DnaRegionReference#

class biopax-explorer.biopax.dnaregionreference.DnaRegionReference(*args, **kwargs)[source]#

Bases: EntityReference

Class DnaRegionReference

Definition: A DNARegionReference is a grouping of several DNARegion entities

that are common in sequence and genomic position. Members can differ in cellular location, sequence features, SNPs, mutations and bound partners.

code generator : rdfobj (author F.Moreews 2023-2024).

Methods

get_absoluteRegion()

Attribute _absoluteRegion getter

get_comment()

Attribute _comment getter

get_displayName()

Attribute _displayName getter

get_entityFeature()

Attribute _entityFeature getter

get_entityReferenceType()

Attribute _entityReferenceType getter

get_evidence()

Attribute _evidence getter

get_memberEntityReference()

Attribute _memberEntityReference getter

get_name()

Attribute _name getter

get_organism()

Attribute _organism getter

get_regionType()

Attribute _regionType getter

get_sequence()

Attribute _sequence getter

get_standardName()

Attribute _standardName getter

get_subRegion()

Attribute _subRegion getter

get_xref()

Attribute _xref getter

attribute_type_by_name

get_uri_string

object_attributes

set_absoluteRegion

set_comment

set_displayName

set_entityFeature

set_entityReferenceType

set_evidence

set_memberEntityReference

set_name

set_organism

set_regionType

set_sequence

set_standardName

set_subRegion

set_uri_string

set_xref

to_json

type_attributes

Methods Summary

attribute_type_by_name()

get_absoluteRegion()

Attribute _absoluteRegion getter

get_organism()

Attribute _organism getter

get_regionType()

Attribute _regionType getter

get_sequence()

Attribute _sequence getter

get_subRegion()

Attribute _subRegion getter

get_uri_string()

object_attributes()

set_absoluteRegion(value)

set_organism(value)

set_regionType(value)

set_sequence(value)

set_subRegion(value)

set_uri_string(uristr)

to_json()

type_attributes()

Methods Documentation

attribute_type_by_name()[source]#
get_absoluteRegion()[source]#
Attribute _absoluteRegion getter

Absolute location as defined by the referenced sequence database record. E.g. an

operon has a absolute region on the DNA molecule referenced by the UnificationXref.

get_organism()[source]#
Attribute _organism getter

An organism, e.g. ‘Homo sapiens’. This is the organism that the entity is found

in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.

get_regionType()[source]#

Attribute _regionType getter

get_sequence()[source]#
Attribute _sequence getter

Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters

representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code.

get_subRegion()[source]#
Attribute _subRegion getter

The sub region of a region or nucleic acid molecule. The sub region must be

wholly part of the region, not outside of it.

get_uri_string()[source]#
object_attributes()[source]#
set_absoluteRegion(value)[source]#
set_organism(value)[source]#
set_regionType(value)[source]#
set_sequence(value)[source]#
set_subRegion(value)[source]#
set_uri_string(uristr)[source]#
to_json()[source]#
type_attributes()[source]#