EntityFeature#
- class biopax-explorer.biopax.entityfeature.EntityFeature(*args, **kwargs)[source]#
Bases:
UtilityClassClass EntityFeature
Description: A characteristic of a physical entity that can change while the
entity still retains its biological identity. Rationale: Two phosphorylated forms of a protein are strictly speaking different chemical molecules. It is, however, standard in biology to treat them as different states of the same entity, where the entity is loosely defined based on sequence. Entity Feature class and its subclassses captures these variable characteristics. A Physical Entity in BioPAX represents a pool of molecules rather than an individual molecule. This is a notion imported from chemistry( See PhysicalEntity). Pools are defined by a set of Entity Features in the sense that a single molecule must have all of the features in the set in order to be considered a member of the pool. Since it is impossible to list and experimentally test all potential features for an entity, features that are not listed in the selection criteria is neglected Pools can also be defined by the converse by specifying features that are known to NOT exist in a specific context. As DNA, RNA and Proteins can be hierarchically organized into families based on sequence homology so can entity features. The memberFeature property allows capturing such hierarchical classifications among entity features. Usage: Subclasses of entity feature describe most common biological instances and should be preferred whenever possible. One common usecase for instantiating entity feature is, for describing active/inactive states of proteins where more specific feature information is not available. Examples: Open/close conformational state of channel proteins, “active”/”inactive” states, excited states of photoreactive groups.
code generator : rdfobj (author F.Moreews 2023-2024).
Methods
get_comment()Attribute _comment getter
Attribute _evidence getter
Attribute _featureLocation getter
Attribute _featureLocationType getter
Attribute _memberFeature getter
attribute_type_by_name
get_uri_string
object_attributes
set_comment
set_evidence
set_featureLocation
set_featureLocationType
set_memberFeature
set_uri_string
to_json
type_attributes
Methods Summary
Attribute _evidence getter
Attribute _featureLocation getter
Attribute _featureLocationType getter
Attribute _memberFeature getter
set_evidence(value)set_featureLocation(value)set_featureLocationType(value)set_memberFeature(value)set_uri_string(uristr)to_json()Methods Documentation
- get_evidence()[source]#
- Attribute _evidence getter
Scientific evidence supporting the existence of the entity as described.
- get_featureLocation()[source]#
- Attribute _featureLocation getter
Location of the feature on the sequence of the interactor. For modification
features this is the modified base or residue. For binding features this is the binding site and for fragment features this is the location of the fragment on the “base” sequence. One feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence. Small Molecules can have binding features but currently it is not possible to define the binding site on the small molecules. In those cases this property should not be specified.
- get_featureLocationType()[source]#
- Attribute _featureLocationType getter
A controlled vocabulary term describing the type of the sequence location of the
feature such as C-Terminal or SH2 Domain.
- get_memberFeature()[source]#
- Attribute _memberFeature getter
An entity feature that belongs to this homology grouping. These features should
be of the same class of this EntityFeature These features should be an EntityFeature of an EntityReference which is a memberEntityReference of the EntityReference of this feature. If this set is not empty than the sequenceLocation of this feature should be non-specified. Example: a homologous phosphorylation site across a protein family.