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Molecular Interaction Map
| Preferred Name | EntityFeature | |
| Synonyms |
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| Definitions |
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. |
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| ID |
http://www.biopax.org/release/biopax-level3.owl#EntityFeature |
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| comment |
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.
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| definition |
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.
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| prefixIRI |
EntityFeature
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| prefLabel |
EntityFeature
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| disjointWith |
http://www.biopax.org/release/biopax-level3.owl#EntityReference http://www.biopax.org/release/biopax-level3.owl#PathwayStep http://www.biopax.org/release/biopax-level3.owl#Xref http://www.biopax.org/release/biopax-level3.owl#Score http://www.biopax.org/release/biopax-level3.owl#Evidence http://www.biopax.org/release/biopax-level3.owl#Stoichiometry http://www.biopax.org/release/biopax-level3.owl#SequenceLocation http://www.biopax.org/release/biopax-level3.owl#Provenance http://www.biopax.org/release/biopax-level3.owl#KPrime http://www.biopax.org/release/biopax-level3.owl#ExperimentalForm |
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| subClassOf |
http://www.biopax.org/release/biopax-level3.owl#UtilityClass |
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