This is the Continuous Integration Build of FHIR (will be incorrect/inconsistent at times).
See the Directory of published versions icon

15.12 Resource SubstanceNucleicAcid - Content

Biomedical Research and Regulation icon

Work Group

Maturity Level: 0

Trial Use

Security Category: Anonymous

Compartments: No defined compartments

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.

15.12.1 Scope and Usage

For an overview of this resource and others in the Medication Definition domain, also see the module page

15.12.2 References to this Resource

Resource References: SubstanceDefinition

Structure

Name	Flags	Card.	Type	Description & Constraints
SubstanceNucleicAcid	TU		DomainResource	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 Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
sequenceType	Σ	0..1	CodeableConcept	The type of the sequence shall be specified based on a controlled vocabulary
numberOfSubunits	Σ	0..1	integer	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
areaOfHybridisation	Σ	0..1	string	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”
oligoNucleotideType	Σ	0..1	CodeableConcept	(TBC)
subunit	Σ	0..*	BackboneElement	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
subunit	Σ	0..1	integer	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
sequence	Σ	0..1	string	Actual nucleotide sequence notation from 5' to 3' 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
length	Σ	0..1	integer	The length of the sequence shall be captured
sequenceAttachment	Σ	0..1	Attachment	(TBC)
fivePrime	Σ	0..1	CodeableConcept	The nucleotide present at the 5’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the first position in the sequence. A separate representation would be redundant
threePrime	Σ	0..1	CodeableConcept	The nucleotide present at the 3’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the last position in the sequence. A separate representation would be redundant
linkage	Σ	0..*	BackboneElement	The linkages between sugar residues will also be captured
connectivity	Σ	0..1	string	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
identifier	Σ	0..1	Identifier	Each linkage will be registered as a fragment and have an ID
name	Σ	0..1	string	Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
residueSite	Σ	0..1	string	Residues shall be captured as described in 5.3.6.8.3
sugar	Σ	0..*	BackboneElement	5.3.6.8.1 Sugar ID (Mandatory)
identifier	Σ	0..1	Identifier	The Substance ID of the sugar or sugar-like component that make up the nucleotide
name	Σ	0..1	string	The name of the sugar or sugar-like component that make up the nucleotide
residueSite	Σ	0..1	string	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
Documentation for this format

See the Extensions for this resource

UML Diagram (Legend)

XML Template

<SubstanceNucleicAcid xmlns="http://hl7.org/fhir"> 
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <sequenceType><!-- 0..1 CodeableConcept The type of the sequence shall be specified based on a controlled vocabulary --></sequenceType>
 <numberOfSubunits value="[integer]"/><!-- 0..1 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 -->
 <areaOfHybridisation value="[string]"/><!-- 0..1 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” -->
 <oligoNucleotideType><!-- 0..1 CodeableConcept (TBC) --></oligoNucleotideType>
 <subunit>  <!-- 0..* 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 -->
  <subunit value="[integer]"/><!-- 0..1 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 -->
  <sequence value="[string]"/><!-- 0..1 Actual nucleotide sequence notation from 5' to 3' 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 -->
  <length value="[integer]"/><!-- 0..1 The length of the sequence shall be captured -->
  <sequenceAttachment><!-- 0..1 Attachment (TBC) --></sequenceAttachment>
  <fivePrime><!-- 0..1 CodeableConcept The nucleotide present at the 5’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the first position in the sequence. A separate representation would be redundant --></fivePrime>
  <threePrime><!-- 0..1 CodeableConcept The nucleotide present at the 3’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the last position in the sequence. A separate representation would be redundant --></threePrime>
  <linkage>  <!-- 0..* The linkages between sugar residues will also be captured -->
   <connectivity value="[string]"/><!-- 0..1 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 -->
   <identifier><!-- 0..1 Identifier Each linkage will be registered as a fragment and have an ID --></identifier>
   <name value="[string]"/><!-- 0..1 Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage -->
   <residueSite value="[string]"/><!-- 0..1 Residues shall be captured as described in 5.3.6.8.3 -->
  </linkage>
  <sugar>  <!-- 0..* 5.3.6.8.1 Sugar ID (Mandatory) -->
   <identifier><!-- 0..1 Identifier The Substance ID of the sugar or sugar-like component that make up the nucleotide --></identifier>
   <name value="[string]"/><!-- 0..1 The name of the sugar or sugar-like component that make up the nucleotide -->
   <residueSite value="[string]"/><!-- 0..1 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 -->
  </sugar>
 </subunit>
</SubstanceNucleicAcid>

