spark_auto_mapper_fhir.backbone_elements.substance_nucleic_acid_subunit

Module Contents

Classes

SubstanceNucleicAcidSubunit

SubstanceNucleicAcid.Subunit
class spark_auto_mapper_fhir.backbone_elements.substance_nucleic_acid_subunit.SubstanceNucleicAcidSubunit(*, id_=None, extension=None, modifierExtension=None, subunit=None, sequence=None, length=None, sequenceAttachment=None, fivePrime=None, threePrime=None, linkage=None, sugar=None)

Bases: spark_auto_mapper_fhir.base_types.fhir_backbone_element_base.FhirBackboneElementBase

SubstanceNucleicAcid.Subunit

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.

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.

param id_

None

param extension

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.

param modifierExtension

May be used to represent additional information that is not part of the basic

definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element’s descendants. Usually modifier elements provide negation or qualification. 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. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

param subunit

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.

param sequence

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.

param length

The length of the sequence shall be captured.

param sequenceAttachment

(TBC).

param fivePrime

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.

param threePrime

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.

param linkage

The linkages between sugar residues will also be captured.

param sugar

5.3.6.8.1 Sugar ID (Mandatory).

Parameters