Article

Towards a visual query interface for phylogenetic databases

Authors:

Hasan M. Jamil,

Giovanni A. Modica,

Maria A. TeranAuthors Info & Claims

CIKM '01: Proceedings of the tenth international conference on Information and knowledge management

Pages 57 - 64

https://doi.org/10.1145/502585.502596

Published: 05 October 2001 Publication History

Abstract

Querying and visualization of phylogenetic databases remain a great challenge due to their complex tree type semi structured nature. Naturally, successful phylogenetic databases such as the Tree of Life database at the University of Arizona are implemented as Web documents in HTML. While Web implementation of such databases facilitate the representation, and in part, visualization of their contents, querying remains an issue. The interoperability of Web-based phylogenetic databases with other similar databases such as TreeBase and RDB which are implemented using traditional database management systems, has not been possible due to the impedance mismatch between the underlying query and data representation framework. In this paper, we present a novel approach to phylogentic database management using existing database technologies without compromising potential opportunities for visualization and interoperability. We present a Web-based tool for the creation, querying and visualization of phylogenetic databases. We demonstrate the functional capabilities and strengths of our system by recreating the Tree of Life database in our system and performing queries that are not possible in the original Tree of Life database.

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Cited By

Chen LJamil HWang N(2004)Automatic composite wrapper generation for semi-structured biological data based on table structure identificationACM SIGMOD Record10.1145/1024694.102470433:2(58-64)Online publication date: 1-Jun-2004
https://dl.acm.org/doi/10.1145/1024694.1024704
Granda W(2003)Strategies for Clustering, Classifying, Integrating, Standardizing and Visualizing Microarray Gene Expression DataA Beginner’s Guide to Microarrays10.1007/978-1-4419-8760-0_8(277-340)Online publication date: 2003
https://doi.org/10.1007/978-1-4419-8760-0_8
Jamil HModica GTeran M(2001)Querying phylogenies visuallyProceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)10.1109/BIBE.2001.974405(3-10)Online publication date: 2001
https://doi.org/10.1109/BIBE.2001.974405

Index Terms

Towards a visual query interface for phylogenetic databases

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cover image ACM Conferences

CIKM '01: Proceedings of the tenth international conference on Information and knowledge management

October 2001

616 pages

ISBN:1581134363

DOI:10.1145/502585

Editors:
Henrique Paques
Georgia Institute of Technology
,
Ling Liu
Georgia Institute of Technology
,
David Grossman
Illinois Institute of Technology
,
General Chair:
Calton Pu
Georgia Institute of Technology

Copyright © 2001 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 05 October 2001

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Cited By

Chen LJamil HWang N(2004)Automatic composite wrapper generation for semi-structured biological data based on table structure identificationACM SIGMOD Record10.1145/1024694.102470433:2(58-64)Online publication date: 1-Jun-2004
https://dl.acm.org/doi/10.1145/1024694.1024704
Granda W(2003)Strategies for Clustering, Classifying, Integrating, Standardizing and Visualizing Microarray Gene Expression DataA Beginner’s Guide to Microarrays10.1007/978-1-4419-8760-0_8(277-340)Online publication date: 2003
https://doi.org/10.1007/978-1-4419-8760-0_8
Jamil HModica GTeran M(2001)Querying phylogenies visuallyProceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)10.1109/BIBE.2001.974405(3-10)Online publication date: 2001
https://doi.org/10.1109/BIBE.2001.974405

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