Crystallographic Information and Data Management
15
2013
39
5 hours 31 minutes
15 results
17:39
1Weiss, ManfredFor biological macromolecules, where structures and experimental data have traditionally been deposited in a central archive (the Protein Data Bank), integrating structural data with derivative publications is more complex. IUCr journals have developed an online publication tool that can extract deposited macromolecular data from the archive, and prompt the author for the additional information required for the fullest characterisation of a macromolecular structure determination. Again, the goal is to maximise the integrity of the scientific discussion.
2013International Union of Crystallography (IUCr)
23:53
5Linden, AnthonyWhen small structures are submitted for publication in IUCr journals, they are analysed as part of the peer review process by the software suite checkCIF. The goal of this analysis is to provide an objective assessment of the quality and reliability of the published structure, with reference both to the available experimental data and the level of consistency with known chemistry. For this to work well, validation protocols have to keep up with advances in structure determination methodologies. Consequently, it is important that CIF tools and definitions are both practical and extended and revised regularly. The purpose and output of validation also have to be understood easily by users, reviewers and journal editors, some of whom may not be expert crystallographers.
2013International Union of Crystallography (IUCr)
18:24
Murray-Rust, PeterThe development of CIF has allowed IUCr journals to capture the structured semantic content of research articles to a very high degree. Hyperlinking between components of the scholarly article (the text, structural data model, experimental data) provides a sound technical basis for mining, validating and reusing scientific data with the help of high-volume robotic tools.
2013International Union of Crystallography (IUCr)
21:58
2Coles, Simon J.Crystal structure determination has become a high-throughput activity, and even at the level of the departmental laboratory, automation is increasingly important in managing the experiment and, crucially, the data collected from the experiment and its subsequent processing, analysis and dissemination. The UK National Crystallography Service is a medium-scale facility which needs to address issues of data management, accountability and dissemination, on top of its efforts to achieve best experimental practice. In providing a service to chemists as well as crystallographers, it has amassed considerable experience in cross-discipline ontology building, data publication via repository platforms, and integration with laboratory management systems.
2013International Union of Crystallography (IUCr)
26:54
2Hodson, SimonAlthough this meeting focuses on the technical aspects of sound data management, because we believe the benefits of this are self-evident to scientists who are used to taking the greatest care in analysing and using data, we should be aware also of the general research policy framework in which so much modern research is located. At the level of national and international science policy, funding bodies increasingly require evidence for best practice in data management; likewise, open-access mandates for publications may become a reality. This presentation contextualises the practice of our science within the evolving policy framework for publicly funded research.
2013International Union of Crystallography (IUCr)
18:38
4Hoyland, Michael A.Structural journals published by the IUCr have an efficient workflow built around the CIF standard. For small-unit-cell structures, authors submit their articles in this format, building on files created directly by their structure solution/refinement software. The processed experimental data from which the structure has been determined (structure factors, Rietveld profiles) are also uploaded in this format, allowing stringent technical peer review of the quality of the structural modelling. All published structures are accompanied by the underlying data that would permit their redetermination, and can be explored in the online publication through three-dimensional visualisation and analysis tools.
2013International Union of Crystallography (IUCr)
22:31
Toby, Brian H.Powder diffraction may well be the impoverished cousin of single crystal diffraction, but for many materials and measurements there is no other choice; structural analyses have been performed from powders for materials ranging from simple salts to proteins. Many other types of material characterizations can be performed with powder diffraction. Excellent instruments are available that measure powder diffraction in different ways, depending on the needs of the study and the type of illumination source. Successful modeling requires that data be kept in a form close to the original measurement, which creates complexity for a powder CIF dictionary (pdCIF). It has been nearly 15 years since the initial pdCIF dictionary was completed and the successes and failures of pdCIF will be considered.
2013International Union of Crystallography (IUCr)
24:30
3Westbrook, JohnA jewel in the crown of structural biology, the Protein Data Bank is an unparalleled archive of protein and nucleic acid structures. Its operation depends on information-rich relational databases, the schemas for which are efficiently expressed in the macromolecular CIF (mmCIF) formalism. Discrete entities that may be stored in the databases are characterised in CIF-format data dictionaries, which express ontologies widely used in areas as diverse as structural genomics, NMR, cryo-electron microscopy and protein production.
2013International Union of Crystallography (IUCr)
24:39
5Yang, EricaThe Rutherford Appleton Laboratory is a UK National Facility that handles a considerable amount of experimental research, and operates many instruments that generate large volumes of data such as the ISIS Pulsed Neutron Source, Central Laser Facility, and Diamond Light Source. It has developed a Core Scientific Metadata Model (CSMD) for the management of the data resources of the facilities in a uniform way. This talk discusses the emerging opportunities opened up by the availability of systematically managed data in a large laboratory setting and the technical barriers of making extensive use of them in real world open data infrastructure developments. The latest developments of CSMD will be presented to highlight the current direction we are undertaking in the context of the PaNData-ODI project, a collaborative European project involving thirteen major world class research laboratories that operate one or more neutron or photon sources in Europe.
