Abstract
BackgroundThe today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing.ResultsIn this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML.ConclusionXML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.
Highlights
Convergent advances in biochemistry techniques, biotechnologies, information technology and computer science provided the basis for the development of bioinformatics and made available huge and growing amounts of biological data [1].(page number not for citation purposes)BMC Bioinformatics 2009, 10(Suppl 12):S7 http://www.biomedcentral.com/1471-2105/10/S12/S7Today’s public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising new problems for their integration and computational processing
The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources
XML provides a large set of other recommendations, standards and approaches that can be exploited for the representation and management of XML within database systems: query languages for querying collections of XML documents and obtaining adequate results; transformation facilities (XSLT [8]), for the presentation of the document contents with different formats (HTML, pdf, doc, etc.); description of schema information (DTD and XML Schema [9]) to enforce integrity constraints; SQL extension to handle at the same timerelational and XML data (SQL/XML facilities [19]); indexing structures ([20]) for the efficient evaluation of queries
Summary
In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches.
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