JSON Template

{
  "resourceType" : "SubstanceNucleicAcid",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "sequenceType" : { CodeableConcept }, // The type of the sequence shall be specified based on a controlled vocabulary
  "numberOfSubunits" : <integer>, // 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
  "areaOfHybridisation" : "<string>", // 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”
  "oligoNucleotideType" : { CodeableConcept }, // (TBC)
  "subunit" : [{ // 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
    "subunit" : <integer>, // 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
    "sequence" : "<string>", // Actual nucleotide sequence notation from 5' to 3' 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
    "length" : <integer>, // The length of the sequence shall be captured
    "sequenceAttachment" : { Attachment }, // (TBC)
    "fivePrime" : { CodeableConcept }, // The nucleotide present at the 5’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the first position in the sequence. A separate representation would be redundant
    "threePrime" : { CodeableConcept }, // The nucleotide present at the 3’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the last position in the sequence. A separate representation would be redundant
    "linkage" : [{ // The linkages between sugar residues will also be captured
      "connectivity" : "<string>", // 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
      "identifier" : { Identifier }, // Each linkage will be registered as a fragment and have an ID
      "name" : "<string>", // Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
      "residueSite" : "<string>" // Residues shall be captured as described in 5.3.6.8.3
    }],
    "sugar" : [{ // 5.3.6.8.1 Sugar ID (Mandatory)
      "identifier" : { Identifier }, // The Substance ID of the sugar or sugar-like component that make up the nucleotide
      "name" : "<string>", // The name of the sugar or sugar-like component that make up the nucleotide
      "residueSite" : "<string>" // 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
    }]
  }]
}

Turtle Template

@prefix fhir: <http://hl7.org/fhir/> .


[ a fhir:SubstanceNucleicAcid;
  fhir:nodeRole fhir:treeRoot; # if this is the parser root

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:sequenceType [ CodeableConcept ] ; # 0..1 The type of the sequence shall be specified based on a controlled vocabulary
  fhir:numberOfSubunits [ integer ] ; # 0..1 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
  fhir:areaOfHybridisation [ string ] ; # 0..1 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”
  fhir:oligoNucleotideType [ CodeableConcept ] ; # 0..1 (TBC)
  fhir:subunit ( [ # 0..* 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
    fhir:subunit [ integer ] ; # 0..1 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
    fhir:sequence [ string ] ; # 0..1 Actual nucleotide sequence notation from 5' to 3' 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
    fhir:length [ integer ] ; # 0..1 The length of the sequence shall be captured
    fhir:sequenceAttachment [ Attachment ] ; # 0..1 (TBC)
    fhir:fivePrime [ CodeableConcept ] ; # 0..1 The nucleotide present at the 5’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the first position in the sequence. A separate representation would be redundant
    fhir:threePrime [ CodeableConcept ] ; # 0..1 The nucleotide present at the 3’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the last position in the sequence. A separate representation would be redundant
    fhir:linkage ( [ # 0..* The linkages between sugar residues will also be captured
      fhir:connectivity [ string ] ; # 0..1 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
      fhir:identifier [ Identifier ] ; # 0..1 Each linkage will be registered as a fragment and have an ID
      fhir:name [ string ] ; # 0..1 Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
      fhir:residueSite [ string ] ; # 0..1 Residues shall be captured as described in 5.3.6.8.3
    ] ... ) ;
    fhir:sugar ( [ # 0..* 5.3.6.8.1 Sugar ID (Mandatory)
      fhir:identifier [ Identifier ] ; # 0..1 The Substance ID of the sugar or sugar-like component that make up the nucleotide
      fhir:name [ string ] ; # 0..1 The name of the sugar or sugar-like component that make up the nucleotide
      fhir:residueSite [ string ] ; # 0..1 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
    ] ... ) ;
  ] ... ) ;
]

Changes from both R4 and R4B

SubstanceNucleicAcid

No Changes

See the Full Difference for further information

This analysis is available for R4 as XML or JSON and for R4B as XML or JSON.