BioSource#
- class biopax-explorer.biopax.biosource.BioSource(*args, **kwargs)[source]#
Bases:
UtilityClassClass BioSource
Definition: The biological source (organism, tissue or cell type) of an Entity.
Usage: Some entities are considered source-neutral (e.g. small molecules), and the biological source of others can be deduced from their constituentss (e.g. complex, pathway). Instances: HeLa cells, Homo sapiens, and mouse liver tissue.
code generator : rdfobj (author F.Moreews 2023-2024).
Methods
Attribute _cellType getter
get_comment()Attribute _comment getter
Attribute _displayName getter
get_name()Attribute _name getter
Attribute _standardName getter
Attribute _tissue getter
get_xref()Attribute _xref getter
attribute_type_by_name
get_uri_string
object_attributes
set_cellType
set_comment
set_displayName
set_name
set_standardName
set_tissue
set_uri_string
set_xref
to_json
type_attributes
Methods Summary
Attribute _cellType getter
Attribute _displayName getter
get_name()Attribute _name getter
Attribute _standardName getter
Attribute _tissue getter
get_xref()Attribute _xref getter
set_cellType(value)set_displayName(value)set_name(value)set_standardName(value)set_tissue(value)set_uri_string(uristr)set_xref(value)to_json()Methods Documentation
- get_cellType()[source]#
- Attribute _cellType getter
A cell type, e.g. ‘HeLa’. This should reference a term in a controlled
vocabulary of cell types. Best practice is to refer to OBO Cell Ontology. http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell
- get_displayName()[source]#
- Attribute _displayName getter
An abbreviated name for this entity, preferably a name that is short enough to
be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application. Warning: Subproperties of name are functional, that is we expect to have only one standardName and shortName for a given entity. If a user decides to assign a different name to standardName or shortName, they have to remove the old triplet from the model too. If the old name should be retained as a synonym a regular “name” property should also be introduced with the old name.
- get_name()[source]#
- Attribute _name getter
Synonyms for this entity. standardName and shortName are subproperties of this
property and if declared they are automatically considered as names. Warning: Subproperties of name are functional, that is we expect to have only one standardName and shortName for a given entity. If a user decides to assign a different name to standardName or shortName, they have to remove the old triplet from the model too. If the old name should be retained as a synonym a regular “name” property should also be introduced with the old name.
- get_standardName()[source]#
- Attribute _standardName getter
The preferred full name for this entity, if exists assigned by a standard
nomenclature organization such as HUGO Gene Nomenclature Committee. Warning: Subproperties of name are functional, that is we expect to have only one standardName and shortName for a given entity. If a user decides to assign a different name to standardName or shortName, they have to remove the old triplet from the model too. If the old name should be retained as a synonym a regular “name” property should also be introduced with the old name.