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Online Journal of Bioinformatics ©OJBTM

Volume 1 (1): 12-21, 2000.

Bioinformatics and Extended Markup Language (XML).

*Vincent H Guerrinia and David Jacksonb and a,bDistributed Systems Technology Centre (DSTC) Pty. Ltd, University of Queensland, Sr Lucia, Queensland 4172, Australia. Present address a Faculty of Sciences, University of Southern Queensland, Toowoomba, Queensland 4350 Australia

ABSTRACT

Guerrini VH, Jackson D,  Bioinformatics and extended markup language (XML), Online J Bioinformatics 1:1-13, 2000.  Bioinformatics is the application of computing to biology; it is mostly used in genomics.  Finding functional genes has become a priority since the human genome was sequenced. However, gene discovery by biologists is restricted by having to analyze multiple sequence databases, compare results from different algorithms, and compute and analyze alignments or linkage results at database level. This report constantly evaluates current terminology, Extended Markup language (XML) and Document Type Declarations (DTD's) genomic files, and genetic databases, for the purpose of creating efficient genomic interfaces. XML files are generated and parsed against their DTD's. Current evaluations suggest that the terminology used in XML-DTD's are not very informative. It was found that many of the current genomic DTD's consisted of general access, formatting, reference and genetic <ELEMENTS> for one XML file. Genetic databases frequently used different terms for the same item. The authors propose the use of more informative genetic terms and the separation of <ELEMENTS> in both XML files and databases.

KEY WORDS: XML, bioinformatics

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