Release 4 5 Preview #3
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11.24 15.12 Resource SubstanceNucleicAcid - Content

Biomedical Research and Regulation Work Group Maturity Level : 0   Trial Use Security Category : Anonymous Compartments : Not linked to any 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.

This resource is referenced by SubstanceSpecification SubstanceDefinition .

This resource does not implement any patterns.

Structure

Name Flags Card. Type Description & Constraints doco
. . SubstanceNucleicAcid Σ 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”
. . . 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

doco Documentation for this format

UML Diagram ( Legend )

SubstanceNucleicAcid ( DomainResource ) The type of the sequence shall be specified based on a controlled vocabulary sequenceType : CodeableConcept [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 numberOfSubunits : integer [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” areaOfHybridisation : string [0..1] (TBC) oligoNucleotideType : CodeableConcept [0..1] Subunit 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 subunit : integer [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 sequence : string [0..1] The length of the sequence shall be captured length : integer [0..1] (TBC) sequenceAttachment : Attachment [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 fivePrime : 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 threePrime : CodeableConcept [0..1] Linkage 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 connectivity : string [0..1] Each linkage will be registered as a fragment and have an ID identifier : Identifier [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 name : string [0..1] Residues shall be captured as described in 5.3.6.8.3 residueSite : string [0..1] Sugar The Substance ID of the sugar or sugar-like component that make up the nucleotide identifier : Identifier [0..1] The name of the sugar or sugar-like component that make up the nucleotide name : 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 residueSite : string [0..1] The linkages between sugar residues will also be captured linkage [0..*] 5.3.6.8.1 Sugar ID (Mandatory) sugar [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 [0..*]

XML Template

<SubstanceNucleicAcid xmlns="http://hl7.org/fhir"> doco
 <!-- 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>
  <</threePrime>

  <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

{doco
  "resourceType" : "",

  "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/> .doco
[ a 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:SubstanceNucleicAcid.sequenceType [ CodeableConcept ]; # 0..1 The type of the sequence shall be specified based on a controlled vocabulary
  fhir:SubstanceNucleicAcid.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:

  fhir:SubstanceNucleicAcid.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:SubstanceNucleicAcid.oligoNucleotideType [ CodeableConcept ]; # 0..1 (TBC)
  fhir:SubstanceNucleicAcid.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:SubstanceNucleicAcid.subunit.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:SubstanceNucleicAcid.subunit.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:SubstanceNucleicAcid.subunit.length [ integer ]; # 0..1 The length of the sequence shall be captured
    fhir:SubstanceNucleicAcid.subunit.sequenceAttachment [ Attachment ]; # 0..1 (TBC)
    fhir:
    fhir:

    fhir:SubstanceNucleicAcid.subunit.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:SubstanceNucleicAcid.subunit.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:SubstanceNucleicAcid.subunit.linkage [ # 0..* The linkages between sugar residues will also be captured
      fhir:

      fhir:SubstanceNucleicAcid.subunit.linkage.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:SubstanceNucleicAcid.subunit.linkage.identifier [ Identifier ]; # 0..1 Each linkage will be registered as a fragment and have an ID
      fhir:SubstanceNucleicAcid.subunit.linkage.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:SubstanceNucleicAcid.subunit.linkage.residueSite [ string ]; # 0..1 Residues shall be captured as described in 5.3.6.8.3
    ], ...;
    fhir:SubstanceNucleicAcid.subunit.sugar [ # 0..* 5.3.6.8.1 Sugar ID (Mandatory)
      fhir:SubstanceNucleicAcid.subunit.sugar.identifier [ Identifier ]; # 0..1 The Substance ID of the sugar or sugar-like component that make up the nucleotide
      fhir:SubstanceNucleicAcid.subunit.sugar.name [ string ]; # 0..1 The name of the sugar or sugar-like component that make up the nucleotide
      fhir:

      fhir:SubstanceNucleicAcid.subunit.sugar.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 since R3

SubstanceNucleicAcid
  • No Changes

This resource did not exist in Release 2 See the Full Difference for further information

This analysis is available as XML or JSON .

