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
      "isSummary" : true,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "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",
      "base" : {
        "path" : "MolecularSequence.structureVariant.inner.start",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "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",
      "base" : {
        "path" : "MolecularSequence.structureVariant.inner.end",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "integer"
      }],
      "isModifier" : false,
      "isSummary" : true
    }]
  },
  "differential" : {
    "element" : [{
      "id" : "MolecularSequence",
      "path" : "MolecularSequence",
      "short" : "Information about a biological sequence",
      "definition" : "Raw data describing a biological sequence.",
      "min" : 0,
      "max" : "*",
      "constraint" : [{
        "key" : "msq-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"
      }]
    },
    {
      "id" : "MolecularSequence.identifier",
      "path" : "MolecularSequence.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" : "FiveWs.identifier"
      }]
    },
    {
      "id" : "MolecularSequence.type",
      "path" : "MolecularSequence.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" : "required",
        "description" : "Type if a sequence -- DNA, RNA, or amino acid sequence.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/sequence-type"
      }
    },
    {
      "id" : "MolecularSequence.coordinateSystem",
      "path" : "MolecularSequence.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" : "MolecularSequence.patient",
      "path" : "MolecularSequence.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" : "MolecularSequence.specimen",
      "path" : "MolecularSequence.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" : "MolecularSequence.device",
      "path" : "MolecularSequence.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" : "MolecularSequence.performer",
      "path" : "MolecularSequence.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" : "MolecularSequence.quantity",
      "path" : "MolecularSequence.quantity",
      "short" : "The number of copies of the sequence of interest.  (RNASeq)",
      "definition" : "The number of copies of the sequence of interest. (RNASeq).",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "Quantity"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq",
      "path" : "MolecularSequence.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" : "msq-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"
      },
      {
        "key" : "msq-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)))"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.chromosome",
      "path" : "MolecularSequence.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.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/chromosome-human"
      }
    },
    {
      "id" : "MolecularSequence.referenceSeq.genomeBuild",
      "path" : "MolecularSequence.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" : "MolecularSequence.referenceSeq.orientation",
      "path" : "MolecularSequence.referenceSeq.orientation",
      "short" : "sense | antisense",
      "definition" : "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.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "code"
      }],
      "isSummary" : true,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "orientationType"
        }],
        "strength" : "required",
        "description" : "Type for orientation.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/orientation-type"
      }
    },
    {
      "id" : "MolecularSequence.referenceSeq.referenceSeqId",
      "path" : "MolecularSequence.referenceSeq.referenceSeqId",
      "short" : "Reference identifier",
      "definition" : "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.",
      "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.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/sequence-referenceSeq"
      }
    },
    {
      "id" : "MolecularSequence.referenceSeq.referenceSeqPointer",
      "path" : "MolecularSequence.referenceSeq.referenceSeqPointer",
      "short" : "A pointer to another MolecularSequence entity as reference sequence",
      "definition" : "A pointer to another MolecularSequence entity as reference sequence.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/StructureDefinition/MolecularSequence"]
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.referenceSeqString",
      "path" : "MolecularSequence.referenceSeq.referenceSeqString",
      "short" : "A string to represent reference sequence",
      "definition" : "A string like \"ACGT\".",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "string"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.strand",
      "path" : "MolecularSequence.referenceSeq.strand",
      "short" : "watson | crick",
      "definition" : "An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "code"
      }],
      "isSummary" : true,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "strandType"
        }],
        "strength" : "required",
        "description" : "Type for strand.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/strand-type"
      }
    },
    {
      "id" : "MolecularSequence.referenceSeq.windowStart",
      "path" : "MolecularSequence.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" : 0,
      "max" : "1",
      "type" : [{
        "code" : "integer"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.referenceSeq.windowEnd",
      "path" : "MolecularSequence.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 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.variant",
      "path" : "MolecularSequence.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" : "MolecularSequence.variant.start",
      "path" : "MolecularSequence.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" : "MolecularSequence.variant.end",
      "path" : "MolecularSequence.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 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.variant.observedAllele",
      "path" : "MolecularSequence.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" : "MolecularSequence.variant.referenceAllele",
      "path" : "MolecularSequence.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" : "MolecularSequence.variant.cigar",
      "path" : "MolecularSequence.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" : "MolecularSequence.variant.variantPointer",
      "path" : "MolecularSequence.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" : "MolecularSequence.observedSeq",
      "path" : "MolecularSequence.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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd.",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "string"
      }],
      "isSummary" : true
    },
    {
      "id" : "MolecularSequence.quality",
      "path" : "MolecularSequence.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" : "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"
      }
    },
    {
      "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"
      }
    },
    {
      "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"
      }
    },
    {
      "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
    }]
  }
}

Примечание к использованию: мы очень стараемся приводить корректные и полезные примеры, но нормативно они не являются частью спецификации.