SubstanceNucleicAcid
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.
- Backends
- PostgreSQLElasticsearch
- Interactions
- CreateReadUpdatePatchDelete
- Search
- 0 of 0 parameters tested
Structure
| Element | Card. | Type | Description |
|---|---|---|---|
sequenceTypeΣ | 0..1 | CodeableConcept | The type of the sequence shall be specified based on a controlled vocabulary |
numberOfSubunitsΣ | 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 |
areaOfHybridisationΣ | 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” |
oligoNucleotideTypeΣ | 0..1 | CodeableConcept | (TBC) |
subunitΣ | 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 |
subunitΣ | 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 |
sequenceΣ | 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 |
lengthΣ | 0..1 | integer | The length of the sequence shall be captured |
sequenceAttachmentΣ | 0..1 | Attachment | (TBC) |
fivePrimeΣ | 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 |
threePrimeΣ | 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 |
linkageΣ | 0..* | BackboneElement | The linkages between sugar residues will also be captured |
connectivityΣ | 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 |
identifierΣ | 0..1 | Identifier | Each linkage will be registered as a fragment and have an ID |
nameΣ | 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 |
residueSiteΣ | 0..1 | string | Residues shall be captured as described in 5.3.6.8.3 |
sugarΣ | 0..* | BackboneElement | 5.3.6.8.1 Sugar ID (Mandatory) |
identifierΣ | 0..1 | Identifier | The Substance ID of the sugar or sugar-like component that make up the nucleotide |
nameΣ | 0..1 | string | The name of the sugar or sugar-like component that make up the nucleotide |
residueSiteΣ | 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 |
Σ in _summary results · ?! modifier element · 1.. required · inherited elements in grey
Search parameters
Query with GET [base]/SubstanceNucleicAcid?[parameter]=[value]. Type decides which modifiers and prefixes apply, see search features.
SubstanceNucleicAcid defines no search parameters of its own; the common parameters below apply.
PG: PostgreSQL, ES: Elasticsearch. passes its TestScript checks, fails, not tested yet. The author of the resource Logical id of this artifact When the resource version last changed Profiles this resource claims to conform to Security Labels applied to this resource Identifies where the resource comes from Tags applied to this resource Derived from the R4B DefinitionCommon parameters on every resource (8)
_haste-health-authorreference _idtoken _lastUpdateddate _profileuri _securitytoken _sourceuri _tagtoken _typetoken