Semantic interoperability and characterization of data provenance in computational molecular engineering

TL;DR

This paper develops ontologies to enable semantic interoperability of simulation workflows in computational molecular engineering, facilitating better data sharing and understanding across diverse platforms.

Contribution

It introduces two formal ontologies, VISO and OSMO, to standardize metadata representation of simulation entities and workflows, enhancing interoperability.

Findings

VISO effectively models software packages and features.

OSMO formalizes simulation workflows based on MODA notation.

Successful application to TaLPas workflow demonstrates practical utility.

Abstract

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.