  By introducing a common representational system for metadata that describe
the employed simulation workflows, diverse sources of data and platforms in
computational molecular engineering, such as workflow management systems, can
become interoperable at the semantic level. To achieve semantic
interoperability, the present work introduces two ontologies that provide a
formal specification of the entities occurring in a simulation workflow and the
relations between them: The software ontology VISO is developed to represent
software packages and their features, and OSMO, an ontology for simulation,
modelling, and optimization, is introduced on the basis of MODA, a previously
developed semi-intuitive graph notation for workflows in materials modelling.
As a proof of concept, OSMO is employed to describe a use case of the TaLPas
workflow management system, a scheduler and workflow optimizer for
particle-based simulations.
