DnaReference#

class biopax-explorer.biopax.dnareference.DnaReference(*args, **kwargs)[source]#

Bases: EntityReference

Class DnaReference

Definition: A DNA reference is a grouping of several DNA entities that are

common in sequence. Members can differ in celular location, sequence features, SNPs, mutations and bound partners. Comments : Note that this is not a reference gene. Genes are non-physical,stateless continuants. Their physical manifestations can span multiple DNA molecules, sometimes even across chromosomes due to regulatory regions. Similarly a gene is not necessarily made up of deoxyribonucleic acid and can be present in multiple copies ( which are different DNA regions).

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

Methods

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_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_comment
set_displayName
set_entityFeature
set_entityReferenceType
set_evidence
set_memberEntityReference
set_name
set_organism
set_sequence
set_standardName
set_subRegion
set_uri_string
set_xref
to_json
type_attributes

Methods Summary

attribute_type_by_name()
get_organism()	Attribute _organism getter
get_sequence()	Attribute _sequence getter
get_subRegion()	Attribute _subRegion getter
get_uri_string()
object_attributes()
set_organism(value)
set_sequence(value)
set_subRegion(value)
set_uri_string(uristr)
to_json()
type_attributes()

Methods Documentation

attribute_type_by_name()[source]#

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_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_organism(value)[source]#

set_sequence(value)[source]#

set_subRegion(value)[source]#

set_uri_string(uristr)[source]#

to_json()[source]#

type_attributes()[source]#