FHIR CI-Build

This is the Continuous Integration Build of FHIR (will be incorrect/inconsistent at times).
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Biomedical Research and Regulation icon Work GroupMaturity Level: 0 Trial UseSecurity Category: Anonymous Compartments: No defined compartments

Detailed Descriptions for the elements in the SubstanceNucleicAcid resource.

SubstanceNucleicAcid
Element Id SubstanceNucleicAcid
Definition

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.

Short Display 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
Cardinality 0..*
Type DomainResource
Summary false
SubstanceNucleicAcid.sequenceType
Element Id SubstanceNucleicAcid.sequenceType
Definition

The type of the sequence shall be specified based on a controlled vocabulary.

Short Display The type of the sequence shall be specified based on a controlled vocabulary
Cardinality 0..1
Type CodeableConcept
Summary true
SubstanceNucleicAcid.numberOfSubunits
Element Id SubstanceNucleicAcid.numberOfSubunits
Definition

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.

Short Display 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
Cardinality 0..1
Type integer
Summary true
SubstanceNucleicAcid.areaOfHybridisation
Element Id SubstanceNucleicAcid.areaOfHybridisation
Definition

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”.

Short Display 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”
Cardinality 0..1
Type string
Summary true
SubstanceNucleicAcid.oligoNucleotideType
Element Id SubstanceNucleicAcid.oligoNucleotideType
Definition

(TBC).

Short Display (TBC)
Cardinality 0..1
Type CodeableConcept
Summary true
SubstanceNucleicAcid.subunit
Element Id SubstanceNucleicAcid.subunit
Definition

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.

Short Display 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
Cardinality 0..*
Summary true
SubstanceNucleicAcid.subunit.subunit
Element Id SubstanceNucleicAcid.subunit.subunit
Definition

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.

Short Display 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
Cardinality 0..1
Type integer
Summary true
SubstanceNucleicAcid.subunit.sequence
Element Id SubstanceNucleicAcid.subunit.sequence
Definition

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.

Short Display 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
Cardinality 0..1
Type string
Summary true
SubstanceNucleicAcid.subunit.length
Element Id SubstanceNucleicAcid.subunit.length
Definition

The length of the sequence shall be captured.

Short Display The length of the sequence shall be captured
Cardinality 0..1
Type integer
Summary true
SubstanceNucleicAcid.subunit.sequenceAttachment
Element Id SubstanceNucleicAcid.subunit.sequenceAttachment
Definition

(TBC).

Short Display (TBC)
Cardinality 0..1
Type Attachment
Summary true
SubstanceNucleicAcid.subunit.fivePrime
Element Id SubstanceNucleicAcid.subunit.fivePrime
Definition

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.

Short Display 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
Cardinality 0..1
Type CodeableConcept
Summary true
SubstanceNucleicAcid.subunit.threePrime
Element Id SubstanceNucleicAcid.subunit.threePrime
Definition

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.

Short Display 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
Cardinality 0..1
Type CodeableConcept
Summary true
SubstanceNucleicAcid.subunit.linkage
Element Id SubstanceNucleicAcid.subunit.linkage
Definition

The linkages between sugar residues will also be captured.

Short Display The linkages between sugar residues will also be captured
Cardinality 0..*
Summary true
SubstanceNucleicAcid.subunit.linkage.connectivity
Element Id SubstanceNucleicAcid.subunit.linkage.connectivity
Definition

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.

Short Display 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
Cardinality 0..1
Type string
Summary true
SubstanceNucleicAcid.subunit.linkage.identifier
Element Id SubstanceNucleicAcid.subunit.linkage.identifier
Definition

Each linkage will be registered as a fragment and have an ID.

Short Display Each linkage will be registered as a fragment and have an ID
Note This is a business identifier, not a resource identifier (see discussion)
Cardinality 0..1
Type Identifier
Summary true
SubstanceNucleicAcid.subunit.linkage.name
Element Id SubstanceNucleicAcid.subunit.linkage.name
Definition

Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage.

Short Display Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
Cardinality 0..1
Type string
Summary true
SubstanceNucleicAcid.subunit.linkage.residueSite
Element Id SubstanceNucleicAcid.subunit.linkage.residueSite
Definition

Residues shall be captured as described in 5.3.6.8.3.

Short Display Residues shall be captured as described in 5.3.6.8.3
Cardinality 0..1
Type string
Summary true
SubstanceNucleicAcid.subunit.sugar
Element Id SubstanceNucleicAcid.subunit.sugar
Definition

5.3.6.8.1 Sugar ID (Mandatory).

Short Display 5.3.6.8.1 Sugar ID (Mandatory)
Cardinality 0..*
Summary true
SubstanceNucleicAcid.subunit.sugar.identifier
Element Id SubstanceNucleicAcid.subunit.sugar.identifier
Definition

The Substance ID of the sugar or sugar-like component that make up the nucleotide.

Short Display The Substance ID of the sugar or sugar-like component that make up the nucleotide
Note This is a business identifier, not a resource identifier (see discussion)
Cardinality 0..1
Type Identifier
Summary true
SubstanceNucleicAcid.subunit.sugar.name
Element Id SubstanceNucleicAcid.subunit.sugar.name
Definition

The name of the sugar or sugar-like component that make up the nucleotide.

Short Display The name of the sugar or sugar-like component that make up the nucleotide
Cardinality 0..1
Type string
Summary true
SubstanceNucleicAcid.subunit.sugar.residueSite
Element Id SubstanceNucleicAcid.subunit.sugar.residueSite
Definition

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.

Short Display 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
Cardinality 0..1
Type string
Summary true