Created by Hevok on Dec. 4, 2012, 3:22 a.m.
The function of a biological entity is determined by its interactions with other entities. The interactions app integrates interaction data from a multitude of resources which are considered as suitable and executes a robust unification schema on interaction information as well as maps the interactors to the correct biological entities via a powerful mapping algorithms that lives in the Annotations App. These enables to generate directional heterogeneous interaction networks of any complexity compromising physical, genetic as well as regulatory interactions.
Specific filters can be applied on entities, defined interaction types, and compartments among others. The interaction app provides basic topology analysis as well as a guilt-by-association algorithm to infer entities highly likely to belong to provided seed list of entities or processes.
Objects can be constructed by combining them with each other (e.g. mitochondria is part of the cytoplasm and an organelle membrane is part of the organelle). The part of entry can be inherited (e.g. cytoplasm is part of the cell, therefore mitochondria are also part of the cell).
The Integrator is the implementation of Denigma's integration protocol. Biological information is distributed among numerous databases, hidden in the literature and web as well as in the minds of scientists. The integrator executes a universal unification schema. Integration can be executed in two fashions. One is implicit, the other is explicit, i.e. mapping discrete biological entities to class-based programming objects. In such data is put together into a conceptional logic which is much more then the sum of its components.