The traditional Protein Data Bank's flat file archival as evolved into a dynamic database based on a Object-Relational Database Management System: 3DB. The development effort attempts to address the needs of the diverse user community served by the PDB and the increasingly richness of solved structures. The 3DB schema supports queries by those interested in answering both crystallographic questions and molecular biology questions. 3DB was designed as an open system, with the expectation that it will shortly be federated with other biological databases, allowing complex queries to be submitted to our database, returning a composite answer built from partial answers that traverse several databases.
A querying tool for accessing this database, 3DB browser , has been developed using readily available elements, like the perl [1] programming language, Web/Genera [2] software toolset and the Glimpse [3] indexing and query system. Users specify search criteria by filling out an HTML form. Software at BNL processes this form and generates the required SQL. System performance is improved by using stored SYBASE SQL procedures that access each predefined object. The fields available are similar to those in our PDBBrowse program, and answer most of the questions that users have been asking.
For those familiar with (or willing to learn about) the OPM protocol [4], access to the object layer will be provided using a high level OPM-based query language. As part of the 3DB open database policy, direct access to the underlying RDBMS will be allowed and actively supported. These queries are not parsed by the 3DB-QA module, so better response time can be expected. This provides third-party developers with the opportunity to either incorporate SQL clients in their products or to learn more of the OPM protocol and, thereby, gain access to all of the benefits that the Object model affords (e.g., active external links, programs, etc.).
The output generator will return query results using a variety of data
interchange formats. PDB will continue to support its current format
in the foreseeable future. We also plan to extend this format to
allow us to represent objects being stored in 3DB. In addition, a "raw
format" is being provided which returns an attribute/value pair. This
form is easily parsed and is more compact than the PDB format.
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