part of
OBO Foundry RO
Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part.
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software".