ProteinReference#
- class biopax-explorer.biopax.proteinreference.ProteinReference(*args, **kwargs)[source]#
Bases:
EntityReferenceClass ProteinReference
Description: A protein reference is a grouping of several protein entities that
are encoded by the same genetic sequence. Members can differ in any combination of cellular location, sequence features and bound partners. Rationale: Protein molecules, encoded by the same genetic sequence can be present in (combinatorially many) different states, as a result of post translational modifications and non-covalent bonds. Each state, chemically, is a different pool of molecules. They are, however, related to each other because: They all share the same “base” genetic sequence. They can only be converted to each other but not to any other protein Comments:Most Protein databases, including UniProt would map one to one with ProteinReferences in BioPAX.
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
Attribute _organism getter
Attribute _sequence getter
get_standardName()Attribute _standardName 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_uri_string
set_xref
to_json
type_attributes
Methods Summary
Attribute _organism getter
Attribute _sequence getter
set_organism(value)set_sequence(value)set_uri_string(uristr)to_json()Methods Documentation
- 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.