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This chapter has described and illustrated the use of object databases in bioinformatics applications It has been argued that object databases contain a range of modeling and programming facilities that makes them suitable for use with complex biological data The two principal weaknesses of the relational model limited modeling facilities and impedance mismatch-prone programming have limited its uptake in bioinformatics, in particular for use in systems that deal with the more complex data sets or that support sophisticated analyses The recent extensions to the relational model, in particular to support abstract data types (also known as data blades or cartridges), allow certain bioinformatics tasks to be supported much more effectively in the database than was previously the case For example, it is possible to envisage a data type sequence for storing protein sequences that supports homology-based sequence comparisons, searching for motifs, and construction of alignments.

Every system has a degree of ef ciency in processing raw materials, information, stimuli, cues, etc. As engineers, we assign an ef ciency metric that provides a ratio of the quantity of output produced for a known quantity on input. Every system has a level of integrity in its ability to deliver systems, products, and services as required despite operating constraints and conditions. To ensure success in accomplishing its mission, every system, product, or service requires resources such as personnel, funding, consumables, expendables; corrective and preventive maintenance; and support such as spares, supplies, and training. Some systems, namely businesses, promote their systems in anticipation of sales via demonstrations, advertising, etc. The promotion activities may require protection and security. EXAMPLE 4.5 A publisher plans to release a new book in a series on a speci c day and time, promote the book via advertising, and impose sale constraints and conditions on bookstore owners. The bookstore owners must keep the book under lock and key (protection) with 24 hour surveillance (security) until the of cial release.

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Every system and its missions may be threatened by competitors or adversaries in its operating environment that may exhibit friendly, benign, or hostile intentions or actions. Because of vulnerabilities or the need for the element of surprise, some systems require camou age or concealment to shield or alter their identity. Every system must have some level of protection to minimize its vulnerability to external threats. (continued)

Support for such facilities within the database would allow sequence analysis and other retrieval tasks to be conducted in a much more integrated environment than has traditionally been the case However, the ODMG standard also provides facilities that fit well with current trends in bioinformatics In particular, object-orientation in general is well suited for use with bioinformatics applications; in fact, all of object-oriented design, programming, and middleware are now prominent in research and development activities The close relationship between the ODMG model and models for design, programming, and interoperation of software systems means that ODMG databases can fit in well with existing technologies To date, a significant proportion of the object database activity in bioinformatics has made use of homegrown object models and systems [Gray 1990]; [Durbin 1991]; [Kosky 1998].

DMTF standards include the Common Information Model (CIM), communication/control protocols like Web-Based Enterprise Management (WBEM) and Web Services for Management (WS-Management), and the Systems Management Architecture for Server Hardware (SMASH) initiative. More information about DMTF s standards and activities can be found in Appendix B and at http://www.dmtf.org.

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This has limited reuse of ideas, software, interfaces, and experience across the different platforms, and has prevented bioinformatics activities from benefiting from the performance and scalability benefits of commercial products Although several industrial and research projects have made use of commercial object databases, such activities are quite thinly spread over organizations and problems However, the success of ACeDB as a repository for genomic data indicates that object database technology can have a significant impact in bioinformatics Furthermore, the rapidly changing face of bioinformatics, with new kinds of data and analyses in the postgenome sequencing phase, means that the data management challenges presented by bioinformatics applications are by no means on the wane.

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