Generated Narrative: StructureDefinition ext-R4-SubstanceNucleicAcid Name Flags Card. Type Description & Constraints Extension 0..* Extension(4.3.0) 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 #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:sequenceType 0..1 Extension The type of the sequence shall be specified based on a controlled vocabulary #xD; url 1..1 uri "sequenceType" #xD; value[x] 0..1 CodeableConcept The type of the sequence shall be specified based on a controlled vocabulary #xD; extension:numberOfSubunits 0..1 Extension 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 #xD; url 1..1 uri "numberOfSubunits" #xD; value[x] 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 #xD; extension:areaOfHybridisation 0..1 Extension 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” #xD; url 1..1 uri "areaOfHybridisation" #xD; value[x] 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” #xD; extension:oligoNucleotideType 0..1 Extension (TBC) #xD; url 1..1 uri "oligoNucleotideType" #xD; value[x] 0..1 CodeableConcept (TBC) #xD; extension:subunit 0..* Extension 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 #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:subunit 0..1 Extension 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 #xD; url 1..1 uri "subunit" #xD; value[x] 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 #xD; extension:sequence 0..1 Extension 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 #xD; url 1..1 uri "sequence" #xD; value[x] 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 #xD; extension:length 0..1 Extension The length of the sequence shall be captured #xD; url 1..1 uri "length" #xD; value[x] 0..1 integer The length of the sequence shall be captured #xD; extension:sequenceAttachment 0..1 Extension (TBC) #xD; url 1..1 uri "sequenceAttachment" #xD; value[x] 0..1 Attachment (TBC) #xD; extension:fivePrime 0..1 Extension 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 #xD; url 1..1 uri "fivePrime" #xD; value[x] 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 #xD; extension:threePrime 0..1 Extension 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 #xD; url 1..1 uri "threePrime" #xD; value[x] 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 #xD; extension:linkage 0..* Extension The linkages between sugar residues will also be captured #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:connectivity 0..1 Extension 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 #xD; url 1..1 uri "connectivity" #xD; value[x] 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 #xD; extension:identifier 0..1 Extension Each linkage will be registered as a fragment and have an ID #xD; url 1..1 uri "identifier" #xD; value[x] 0..1 Identifier Each linkage will be registered as a fragment and have an ID #xD; extension:name 0..1 Extension Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage #xD; url 1..1 uri "name" #xD; value[x] 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 #xD; extension:residueSite 0..1 Extension Residues shall be captured as described in 5.3.6.8.3 #xD; url 1..1 uri "residueSite" #xD; value[x] 0..1 string Residues shall be captured as described in 5.3.6.8.3 #xD; url 1..1 uri "linkage" #xD; extension:sugar 0..* Extension 5.3.6.8.1 Sugar ID (Mandatory) #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:identifier 0..1 Extension The Substance ID of the sugar or sugar-like component that make up the nucleotide #xD; url 1..1 uri "identifier" #xD; value[x] 0..1 Identifier The Substance ID of the sugar or sugar-like component that make up the nucleotide #xD; extension:name 0..1 Extension The name of the sugar or sugar-like component that make up the nucleotide #xD; url 1..1 uri "name" #xD; value[x] 0..1 string The name of the sugar or sugar-like component that make up the nucleotide #xD; extension:residueSite 0..1 Extension 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 #xD; url 1..1 uri "residueSite" #xD; value[x] 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 #xD; url 1..1 uri "sugar" #xD; url 1..1 uri "subunit" #xD; url 1..1 uri "http://hl7.org/fhir/4.0/StructureDefinition/extension-SubstanceNucleicAcid" #xD; Documentation for this format
Cross-version Extension for R4.SubstanceNucleicAcid for use in FHIR R4B
This cross-version extension represents SubstanceNucleicAcid from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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
All FHIR elements must have a @value or children unless an empty Parameters resource
hasValue() or (children().count() > id.count()) or $this is Parameters
Must have either extensions or value[x], not both
exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Extensions are always sliced by (at least) url
All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
The type of the sequence shall be specified based on a controlled vocabulary
This cross-version extension represents SubstanceNucleicAcid.sequenceType from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
Additional content defined by implementations
May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Source of the definition for the extension code - a logical name or a URL.
The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
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
This cross-version extension represents SubstanceNucleicAcid.numberOfSubunits from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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”
This cross-version extension represents SubstanceNucleicAcid.areaOfHybridisation from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
This cross-version extension represents SubstanceNucleicAcid.oligoNucleotideType from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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
This cross-version extension represents SubstanceNucleicAcid.subunit from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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
This cross-version extension represents SubstanceNucleicAcid.subunit.subunit from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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
This cross-version extension represents SubstanceNucleicAcid.subunit.sequence from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
The length of the sequence shall be captured
This cross-version extension represents SubstanceNucleicAcid.subunit.length from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
This cross-version extension represents SubstanceNucleicAcid.subunit.sequenceAttachment from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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
This cross-version extension represents SubstanceNucleicAcid.subunit.fivePrime from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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
This cross-version extension represents SubstanceNucleicAcid.subunit.threePrime from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
The linkages between sugar residues will also be captured
This cross-version extension represents SubstanceNucleicAcid.subunit.linkage from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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
This cross-version extension represents SubstanceNucleicAcid.subunit.linkage.connectivity from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
Each linkage will be registered as a fragment and have an ID
This cross-version extension represents SubstanceNucleicAcid.subunit.linkage.identifier from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
This cross-version extension represents SubstanceNucleicAcid.subunit.linkage.name from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
Residues shall be captured as described in 5.3.6.8.3
This cross-version extension represents SubstanceNucleicAcid.subunit.linkage.residueSite from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4B/extensibility.html) for a list).
This cross-version extension represents SubstanceNucleicAcid.subunit.sugar from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
The Substance ID of the sugar or sugar-like component that make up the nucleotide
This cross-version extension represents SubstanceNucleicAcid.subunit.sugar.identifier from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
The name of the sugar or sugar-like component that make up the nucleotide
This cross-version extension represents SubstanceNucleicAcid.subunit.sugar.name from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.
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
This cross-version extension represents SubstanceNucleicAcid.subunit.sugar.residueSite from http://hl7.org/fhir/StructureDefinition/SubstanceNucleicAcid|4.0.1 for use in FHIR R4B.