Extension of the sasCIF format and its applications for data processing and deposition
- Hamburg Outstation (Germany). European Molecular Biology Lab.
- Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology and Center for Integrative Proteomics Research
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. Lastly, 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.
- Research Organization:
- Rutgers Univ., Piscataway, NJ (United States)
- Sponsoring Organization:
- USDOE
- Grant/Contract Number:
- SC0008434
- OSTI ID:
- 1345572
- Journal Information:
- Journal of Applied Crystallography (Online), Vol. 49, Issue 1; ISSN 1600-5767
- Publisher:
- International Union of CrystallographyCopyright Statement
- Country of Publication:
- United States
- Language:
- English
Web of Science
2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update
|
journal | August 2017 |
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
|
journal | April 2019 |
Archiving and disseminating integrative structure models
|
journal | July 2019 |
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