XML-based approaches for the integration of heterogeneous bio-molecular data

• Published in: BMC bioinformatics 2009-10, Vol.10 Suppl 12 (S12), p.S7-S7, Article S7
• Main Authors: Mesiti, Marco, Jiménez-Ruiz, Ernesto, Sanz, Ismael, Berlanga-Llavori, Rafael, Perlasca, Paolo, Valentini, Giorgio, Manset, David
• Format: Article
• Language: English
• Subjects: Computational Biology - methods; Databases, Factual; Databases, Genetic; Genomics; Mutation; Polymorphism, Genetic; Programming Languages
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-10-S12-S7

The 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. 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. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML 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.