Semantic interoperability and characterization of data provenance in computational molecular engineering
arXiv:1908.02335 · doi:10.1021/acs.jced.9b00739
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.
References in corpus (7)
- AiiDA: Automated Interactive Infrastructure and Database for Computational Science
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- ms2: A molecular simulation tool for thermodynamic properties, new version release
- ls1 mardyn: The massively parallel molecular dynamics code for large systems
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- An Ontology for the Materials Design Domain
- Heterogeneous Multi-Rate mass transfer models in OpenFOAM
- Reliable and interoperable computational molecular engineering: 2. Semantic interoperability based on the European Materials and Modelling Ontology
- KnowTD-An Actionable Knowledge Representation System for Thermodynamics
- Using Large Language Models for Solving Thermodynamic Problems