spark_auto_mapper_fhir.backbone_elements.molecular_sequence_reference_seq

Module Contents

Classes

MolecularSequenceReferenceSeq

MolecularSequence.ReferenceSeq
class spark_auto_mapper_fhir.backbone_elements.molecular_sequence_reference_seq.MolecularSequenceReferenceSeq(*, id_=None, extension=None, modifierExtension=None, chromosome=None, genomeBuild=None, orientation=None, referenceSeqId=None, referenceSeqPointer=None, referenceSeqString=None, strand=None, windowStart=None, windowEnd=None)

Bases: spark_auto_mapper_fhir.base_types.fhir_backbone_element_base.FhirBackboneElementBase

MolecularSequence.ReferenceSeq

Raw data describing a biological sequence.

Raw data describing a biological sequence.

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 chromosome

Structural unit composed of a nucleic acid molecule which controls its own

replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/c urrent_svn/term/SO:0000340)).

param genomeBuild

The Genome Build used for reference, following GRCh build versions e.g. ‘GRCh

37’. Version number must be included if a versioned release of a primary build was used.

param orientation

A relative reference to a DNA strand based on gene orientation. The strand

that contains the open reading frame of the gene is the “sense” strand, and the opposite complementary strand is the “antisense” strand.

param referenceSeqId

Reference identifier of reference sequence submitted to NCBI. It must match

the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.

param referenceSeqPointer

A pointer to another MolecularSequence entity as reference sequence.

param referenceSeqString

A string like “ACGT”.

param strand

An absolute reference to a strand. The Watson strand is the strand whose

5’-end is on the short arm of the chromosome, and the Crick strand as the one whose 5’-end is on the long arm.

param windowStart

Start position of the window on the reference sequence. If the coordinate

system is either 0-based or 1-based, then start position is inclusive.
param windowEnd

End position of the window on the reference sequence. If the coordinate system

is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Parameters