Section 5.3.8.2.  OpenMMS

In practice, the ontology was developed in a `metamodel' that combined the definitions and relationships between data items specified in the mmCIF dictionary with a generic metamodel framework. The metamodel extracts the information in the mmCIF dictionary but maintains it in a representation that is independent of the mmCIF STAR or any other file format. The standard building block of the metamodel is an Entry object, modelling a single macromolecular structure.

From a suitable metamodel, it then becomes relatively straightforward to generate alternative expressions of the information to suit different access requirements. The OpenMMS toolkit (Greer et al., 2002) was built using Java source code to generate a Corba interface, an SQL schema for relational database loading and an XML representation of macromolecular data sets (Fig. 5.3.8.1).

Figure 5.3.8.1 | top | pdf | The OpenMMS metamodel and data flow.

The toolkit contains an mmCIF parsing module capable of direct access to the underlying data archive of mmCIF data files. This is important, because the data files represent a common reference for all the derived representations. Any errors or discrepancies between the expressed forms of the Corba, XML or SQL representations are resolved against the standard mmCIF reference form.

The relational database supporting an SQL-92 compatible interface provides an appropriate API for many applications, particularly ones that require extensive string searches. The close relationship between the mmCIF data model and relational database models has already been described earlier in this volume (Chapter 2.6 ).

Advantages of the SQL interface are that it provides rapid access direct to the binary data storage representation and that individual components of a data set may be efficiently retrieved without the need to search sequentially through an entire entry.

This efficiency of access and the ability to retrieve individual MMS data elements from a remote server is best realized through the Corba interface, the primary purpose of which is indeed to facilitate such high-performance access.

The bulk exchange of data is addressed through the generation of XML files. XML is a simple, powerful and widely used standard for interchanging data, and its use for transporting macromolecular data obviates the need for target applications to build their own STAR parsers. However, the use of markup tags around every individual data element does make the files much larger than their mmCIF progenitors. This is not an insurmountable problem in large-scale application environments, but it can undermine the effectiveness of XML as a representation mechanism in such applications as web browsers. A possible approach to this could be to define different, less verbose, XML representations and populate these on demand from a database store, either by SQL or XML queries. This is not an approach that the current OpenMMS toolkit supports directly.

Fig. 5.3.8.2 is an extract from an XML data file generated from the PDB structure 1xy2. The XML uses a reserved name space PDBx conforming to the schema http://deposit.pdb.org/pdbML/pdbx-v0.905.xsd . Data tags map cleanly to the corresponding data names in the mmCIF dictionary formed by concatenating the XML element name with its parent category name. For example, the entry 〈PDBx:length_a〉27.080〈/PDBx:length_a〉 included in the 〈PDBx:cellCategory〉 container tag can be directly translated to the corresponding mmCIF data item _cell.length_a 27.080. CIF data loops are represented by repeated instances of the XML tag representing the corresponding CIF data name (for example, the multiple 〈PDBx:audit_author name〉 tags are equivalent to a CIF loop_ _audit_author.name construct). Nonstandard items with a pdbx_ prefix (e.g. 〈PDBx:pdbx_description〉 in the 〈PDBx:entityCategory〉 group) refer to private data names in the PDB extension dictionary (Appendix 3.6.2 ).

Figure 5.3.8.2 | top | pdf | Sample XML output from the OpenMMS XML generator. Lines have been omitted or wrapped to fit the present column width.