[April 21, 2000] StarDOM has been created by Jens Linge and Lutz Ehrlich of the European Molecular Biology Laboratory, Heidelberg, Germany. "StarDOM is a software package to transform data provided in the Self Defining Text Archival and Retrieval (STAR) format into XML. The Self-Defining Text Archival and Retrieval (STAR) format has become a standard in structural biology. Several scientific databases (e.g., PDB, CCDC, ICDD, BioMagResBank) use the STAR format to store structural, crystallographic diffraction and NMR data. A growing number of programs (e.g., CNS, NMRView, MODELFREE) can utilize the STAR format for their respective data output. The transform is achieved by transferring the data tree inherent in a STAR file to a [W3C] Document Object Model. This opens new possibilities for visual editing, archiving, parsing and structured queries of structural biology data. The strategy allows interactive navigation by using the Document Object Model representation of the data as well as easy access by XML query languages. As an example application, the entire BioMagResBank has been transformed into XML format [conforming to the StarDOM XML DTD]. Using an XML query language, statistical queries on the collected NMR data sets can be constructed with very little effort... The core functionality of StarDOM is implemented in a package written in the Python programming language. It relies on an implementation of the Document Object Model (DOM). Currently, there are two DOM implementations freely availabe for noncommercial purposes: 4DOM is the implementation of FourThought which adheres closely to the W3C DOM recommendation, whereas the implementation provided by the Python XML-special interest group (XML-SIG) lends itself to easier programmatic manipulation of the DOM objects. StarDOM is written in a way which allows the use of either package. As the 4DOM implementation can be used to access DOM objects as CORBA servers, the additional effort in programming might be worth it if you plan to create distributed data repositories."
References:
"StarDOM: From STAR format to XML." Presentation by Lutz Ehrlich.
StarDOM DTD; [cache]
[April 21, 2000] "StarDOM: From STAR Format to XML." By Jens P. Linge, Michael Nilges, and Lutz Ehrlich. In Journal of Biomolecular NMR Volume 15, Number 2 (October 1999), pages 169-172. [ISSN: 0925-2738, Kluwer Academic Press] "StarDOM is a software package for the representation of STAR files as document object models and the conversion of STAR files into XML. This allows interactive navigation by using the Document Object Model representation of the data as well as easy access by XML query languages. As an example application, the entire BioMagResBank has been transformed into XML format. Using an XML query language, statistical queries on the collected NMR data sets can be constructed with very little effort. The BioMagResBank/XML data and the software can be obtained at http://www.nmr.embl-heidelberg.de/nmr/StarDOM/."
