From ReactomeWiki

EntitySets

Use

There are three types:

• CandidateSet - Good Example
• DefinedSet - Good Example
• OpenSet - Good Example

When/how should I use sets?

Example 1.

When multiple entities can take part in the same reaction, it may be simpler to represent this as a single "generic" reaction using sets as input. For example, suppose protein A +protein B -> complex AB but A could be 1 of 10 related proteins. You could create a reaction I in which:

Reaction I:

DefinedSet A + protein B= complex AB where

Input = DefinedSet A = (Protein 1, Protein 2, protein 3,......protein 10) Input= protein B

Output = Complex AB= DefinedSet A + protein B

Caveats:

1. Members of a DefinedSet must all be of the same class (e.g all EWASs OR all Complexes, OR all simpleEntities.....)

2. If you need to use to a specific reaction that is represented by the "generic" Reaction I above (say as a precedingEvent for a new reaction), you MUST create a specific instance of this Reaction I.

For example, for the reaction:

(Protein 2:protein B) complex + Protein C -> ((Protein 2:protein B):protein C) complex

Say you need a preceding event to represent the formation of (Protein 2:protein B) complex.

You can't simply use Reaction I as the preceding event. You must create a new reaction:

Reaction II:

protein 2 + protein B= (protein 2: protein B) complex

Input = protein 2 Input= protein B Output = (protein 2: protein B) complex

Reaction II can be added to the "has member" slot of Reaction I.

NYCCM08 Notes

Surprisingly there was very little discussion of these. Maybe it is not as hard as I thought.

• We need good examples above.