PhysicalEntity#
- class biopax-explorer.biopax.physicalentity.PhysicalEntity(*args, **kwargs)[source]#
Bases:
EntityClass PhysicalEntity
Definition: A pool of molecules or molecular complexes. Comments: Each
PhysicalEntity is defined by a sequence or structure based on an EntityReference AND any set of Features that are given. For example, ser46 phosphorylated p53 is a physical entity in BioPAX defined by the p53 sequence and the phosphorylation feature on the serine at position 46 in the sequence. Features are any combination of cellular location, covalent and non-covalent bonds with other molecules and covalent modifications. For a specific molecule to be a member of the pool it has to satisfy all of the specified features. Unspecified features are treated as unknowns or unneccesary. Features that are known to not be on the molecules should be explicitly stated with the “not feature” property. A physical entity in BioPAX never represents a specific molecular instance. Physical Entity can be heterogenous and potentially overlap, i.e. a single molecule can be counted as a member of multiple pools. This makes BioPAX semantics different than regular chemical notation but is necessary for dealing with combinatorial complexity. Synonyms: part, interactor, object, species Examples: extracellular calcium, ser 64 phosphorylated p53
code generator : rdfobj (author F.Moreews 2023-2024).
Methods
get_availability()Attribute _availability getter
Attribute _cellularLocation getter
get_comment()Attribute _comment getter
get_dataSource()Attribute _dataSource getter
get_displayName()Attribute _displayName getter
get_evidence()Attribute _evidence getter
Attribute _feature getter
Attribute _memberPhysicalEntity getter
get_name()Attribute _name getter
Attribute _notFeature getter
get_standardName()Attribute _standardName getter
get_xref()Attribute _xref getter
attribute_type_by_name
get_uri_string
object_attributes
set_availability
set_cellularLocation
set_comment
set_dataSource
set_displayName
set_evidence
set_feature
set_memberPhysicalEntity
set_name
set_notFeature
set_standardName
set_uri_string
set_xref
to_json
type_attributes
Methods Summary
Attribute _cellularLocation getter
Attribute _feature getter
Attribute _memberPhysicalEntity getter
Attribute _notFeature getter
set_cellularLocation(value)set_feature(value)set_memberPhysicalEntity(value)set_notFeature(value)set_uri_string(uristr)to_json()Methods Documentation
- get_cellularLocation()[source]#
- Attribute _cellularLocation getter
A cellular location, e.g. ‘cytoplasm’. This should reference a term in the Gene
Ontology Cellular Component ontology. The location referred to by this property should be as specific as is known. If an interaction is known to occur in multiple locations, separate interactions (and physicalEntities) must be created for each different location. If the location of a participant in a complex is unspecified, it may be assumed to be the same location as that of the complex. A molecule in two different cellular locations are considered two different physical entities.
- get_memberPhysicalEntity()[source]#
- Attribute _memberPhysicalEntity getter
This property stores the members of a generic physical entity. For
representing homology generics a better way is to use generic entity references and generic features. However not all generic logic can be captured by this, such as complex generics or rare cases where feature cardinality is variable. Usages of this property should be limited to such cases.