15.12.8 JSON Schema for SubstanceNucleicAcid

Biomedical Research and Regulation Work Group

Maturity Level: N/A

Standards Status: Informative

Compartments: Not linked to any defined compartments

This is a representation of the json schema for SubstanceNucleicAcid, which is just a part of the full JSON Schema.

{
  "$schema": "http://json-schema.org/draft-06/schema#",
  "id": "http://hl7.org/fhir/json-schema/SubstanceNucleicAcid",
  "$ref": "#/definitions/SubstanceNucleicAcid",
  "description": "see http://hl7.org/fhir/json.html#schema for information about the FHIR Json Schemas",
  "definitions": {
    "SubstanceNucleicAcid": {
      "description": "Nucleic acids are defined by three distinct elements: the base, sugar and linkage. Individual substance/moiety IDs will be created for each of these elements. The nucleotide sequence will be always entered in the 5’-3’ direction.",
      "properties": {
        "resourceType": {
          "description": "This is a SubstanceNucleicAcid resource",
          "const": "SubstanceNucleicAcid"
        },
        "id": {
          "description": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.",
          "$ref": "id.schema.json#/definitions/id"
        },
        "meta": {
          "description": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.",
          "$ref": "Meta.schema.json#/definitions/Meta"
        },
        "implicitRules": {
          "description": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.",
          "$ref": "#/definitions/uri"
        },
        "_implicitRules": {
          "description": "Extensions for implicitRules",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "language": {
          "description": "The base language in which the resource is written.",
          "$ref": "#/definitions/code"
        },
        "_language": {
          "description": "Extensions for language",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "text": {
          "description": "A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.",
          "$ref": "Narrative.schema.json#/definitions/Narrative"
        },
        "contained": {
          "description": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, nor can they have their own independent transaction scope. This is allowed to be a Parameters resource if and only if it is referenced by a resource that provides context/meaning.",
          "items": {
            "$ref": "ResourceList.schema.json#/definitions/ResourceList"
          },
          "type": "array"
        },
        "extension": {
          "description": "May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance  applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
          "items": {
            "$ref": "Extension.schema.json#/definitions/Extension"
          },
          "type": "array"
        },
        "modifierExtension": {
          "description": "May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
          "items": {
            "$ref": "Extension.schema.json#/definitions/Extension"
          },
          "type": "array"
        },
        "sequenceType": {
          "description": "The type of the sequence shall be specified based on a controlled vocabulary.",
          "$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
        },
        "numberOfSubunits": {
          "description": "The number of linear sequences of nucleotides linked through phosphodiester bonds shall be described. Subunits would be strands of nucleic acids that are tightly associated typically through Watson-Crick base pairing. NOTE: If not specified in the reference source, the assumption is that there is 1 subunit.",
          "$ref": "#/definitions/integer"
        },
        "_numberOfSubunits": {
          "description": "Extensions for numberOfSubunits",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "areaOfHybridisation": {
          "description": "The area of hybridisation shall be described if applicable for double stranded RNA or DNA. The number associated with the subunit followed by the number associated to the residue shall be specified in increasing order. The underscore “” shall be used as separator as follows: “Subunitnumber Residue”.",
          "$ref": "#/definitions/string"
        },
        "_areaOfHybridisation": {
          "description": "Extensions for areaOfHybridisation",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "oligoNucleotideType": {
          "description": "(TBC).",
          "$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
        },
        "subunit": {
          "description": "Subunits are listed in order of decreasing length; sequences of the same length will be ordered by molecular weight; subunits that have identical sequences will be repeated multiple times.",
          "items": {
            "$ref": "#/definitions/SubstanceNucleicAcid_Subunit"
          },
          "type": "array"
        }
      },
      "type": "object",
      "additionalProperties": false,
      "required": [
        "resourceType"
      ]
    },
    "SubstanceNucleicAcid_Subunit": {
      "description": "Nucleic acids are defined by three distinct elements: the base, sugar and linkage. Individual substance/moiety IDs will be created for each of these elements. The nucleotide sequence will be always entered in the 5’-3’ direction.",
      "properties": {
        "id": {
          "description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
          "$ref": "string.schema.json#/definitions/string"
        },
        "extension": {
          "description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance  applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
          "items": {
            "$ref": "Extension.schema.json#/definitions/Extension"
          },
          "type": "array"
        },
        "modifierExtension": {
          "description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
          "items": {
            "$ref": "Extension.schema.json#/definitions/Extension"
          },
          "type": "array"
        },
        "subunit": {
          "description": "Index of linear sequences of nucleic acids in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts.",
          "$ref": "#/definitions/integer"
        },
        "_subunit": {
          "description": "Extensions for subunit",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "sequence": {
