Kegg example - Control subclasses: Catalysis/Modulation
From the Biopax doc:
Mother class: Control
controller - (0 or more object:PhysicalEntity or object:Pathway) In for example, a biochemical reaction, an enzyme is the controlling entity of the reaction. Physical entities pathways can be controllers (e.g. protein enzyme catalyzes a reaction, a pathway activates a reaction, caspase cascade activates apoptosis). Multiple controllers are all required for the control to occur (AND relationship). OR relationships are defined using multiple control interaction instances. controller is a sub-property of participant.
Sub-class: Catalysis
Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy. Instances of this class describe a pairing between a catalyzing entity and a catalyzed conversion. Comment: A separate catalysis instance should be created for each different conversion that a physicalEntity may catalyze and for each different physicalEntity that may catalyze a conversion.
Note:
- it seems that several controllers are not allowed for Catalysis and Modulation classes. => Edit: False
From PathwayCommons10.kegg.BIOPAX:
<bp:Catalysis rdf:ID="Catalysis_6f3d86639e31e9205ac742142ce63c35">
<bp:controller rdf:resource="#Protein_120bd3b428a3705b674f4588b5accedc" />
<bp:controller rdf:resource="#Protein_938989884443d841826be52ccdc7d13b" />
<bp:controller rdf:resource="#Protein_5b1083d6ed19683fd06825a9450cc9ea" />
<bp:controller rdf:resource="#Protein_bcefc23f2e55820bb4265e28624b47e9" />
<bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">rn:R06025_Catalysis</bp:displayName>
<bp:controlled rdf:resource="#BiochemicalReaction_b25cedc4d2d003016cd99febf1e3629d" />
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://www.ra.cs.uni-tuebingen.de/software/KEGGtranslator/rnR06025</bp:comment>
<bp:dataSource rdf:resource="#kegg" />
</bp:Catalysis>
Problems:
-
Multiple controllers for 1 Catalysis while it seems to be explicitly forbidden in the standard. -
No controlType that defines the nature of the control relationship between the controller and the controlled entities.
Solutions:
-
Catalysis is a control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy. => So default controlType will be "ACTIVATION"