Structure

Name Flags Card. Type Description & Constraints doco
. . SubstanceNucleicAcid Σ 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”
. . . 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

doco Documentation for this format

UML Diagram ( Legend )

SubstanceNucleicAcid ( DomainResource ) The type of the sequence shall be specified based on a controlled vocabulary sequenceType : CodeableConcept [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 numberOfSubunits : integer [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” areaOfHybridisation : string [0..1] (TBC) oligoNucleotideType : CodeableConcept [0..1] Subunit 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 subunit : integer [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 sequence : string [0..1] The length of the sequence shall be captured length : integer [0..1] (TBC) sequenceAttachment : Attachment [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 fivePrime : 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 threePrime : CodeableConcept [0..1] Linkage 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 connectivity : string [0..1] Each linkage will be registered as a fragment and have an ID identifier : Identifier [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 name : string [0..1] Residues shall be captured as described in 5.3.6.8.3 residueSite : string [0..1] Sugar The Substance ID of the sugar or sugar-like component that make up the nucleotide identifier : Identifier [0..1] The name of the sugar or sugar-like component that make up the nucleotide name : 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 residueSite : string [0..1] The linkages between sugar residues will also be captured linkage [0..*] 5.3.6.8.1 Sugar ID (Mandatory) sugar [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 [0..*]

XML Template

<SubstanceNucleicAcid xmlns="http://hl7.org/fhir"> doco
 <!-- 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>
  <</threePrime>

  <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

{doco
  "resourceType" : "",

  "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/> .doco
[ a 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:SubstanceNucleicAcid.sequenceType [ CodeableConcept ]; # 0..1 The type of the sequence shall be specified based on a controlled vocabulary
  fhir:SubstanceNucleicAcid.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:

  fhir:SubstanceNucleicAcid.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:SubstanceNucleicAcid.oligoNucleotideType [ CodeableConcept ]; # 0..1 (TBC)
  fhir:SubstanceNucleicAcid.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:SubstanceNucleicAcid.subunit.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:SubstanceNucleicAcid.subunit.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:SubstanceNucleicAcid.subunit.length [ integer ]; # 0..1 The length of the sequence shall be captured
    fhir:SubstanceNucleicAcid.subunit.sequenceAttachment [ Attachment ]; # 0..1 (TBC)
    fhir:
    fhir:

    fhir:SubstanceNucleicAcid.subunit.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:SubstanceNucleicAcid.subunit.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:SubstanceNucleicAcid.subunit.linkage [ # 0..* The linkages between sugar residues will also be captured
      fhir:

      fhir:SubstanceNucleicAcid.subunit.linkage.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:SubstanceNucleicAcid.subunit.linkage.identifier [ Identifier ]; # 0..1 Each linkage will be registered as a fragment and have an ID
      fhir:SubstanceNucleicAcid.subunit.linkage.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:SubstanceNucleicAcid.subunit.linkage.residueSite [ string ]; # 0..1 Residues shall be captured as described in 5.3.6.8.3
    ], ...;
    fhir:SubstanceNucleicAcid.subunit.sugar [ # 0..* 5.3.6.8.1 Sugar ID (Mandatory)
      fhir:SubstanceNucleicAcid.subunit.sugar.identifier [ Identifier ]; # 0..1 The Substance ID of the sugar or sugar-like component that make up the nucleotide
      fhir:SubstanceNucleicAcid.subunit.sugar.name [ string ]; # 0..1 The name of the sugar or sugar-like component that make up the nucleotide
      fhir:

      fhir:SubstanceNucleicAcid.subunit.sugar.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 since Release 3

SubstanceNucleicAcid
  • No Changes

This resource did not exist in Release 2 See the Full Difference for further information

This analysis is available as XML or JSON .

 

See the Profiles & Extensions and the alternate definitions: Master Definition XML + JSON , XML Schema / Schematron + JSON Schema , ShEx (for Turtle ) + see the extensions , the spreadsheet version & the dependency analysis a