          "description": "Actual nucleotide sequence notation from 5\u0027 to 3\u0027 end using standard single letter codes. In addition to the base sequence, sugar and type of phosphate or non-phosphate linkage should also be captured.",
          "$ref": "#/definitions/string"
        },
        "_sequence": {
          "description": "Extensions for sequence",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "length": {
          "description": "The length of the sequence shall be captured.",
          "$ref": "#/definitions/integer"
        },
        "_length": {
          "description": "Extensions for length",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "sequenceAttachment": {
          "description": "(TBC).",
          "$ref": "Attachment.schema.json#/definitions/Attachment"
        },
        "fivePrime": {
          "description": "The nucleotide present at the 5’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5\u0027 to the 3\u0027 end, the 5’ prime nucleotide is the letter at the first position in the sequence. A separate representation would be redundant.",
          "$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
        },
        "threePrime": {
          "description": "The nucleotide present at the 3’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5\u0027 to the 3\u0027 end, the 5’ prime nucleotide is the letter at the last position in the sequence. A separate representation would be redundant.",
          "$ref": "CodeableConcept.schema.json#/definitions/CodeableConcept"
        },
        "linkage": {
          "description": "The linkages between sugar residues will also be captured.",
          "items": {
            "$ref": "#/definitions/SubstanceNucleicAcid_Linkage"
          },
          "type": "array"
        },
        "sugar": {
          "description": "5.3.6.8.1 Sugar ID (Mandatory).",
          "items": {
            "$ref": "#/definitions/SubstanceNucleicAcid_Sugar"
          },
          "type": "array"
        }
      },
      "type": "object",
      "additionalProperties": false
    },
    "SubstanceNucleicAcid_Linkage": {
      "description": "Nucleic acids are defined by three distinct elements: the base, sugar and linkage. Individual substance/moiety IDs will be created for each of these elements. The nucleotide sequence will be always entered in the 5’-3’ direction.",
      "properties": {
        "id": {
          "description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
          "$ref": "string.schema.json#/definitions/string"
        },
        "extension": {
          "description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance  applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
          "items": {
            "$ref": "Extension.schema.json#/definitions/Extension"
          },
          "type": "array"
        },
        "modifierExtension": {
          "description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
          "items": {
            "$ref": "Extension.schema.json#/definitions/Extension"
          },
          "type": "array"
        },
        "connectivity": {
          "description": "The entity that links the sugar residues together should also be captured for nearly all naturally occurring nucleic acid the linkage is a phosphate group. For many synthetic oligonucleotides phosphorothioate linkages are often seen. Linkage connectivity is assumed to be 3’-5’. If the linkage is either 3’-3’ or 5’-5’ this should be specified.",
          "$ref": "#/definitions/string"
        },
        "_connectivity": {
          "description": "Extensions for connectivity",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "identifier": {
          "description": "Each linkage will be registered as a fragment and have an ID.",
          "$ref": "Identifier.schema.json#/definitions/Identifier"
        },
        "name": {
          "description": "Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage.",
          "$ref": "#/definitions/string"
        },
        "_name": {
          "description": "Extensions for name",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "residueSite": {
          "description": "Residues shall be captured as described in 5.3.6.8.3.",
          "$ref": "#/definitions/string"
        },
        "_residueSite": {
          "description": "Extensions for residueSite",
          "$ref": "Element.schema.json#/definitions/Element"
        }
      },
      "type": "object",
      "additionalProperties": false
    },
    "SubstanceNucleicAcid_Sugar": {
      "description": "Nucleic acids are defined by three distinct elements: the base, sugar and linkage. Individual substance/moiety IDs will be created for each of these elements. The nucleotide sequence will be always entered in the 5’-3’ direction.",
      "properties": {
        "id": {
          "description": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
          "$ref": "string.schema.json#/definitions/string"
        },
        "extension": {
          "description": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance  applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
          "items": {
            "$ref": "Extension.schema.json#/definitions/Extension"
          },
          "type": "array"
        },
        "modifierExtension": {
          "description": "May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element\u0027s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
          "items": {
            "$ref": "Extension.schema.json#/definitions/Extension"
          },
          "type": "array"
        },
        "identifier": {
          "description": "The Substance ID of the sugar or sugar-like component that make up the nucleotide.",
          "$ref": "Identifier.schema.json#/definitions/Identifier"
        },
        "name": {
          "description": "The name of the sugar or sugar-like component that make up the nucleotide.",
          "$ref": "#/definitions/string"
        },
        "_name": {
          "description": "Extensions for name",
          "$ref": "Element.schema.json#/definitions/Element"
        },
        "residueSite": {
          "description": "The residues that contain a given sugar will be captured. The order of given residues will be captured in the 5‘-3‘direction consistent with the base sequences listed above.",
          "$ref": "#/definitions/string"
        },
        "_residueSite": {
          "description": "Extensions for residueSite",
          "$ref": "Element.schema.json#/definitions/Element"
        }
      },
      "type": "object",
      "additionalProperties": false
    }
  }
}