2013International Union of Crystallography (IUCr)
24:14
3Bernstein, Herbert J.A specific aspect of interoperability within large scientific facilities is the management of different data formats associated with different fields. NeXus, HDF5 and CIF are scientific data formats that overlap in some areas (e.g. in the capture and management of X-ray diffraction images), and there is considerable benefit to be gained by harmonising their content and working towards maximum interoperability. Format conversion at the syntactic level can be a straightforward process, but truly interoperable software applications require functional mappings between different representation standards. An initial approach to this is being attempted by constructing a DDL2 dictionary, acting as a concordance between the existing NeXus and imgCIF formats. Full interconvertibility between NeXus and imgCIF relies on methods evaluation, and may be possible using the new dictionary definition language DDLm and an evaluation engine (such as dREL).
2013International Union of Crystallography (IUCr)
20:59
3Spadaccini, NickWhen CIF was adopted as an information exchange standard by the IUCr in 1991, it was, if anything, ahead of the then state of the art. Free-format, extensible, low-overhead - it offered an easy route to implementation by scientific software, much still written in Fortran. By externalising the semantics of its tags to external dictionaries, it allowed ontology development to be decoupled from format, and thus had an important role to play in interoperability between purely crystallographic applications and the wider worlds of structural biology, chemical informatics and laboratory data management, as illustrated elsewhere in this symposium. The latest enhancements to CIF, with the introduction of an even more powerful dictionary definition language that support methods definitions and multiple data models, provide unrivalled potential for taking computer ontologies into completely new territories.
2013International Union of Crystallography (IUCr)
25:08
4Velankar, SameerIncreasingly, the structural biology community is aware that the quality of structures deposited in the Protein Data Bank (PDB) needs critical assessment using informative, well-defined and community-accepted validation methods. To obtain recommendations on validation methods and criteria to be applied to newly deposited as well as existing structures in the PDB, the Worldwide Protein Data Bank (wwPDB) has convened several Validation Task Forces (VTFs). The validation methods and criteria suggested by the wwPDB X-ray VTF will be used to validate all X-ray structures deposited in the PDB as well as all crystal structures already in the archive. The talk will highlight the importance of validation and describe the implementation of the recommendations of the X-ray VTF. Salient features of the validation reports generated by the new wwPDB X-ray validation pipeline will also be discussed. It is hoped that all journals that publish biomacromolecular structure papers will make submission of these reports mandatory whenever they receive a manuscript describing a new structure.
2013International Union of Crystallography (IUCr)
22:31
1Helliwell, John R.The IUCr Executive Committee has charged a Working Group with an assessment of the potential benefits of depositing raw experimental data sets (with initial emphasis on X-ray diffraction images), and the cost, technical and structural ramifications of doing so. There are a number of potential locations for depositing raw images that allow their reuse in validation, re-refinements, reanalysis for new science, education and software development - for example, in discipline-specific data centres, in large-scale instrument facilities, or in institutional repositories. These are not necessarily exclusive (for example, a central data centre might archive only data sets associated with published structures), and initiatives such as the Australian TARDIS demonstrate approaches to federating separate repository platforms. Crucial to interoperability between such federated archives will be well-defined metadata and procedural standards.
2013International Union of Crystallography (IUCr)
20:05
5Groom, ColinThe Cambridge Structural Database of organic and metal-organic structures is one example of the curated archives of structural data that have been crucially important crystallographic and chemical resources for many decades. Many structural analyses based on the holdings in such databases rely on the quality and reliability of the individual structures. Historically, CCDC's Scientific Editors have worked hard to validate the individual depositions, a task greatly helped by the adoption of CIF as a community standard format. CCDC now applies probabilistic computational tools to determine the 'chemistry' represented by a CIF alongside expert human analysis.
2013International Union of Crystallography (IUCr)
19:29
1McMahon, BrianFrom its beginnings as a descriptive framework for structure determination experiments, CIF has grown to be a powerful framework for many aspects of crystallographic practice. It describes or is actively used in raw data collection (such as diffraction images), data reduction (e.g. as structure factors or Rietveld profiles), structure solution and refinement, and the publication, database curation and visualisation of crystal and molecular structures. Although not the only format in common use in the structural sciences, it is central to structure determination of small-unit-cell and macromolecular structures, and its ontologic approach informs the best practice of information and data handling throughout crystallographic researches.
2013International Union of Crystallography (IUCr)