Name	Flags	Card.	Type	Description & Constraints
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”
oligoNucleotideType	Σ	0..1	CodeableConcept	(TBC)
subunit	Σ	0..*	BackboneElement	Subunits are listed in order of decreasing length; sequences of the same length will be ordered by molecular weight; subunits that have identical sequences will be repeated multiple times
subunit	Σ	0..1	integer	Index of linear sequences of nucleic acids in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts
sequence	Σ	0..1	string	Actual nucleotide sequence notation from 5' to 3' end using standard single letter codes. In addition to the base sequence, sugar and type of phosphate or non-phosphate linkage should also be captured
length	Σ	0..1	integer	The length of the sequence shall be captured
sequenceAttachment	Σ	0..1	Attachment	(TBC)
fivePrime	Σ	0..1	CodeableConcept	The nucleotide present at the 5’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the first position in the sequence. A separate representation would be redundant
threePrime	Σ	0..1	CodeableConcept	The nucleotide present at the 3’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the last position in the sequence. A separate representation would be redundant
linkage	Σ	0..*	BackboneElement	The linkages between sugar residues will also be captured
connectivity	Σ	0..1	string	The entity that links the sugar residues together should also be captured for nearly all naturally occurring nucleic acid the linkage is a phosphate group. For many synthetic oligonucleotides phosphorothioate linkages are often seen. Linkage connectivity is assumed to be 3’-5’. If the linkage is either 3’-3’ or 5’-5’ this should be specified
identifier	Σ	0..1	Identifier	Each linkage will be registered as a fragment and have an ID
name	Σ	0..1	string	Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
residueSite	Σ	0..1	string	Residues shall be captured as described in 5.3.6.8.3
sugar	Σ	0..*	BackboneElement	5.3.6.8.1 Sugar ID (Mandatory)
identifier	Σ	0..1	Identifier	The Substance ID of the sugar or sugar-like component that make up the nucleotide
name	Σ	0..1	string	The name of the sugar or sugar-like component that make up the nucleotide
residueSite	Σ	0..1	string	The residues that contain a given sugar will be captured. The order of given residues will be captured in the 5‘-3‘direction consistent with the base sequences listed above
Documentation for this format