spark_auto_mapper_fhir.resources.substance_nucleic_acid

Module Contents

Classes

SubstanceNucleicAcid

SubstanceNucleicAcid
class spark_auto_mapper_fhir.resources.substance_nucleic_acid.SubstanceNucleicAcid(*, id_=None, meta=None, implicitRules=None, language=None, text=None, contained=None, extension=None, modifierExtension=None, sequenceType=None, numberOfSubunits=None, areaOfHybridisation=None, oligoNucleotideType=None, subunit=None)

Bases: spark_auto_mapper_fhir.base_types.fhir_resource_base.FhirResourceBase

SubstanceNucleicAcid substancenucleicacid.xsd

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.

If the element is present, it must have either a @value, an @id, or extensions

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.

If the element is present, it must have either a @value, an @id, or extensions

param id_

The logical id of the resource, as used in the URL for the resource. Once

assigned, this value never changes.
param meta

The metadata about the resource. This is content that is maintained by the

infrastructure. Changes to the content might not always be associated with version changes to the resource.

param implicitRules

A reference to a set of rules that were followed when the resource was

constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.

param language

The base language in which the resource is written.

param text

A human-readable narrative that contains a summary of the resource and can be

used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it “clinically safe” for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.

param contained

These resources do not have an independent existence apart from the resource

that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.

param extension

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

definition of the resource. 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 resource and that modifies the understanding of the element that contains it 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 is allowed to 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 sequenceType

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

param numberOfSubunits

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.

param areaOfHybridisation

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”.

param oligoNucleotideType

(TBC).

param subunit

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.

Parameters
get_schema(self, include_extension)
Parameters

include_extension (bool) –

Return type

Optional[Union[pyspark.sql.types.StructType, pyspark.sql.types.DataType]]