#72 prerequisite conditions

[lululi]

As discussed during the PSIMEx meeting 2011 in Heidelberg, it would be important to implement the PSI-MI 2.5 XML format in order to better describe the dynamic and complexity of an interaction.
Some interactions occur only in specific biological conditions, such as for example, after an external stimuli or a genetic perturbation or in a specific time or location. We could insert, at the interaction level, some prerequisite conditions that explain the biological environment in which the interaction occurs.

See below some examples of ontologies that could be used or extended:

Time (cell cycle, differentiation, apoptosis, etc.) using Gene Ontology Biological process:
Mitotic cell cycle: GO:0000278
Chondroblast differentiation: GO:0060591
Induction of apoptosis: GO:0006917

Localization using Gene Ontology Cellular component:
Nucleus: GO:0005634
Plasma membrane: GO:0005886
Trans-Golgi network: GO:0005802

Pathological conditions using DOID Ontology:
Cancer: DOID:162
Long QT syndrome: DOID:2843
Ataxia telangiectasia: DOID:12704

Perturbation or external stimuli (Starvation, oxidative stress, growth conditions, drugs, etc) using ChEBI Ontology and Gene Ontology Biological process:
Genotoxin: CHEBI:50902
Cisplatin: CHEBI:27899
Cellular response to amino acid starvation: GO:0034198
Response to oxidative stress: GO:0006979

Growth conditions need a specific ontology.

To add an extra component (protein, RNA, DNA, macromolecule), that is not necessary an interactor itself, but it is fundamental to the interaction.