Abstract
Recent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and provide independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files (sasCIFtools) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. This update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.
Highlights
The broad availability of advanced experimental facilities for small-angle scattering (SAS) of X-rays (SAXS) and neutrons (SANS), together with novel data analysis methods, have prompted a dramatic increase in the popularity of the method, most notably its use in investigating the overall structures of biological macromolecules in solution (Graewert & Svergun, 2013)
The sasCIF file can be submitted to a SAS database to be accessible for the community. This new version of the sasCIF format is intended to provide a major step towards standardizing the representation and exchange of SAS data and SAS-based models
The open source sasCIFtools developed for the processing of sasCIF files facilitate the conversion of the experimental SAS data files and models to the updated sasCIF format and vice versa
Summary
The broad availability of advanced experimental facilities for small-angle scattering (SAS) of X-rays (SAXS) and neutrons (SANS), together with novel data analysis methods, have prompted a dramatic increase in the popularity of the method, most notably its use in investigating the overall structures of biological macromolecules in solution (Graewert & Svergun, 2013) This increase has led to an upsurge in the number of objects studied, the experimental data available and the structural models generated. Cross-platform exchange of experimental data, analysis protocols, general experimental information, and the results obtained using various instruments and radiation sources (X-rays or neutrons) is hindered by the lack of a consistent and user-friendly file structure Discussions on this issue within the SAS community resulted in the recommendation by the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank (wwPDB) to develop a federated approach to SAS data and model archiving. A data block may be named by appending a text string after the data_ directive and a data block is terminated either by another data_ directive or by the end of the file
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