phosphorilation
type: Class
subclass of: interaction
disjoint with: physical_interaction

physical_interaction
type: Class
subclass of: interaction
disjoint with: phosphorilation

InteractorRoleInteractionDomain
type: Class
additional information: See also the following paper: M. Dumontier. Biological situational modeling: Defining Molecular Roles in Pathways and Reactions. 2008. OWL Experiences and Design (OWLED-EU 2008)
aim: To model different interactions where the interactors can have different roles
classification: Domain Modelling
elements: Three object properties are needed: HasRole, RoleInInteraction, and HasParticipant. This ODP has got two aims: close the interactors an interaction can have, and decouple roles from interactions. An interaction is a unique combination of interactors and roles, whereas an interactor can have at the same time many roles and participate in many different interactions (but never with different roles in the same interaction)
implementation: The three object properties must be created first (HasRole, RoleInInteraction and HasParticipant). Each interaction bears a closure, so apart of an axiom [HasParticipant exactly 1 InteractorX], an axiom of the type [HasParticipant only (Interactor1 or InteractorN)] should be used. For each interactor, add an axiom of the type [HasRole some (Role and RoleInInteraction Interaction), so queries can be decomposed for roles or participation in interactions, or participations in interactions with certain roles
motivation: Protein Protein Interactions (PPI) are the base for most of the biological processes at a molecular level. For example (http://www.ebi.ac.uk/intact/binary-search/faces/search.xhtml?query=BRCA2)
name: Interactor Role Interaction
reference: http://odps.sourceforge.net
reference: http://www.cellcycleontology.org/
result: The participation events and the role with which interactors participate in concrete interactions are decoupled. Also, each interaction has a given set of interactors and not more
sample: ../img/Interactor_Role_Interaction_instance.png
structure: ../img/Interactor_Role_Interaction_abstract.png
subclass of: Thing

Thing
on class: brca2
qualified cardinality: 1

Thing
on class: fancd2
qualified cardinality: 1

Thing
on class: rad51
qualified cardinality: 1

Thing
on class: brca2
qualified cardinality: 1