Developing and Accessing Scientific Databases with the

The Object-Protocol Model (OPM) data management tools provide facilities for rapid development, documentation, and flexible exploration of scientific databases. The tools are based on OPM, an object-oriented data model which is similar to the ODMG standard, but also supports extensions for modeling scientific data. Databases designed using OPM can be implemented using a variety of commercial relational DBMSs, using schema translation tools that generate complete DBMS database definitions from OPM schemas. Further, OPM schemas can be retrofitted on top of existing databases defined using a variety of notations, such as the relational data model or the ASN.l data exchange format, using OPM retrojitting tools. Several archival molecular biology databases have been designed and implemented using the OPM tools, including the Genome Database (GDB) and the Protein Data Bank (PDB), while other scientific databases, such as the Genome Sequence Database (GSDB), have been retrofitted with semantically enhanced views using the OPM tools. Tools for querying (native or retrofitted) OPM databases include a query language translator, which interprets queries expressed in the OPM query language (OPM-QL) and translates them into the languages supported by the underlying DBMS. OPM-QL is similar to the ODMG standard for object-oriented database query languages, with extensions supporting the unique features of OPM. JAVA-based schema browsing and query tools provide access to OPM databases via the Web. The OPM schema browser allows exploring OPM schemas represented graphically, while the OPM query interface allows graphical construction of ad hoc OPM queries, and can also be used for generating HTML query forms. OPM schema publishing tools allow documenting OPM databases in a variety of formats and