International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 5.5, p. 541

Section 5.5.2.3. Supporting other data formats and data delivery methods

J. D. Westbrook,a* H. Yang,a Z. Fenga and H. M. Bermana

aProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Correspondence e-mail:  jwest@rcsb.rutgers.edu

5.5.2.3. Supporting other data formats and data delivery methods

| top | pdf |

One of the greatest benefits of a dictionary-based informatics infrastructure is the flexibility that it provides in supporting alternative data formats and delivery methods. Because the data and all of their defining attributes are electronically encoded, translation between data and dictionary formats can be achieved using light-weight software filters without loss of any information.

XML provides a particularly good example of the ease with which data can be converted to and from the mmCIF format. XML translations of mmCIF data files are currently provided on the Worldwide PDB ftp site (ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/XML/ ). These XML files use mmCIF dictionary data-item names as XML tags. These files were created by a translation tool (http://sw-tools.pdb.org/apps/MMCIF-XML-UTIL/ ) that translates mmCIF data files to XML in compliance with an XML schema. The XML schema is similarly software-translated from the PDB exchange data dictionary.

Other delivery methods such as Corba (http://www.omg.org/cgi-bin/doc?lifesci/00–02-02 ) do not require a data format, as data are exchanged using an application program interface (API). A Corba API for macromolecular structure (Greer et al., 2002[link]) based on the content of the mmCIF data dictionary has been approved by the Object Management Group (OMG). Software tools supporting this Corba API (OpenMMS, http://openmms.sdsc.edu , and FILM, http://sw-tools.pdb.org/apps/FILM ) take full advantage of the data dictionary in building the interface definitions and supporting server on which the API is based (see also Section 5.3.8.2[link] ).

References

Greer, D. S., Westbrook, J. D. & Bourne, P. E. (2002). An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics, 18, 1280–1281.








































to end of page
to top of page