title: Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.
abstract: Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations.
authors.affiliation: a Department of Biomedical Informatics , University of Utah , Salt Lake City , Utah , USA.
authors.forename: J C
authors.initials: JC
authors.lastname: Thibault
authors.affiliation: b Department of Medicinal Chemistry , University of Utah , Salt Lake City , Utah , USA.
authors.forename: D R
authors.initials: DR
authors.lastname: Roe
authors.affiliation: a Department of Biomedical Informatics , University of Utah , Salt Lake City , Utah , USA.
authors.forename: K
authors.initials: K
authors.lastname: Eilbeck
authors.affiliation: b Department of Medicinal Chemistry , University of Utah , Salt Lake City , Utah , USA.|c Center for High Performance Computing , University of Utah , Salt Lake City , Utah , USA.
authors.forename: T E
authors.initials: TE
authors.lastname: Cheatham
authors.affiliation: a Department of Biomedical Informatics , University of Utah , Salt Lake City , Utah , USA.
authors.forename: J C
authors.initials: JC
authors.lastname: Facelli
mesh_terms: D064229:Biological Ontologies; D019295:Computational Biology / Q000379:methods / Q000458:organization & administration*; D003195:Computer Communication Networks; D003198:Computer Simulation; D033181:Information Dissemination; D008958:Models, Molecular; D015394:Molecular Structure; D021281:Quantitative Structure-Activity Relationship; D018875:Vocabulary, Controlled
keywords: data repositories; data sharing; distributed computing; molecular simulations; ontologies; vocabularies