Biochemical Space

Entity

Entity is a cornerstone of space hierarchy and represents an object from a wide range of functions – from individual particles to huge complexes. However, to avoid enumerating huge number of individual entities, one entity can represent a group of entities with similar properties.

Attributes of an entity:

1. ID - unique identifier of the entity *
2. Name - suitable name for the entity
3. States - a set of allowed states **
4. Composition - enumeration of subordinate entities **
5. Locations - set of allowed compartments where the entity might occur *
6. Classification - short description of general functionality of the entity
7. Description - detailed characterization of the entity
8. Annotation - links to databases with appropriate annotations *
9. Organisms - set of organisms where the entity might occur *
10. Notes - additional information

* mandatory (cannot be empty)

** exactly one of States or Composition must be filled

Moreover, entity detail provides:

• information about associated models and rules,
• link to the process hierarchy.