Entity#
- class biopax-explorer.biopax.entity.Entity(*args, **kwargs)[source]#
Bases:
objectClass Entity
Definition: A discrete biological unit used when describing pathways.
Rationale: Entity is the most abstract class for representing components of a pathway. It includes both occurents (interactions and pathways) and continuants (physical entities and genes). Loosely speaking, BioPAX Entity is an atomic scientific statement with an associated source, evidence and references. Usage: There is no recommended use-cases for instantiating this class. Please, use its subclasses instead. Synonyms: element, thing,biological unit, statement, observable.
code generator : rdfobj (author F.Moreews 2023-2024).
Methods
Attribute _availability getter
Attribute _comment getter
Attribute _dataSource getter
Attribute _displayName getter
Attribute _evidence getter
get_name()Attribute _name getter
Attribute _standardName getter
get_xref()Attribute _xref getter
attribute_type_by_name
get_uri_string
object_attributes
set_availability
set_comment
set_dataSource
set_displayName
set_evidence
set_name
set_standardName
set_uri_string
set_xref
to_json
type_attributes
Methods Summary
Attribute _availability getter
Attribute _comment getter
Attribute _dataSource getter
Attribute _displayName getter
Attribute _evidence getter
get_name()Attribute _name getter
Attribute _standardName getter
get_xref()Attribute _xref getter
set_availability(value)set_comment(value)set_dataSource(value)set_displayName(value)set_evidence(value)set_name(value)set_standardName(value)set_uri_string(uristr)set_xref(value)to_json()Methods Documentation
- get_availability()[source]#
- Attribute _availability getter
Describes the availability of this data (e.g. a copyright statement).
- get_comment()[source]#
- Attribute _comment getter
Comment on the data in the container class. This property should be used instead
of the OWL documentation elements (rdfs:comment) for instances because information in ‘comment’ is data to be exchanged, whereas the rdfs:comment field is used for metadata about the structure of the BioPAX ontology.
- get_dataSource()[source]#
- Attribute _dataSource getter
A free text description of the source of this data, e.g. a database or person
name. This property should be used to describe the source of the data. This is meant to be used by databases that export their data to the BioPAX format or by systems that are integrating data from multiple sources. The granularity of use (specifying the data source in many or few instances) is up to the user. It is intended that this property report the last data source, not all data sources that the data has passed through from creation.
- 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_evidence()[source]#
- Attribute _evidence getter
Scientific evidence supporting the existence of the entity as described.
- 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.