Journal Article

HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees.

Y Zhong, Y Luo, S Pramanik and J H Beaman

in Bioinformatics

Volume 15, issue 2, pages 149-156
Published in print February 1999 | ISSN: 1367-4803
Published online February 1999 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/15.2.149
HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees.

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MOTIVATION: Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups. RESULTS: An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees. AVAILABILITY: Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/ CONTACT: pramanik@cps.msu.edu; lotus@wipm.whcnc.ac.cn

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Subjects: Bioinformatics and Computational Biology

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