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Semantic interoperability and characterization of data provenance in computational molecular engineering

: Horsch, Martin Thomas; Niethammer, Christoph; Boccardo, Gianluca; Carbone, Paola; Chiacchiera, Silvia; Chiricotto, Mara; Elliott, Joshua D.; Lobaskin, Vladimir; Neumann, Philipp; Schiffels, Peter; Seaton, Michael A.; Todorov, Ilian T.; Vrabec, Jadran; Leite Cavalcanti, Welchy


Journal of Chemical and Engineering Data 65 (2020), Nr.3, S.1313-1329
ISSN: 0021-9568
ISSN: 1520-5134
Fraunhofer IFAM ()
molecular modeling; molecular engineering; Software; materials; computer simulation

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, modeling, and optimization, is introduced on the basis of MODA, a previously developed semi-intuitive graph notation for workflows in materials modeling. 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.