©1996-2009 All Rights Reserved. Online Journal of Bioinformatics. You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJVR publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors.
OJBTM
Online Journal of Bioinformatics
Volume 1 (1): 12-21, 2000.
Bioinformatics and Extended Markup Language (XML).
*Vincent H Guerrinia and David Jacksonb
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
©1996-2004 All Rights Reserved. Online Journal of Bioinformatics. You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJVR publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors.