Abstract
BackgroundFew environments have been developed or deployed to widely share biomolecular simulation data or to enable collaborative networks to facilitate data exploration and reuse. As the amount and complexity of data generated by these simulations is dramatically increasing and the methods are being more widely applied, the need for new tools to manage and share this data has become obvious. In this paper we present the results of a process aimed at assessing the needs of the community for data representation standards to guide the implementation of future repositories for biomolecular simulations.ResultsWe introduce a list of common data elements, inspired by previous work, and updated according to feedback from the community collected through a survey and personal interviews. These data elements integrate the concepts for multiple types of computational methods, including quantum chemistry and molecular dynamics. The identified core data elements were organized into a logical model to guide the design of new databases and application programming interfaces. Finally a set of dictionaries was implemented to be used via SQL queries or locally via a Java API built upon the Apache Lucene text-search engine.ConclusionsThe model and its associated dictionaries provide a simple yet rich representation of the concepts related to biomolecular simulations, which should guide future developments of repositories and more complex terminologies and ontologies. The model still remains extensible through the decomposition of virtual experiments into tasks and parameter sets, and via the use of extended attributes. The benefits of a common logical model for biomolecular simulations was illustrated through various use cases, including data storage, indexing, and presentation. All the models and dictionaries introduced in this paper are available for download at http://ibiomes.chpc.utah.edu/mediawiki/index.php/Downloads.
Highlights
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci 1988, 28(1):31–36.39
In this paper we introduce a list of common data elements and a data model that will help iBIOMES and future biomolecular simulation data repository developments move towards semantic interoperability
Data elements were missing for the representation of both Molecular dynamics (MD) and Quantum Mechanics (QM)-specific parameters
Summary
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci 1988, 28(1):31–36.39. While the use of quantum mechanics (QM) is still limited to the modelling of small biomolecules [1] composed of less than a couple hundred of atoms, atomistic or coarser-grain molecular representations have allowed researchers to simulate large biomolecular systems One of the problems with such repositories is that the published data was generated in a specialized environment to study a given biological process (e.g. protein folding), resulting in fairly homogeneous data compared to the range of methods and software available to the community. Note that other efforts to build repositories and scientific gateways, such as the BioSimGrid project [7] and work by Terstyanszky et al [8], have been undertaken but so far none has been widely adopted outside their original deploying institution or organization
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