Reset password

Biochemical Space



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.

Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI