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Date

22. 3.2008 12:21:28

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Footnote

Relational database Management systems have been one of the great success stories of recent times and sensitive to the market, Most major vendors have responded by extending their products to handle XML data while still exploiting the range of facilities that a modern RDBMS affords. No book of this type would be complete without consideration of the "big these" (Oracle 9i, DB2, and SQL Server 2000 which each get a dedicated chapter) and though occasionally overtly piece-meal and descriptive the authors all note the shortcomings as well as the strengths of the respective systems. This part of the book is somewhat dichotomous, these chapters being followed by two that propose detailed solutions to somewhat theoretical problems, a generic architecture for storing XML in a RDBMS and using an object-relational approach to building an XML repository. The biography of the author of the latter (Paul Brown) contains the curious but strangely reassuring admission that "he remains puzzled by XML." The first five components are in-depth case studies of XMLdatabase applications. Necessarily diverse, few will be interested in all the topics presented but I was particularly interested in the first case study an bioinformatics. One of the twentieth century's greatest scientific undertakings was the Human Genome Project, the quest to list the information encoded by the sequence of DNA that makes up our genes and which has been referred to as "a paradigm for information Management in the life sciences" (Pearson & Soll, 1991). After a brief introduction to molecular biology to give the background to the information management problems, the authors turn to the use of XML in bioinformatics. Some of the data are hierarchical (e.g., the Linnaean classification of a human as a primate, primates as mammals, mammals are all vertebrates, etc.) but others are far more difficult to model. The Human Genome Project is virtually complete as far as the data acquisition phase is concerned and the immense volume of genome sequence data is no longer a very significant information Management issue per se. However bioinformaticians now need to interpret this information. Some data are relatively straightforward, e.g., the positioning of genes and sequence elements (e.g., promoters) within the sequences, but there is often little or no knowledge available an the direct and indirect interactions between them. There are vast numbers of such interrelationships; many complex data types and novel ones are constantly emerging, necessitating an extensible approach and the ability to manage semi-structured data. In the past, object databases such as AceDB (Durbin & Mieg, 1991) have gone some way to Meeting these aims but it is the combination of XML and databases that more completely addresses knowledge Management requirements of bioinformatics. XML is being enthusiastically adopted with a plethora of XML markup standards being developed, as authors Direen and Jones note "The unprecedented degree and flexibility of XML in terms of its ability to capture information is what makes it ideal for knowledge Management and for use in bioinformatics."
After several detailed examples of XML, Direen and Jones discuss sequence comparisons. The ability to create scored comparisons by such techniques as sequence alignment is fundamental to bioinformatics. For example, the function of a gene product may be inferred from similarity with a gene of known function but originating from a different organism and any information modeling method must facilitate such comparisons. One such comparison tool, BLAST utilizes a heuristic method has become the tool of choice for many years and is integrated into the NeoCore XMS (XML Management System) described herein. Any set of sequences that can be identified using an XPath query may thus become the targets of an embedded search. Again examples are given, though a BLASTp (protein) search is labeled as being BLASTn (nucleotide sequence) in one of them. Some variants of BLAST are computationally intensive, e.g., tBLASTx where a nucleotide sequence is dynamically translated in all six reading frames and compared against similarly translated database sequences. Though these variants are implemented in NeoCore XMS, it would be interesting to see runtimes for such comparisons. Obviously the utility of this and the other four quite specific examples will depend an your interest in the application area but two that are more research-oriented and general follow them. These chapters (on using XML with inductive databases and an XML warehouses) are both readable critical reviews of their respective subject areas. For those involved in the implementation of performance-critical applications an examination of benchmark results is mandatory, however very few would examine the benchmark tests themselves. The picture that emerges from this section is that no single set is comprehensive and that some functionalities are not addressed by any available benchmark. As always, there is no Substitute for an intimate knowledge of your data and how it is used. In a direct comparison of an XML-enabled and a native XML database system (unfortunately neither is named), the authors conclude that though the native system has the edge in handling large documents this comes at the expense of increasing index and data file size. The need to use legacy data and software will certainly favor the all-pervasive XML-enabled RDBMS such as Oracle 9i and IBM's DB2. Of more general utility is the chapter by Schmauch and Fellhauer comparing the approaches used by database systems for the storing of XML documents. Many of the limitations of current XML-handling systems may be traced to problems caused by the semi-structured nature of the documents and while the authors have no panacea, the chapter forms a useful discussion of the issues and even raises the ugly prospect that a return to the drawing board may be unavoidable. The book concludes with an appraisal of the current status of XML by the editors that perhaps focuses a little too little an the database side but overall I believe this book to be very useful indeed. Some of the indexing is a little idiosyncratic, for example some tags used in the examples are indexed (perhaps a separate examples index would be better) and Ron Bourret's excellent web site might be better placed under "Bourret" rather than under "Ron" but this doesn't really detract from the book's qualities. The broad spectrum and careful balance of theory and practice is a combination that both database and XML professionals will find valuable."

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Classification

303.48/33 22 (LoC)

DDC

303.48/33 22 (LoC)