Michael A. Seaton

Martin Thomas Horsch, Silvia Chiacchiera, Björn Schembera et al.

The European Materials and Modelling Ontology (EMMO) has recently been advanced in the computational molecular engineering and multiscale modelling communities as a top-level ontology, aiming to support semantic interoperability and data integration solutions, e.g., for research data infrastructures. The present work explores how top-level ontologies that are based on the same paradigm - the same set of fundamental postulates - as the EMMO can be applied to models of physical systems and their use in computational engineering practice. This paradigm, which combines mereology (in its extension as mereotopology) and semiotics (following Peirce's approach), is here referred to as mereosemiotics. Multiple conceivable ways of implementing mereosemiotics are compared, and the design space consisting of the possible types of top-level ontologies following this paradigm is characterized.

Martin Thomas Horsch, Silvia Chiacchiera, Michael A. Seaton et al.

The Virtual Materials Marketplace (VIMMP) project, which develops an open platform for providing and accessing services related to materials modelling, is presented with a focus on its ontology development and data technology aspects. Within VIMMP, a system of marketplace-level ontologies is developed to characterize services, models, and interactions between users; the European Materials and Modelling Ontology (EMMO) is employed as a top-level ontology. The ontologies are used to annotate data that are stored in the ZONTAL Space component of VIMMP and to support the ingest and retrieval of data and metadata at the VIMMP marketplace frontend.

M. T. Horsch, C. Niethammer, G. Boccardo et al.

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.