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11.24 Resource SubstanceNucleicAcid - Content

Biomedical Research and Regulation Work GroupMaturity Level: 0 Trial UseSecurity 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

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. SubstanceNucleicAcid ΣTUDomainResourceNucleic 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 Σ0..1CodeableConceptThe type of the sequence shall be specified based on a controlled vocabulary
... numberOfSubunits Σ0..1integerThe 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 Σ0..1stringThe 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 Σ0..1CodeableConcept(TBC)
... subunit Σ0..*BackboneElementSubunits 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 Σ0..1integerIndex 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 Σ0..1stringActual 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 Σ0..1integerThe length of the sequence shall be captured
.... sequenceAttachment Σ0..1Attachment(TBC)
.... fivePrime Σ0..1CodeableConceptThe 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 Σ0..1CodeableConceptThe 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 Σ0..*BackboneElementThe linkages between sugar residues will also be captured
..... connectivity Σ0..1stringThe 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 Σ0..1IdentifierEach linkage will be registered as a fragment and have an ID
..... name Σ0..1stringEach linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
..... residueSite Σ0..1stringResidues shall be captured as described in 5.3.6.8.3
.... sugar Σ0..*BackboneElement5.3.6.8.1 Sugar ID (Mandatory)
..... identifier Σ0..1IdentifierThe Substance ID of the sugar or sugar-like component that make up the nucleotide
..... name Σ0..1stringThe name of the sugar or sugar-like component that make up the nucleotide
..... residueSite Σ0..1stringThe 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 vocabularysequenceType : 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 subunitnumberOfSubunits : 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]SubunitIndex 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 subscriptssubunit : 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 capturedsequence : string [0..1]The length of the sequence shall be capturedlength : 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 redundantfivePrime : 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 redundantthreePrime : CodeableConcept [0..1]LinkageThe 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 specifiedconnectivity : string [0..1]Each linkage will be registered as a fragment and have an IDidentifier : 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 linkagename : string [0..1]Residues shall be captured as described in 5.3.6.8.3residueSite : string [0..1]SugarThe Substance ID of the sugar or sugar-like component that make up the nucleotideidentifier : Identifier [0..1]The name of the sugar or sugar-like component that make up the nucleotidename : 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 aboveresidueSite : string [0..1]The linkages between sugar residues will also be capturedlinkage[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 timessubunit[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><!-- 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" : "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: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: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: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: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: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

This resource did not exist in Release 2

This analysis is available as XML or JSON.

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. SubstanceNucleicAcid ΣTUDomainResourceNucleic 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 Σ0..1CodeableConceptThe type of the sequence shall be specified based on a controlled vocabulary
... numberOfSubunits Σ0..1integerThe 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 Σ0..1stringThe 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 Σ0..1CodeableConcept(TBC)
... subunit Σ0..*BackboneElementSubunits 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 Σ0..1integerIndex 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 Σ0..1stringActual 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 Σ0..1integerThe length of the sequence shall be captured
.... sequenceAttachment Σ0..1Attachment(TBC)
.... fivePrime Σ0..1CodeableConceptThe 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 Σ0..1CodeableConceptThe 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 Σ0..*BackboneElementThe linkages between sugar residues will also be captured
..... connectivity Σ0..1stringThe 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 Σ0..1IdentifierEach linkage will be registered as a fragment and have an ID
..... name Σ0..1stringEach linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
..... residueSite Σ0..1stringResidues shall be captured as described in 5.3.6.8.3
.... sugar Σ0..*BackboneElement5.3.6.8.1 Sugar ID (Mandatory)
..... identifier Σ0..1IdentifierThe Substance ID of the sugar or sugar-like component that make up the nucleotide
..... name Σ0..1stringThe name of the sugar or sugar-like component that make up the nucleotide
..... residueSite Σ0..1stringThe 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 vocabularysequenceType : 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 subunitnumberOfSubunits : 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]SubunitIndex 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 subscriptssubunit : 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 capturedsequence : string [0..1]The length of the sequence shall be capturedlength : 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 redundantfivePrime : 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 redundantthreePrime : CodeableConcept [0..1]LinkageThe 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 specifiedconnectivity : string [0..1]Each linkage will be registered as a fragment and have an IDidentifier : 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 linkagename : string [0..1]Residues shall be captured as described in 5.3.6.8.3residueSite : string [0..1]SugarThe Substance ID of the sugar or sugar-like component that make up the nucleotideidentifier : Identifier [0..1]The name of the sugar or sugar-like component that make up the nucleotidename : 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 aboveresidueSite : string [0..1]The linkages between sugar residues will also be capturedlinkage[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 timessubunit[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><!-- 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" : "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: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: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: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: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: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

This resource did not exist in Release 2

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 dependency analysis