## Journal article: Visual Understanding of Metabolic Pathways Across Organisms using Layout in Two and a Half Dimensions

No Thumbnail Available
2004
Dwyer, Tim
Journal article
##### Abstract
We propose a method for visualizing a set of related metabolic pathways across organisms using 2 1/2 dimensional graph visualization. Interdependent,two-dimensional layouts of each pathway are stacked on top of each other so that biologists get a full picture of subtle and significant differences among the pathways. The (dis)similarities between pathways are expressed by the Hamming distances of the underlying graphs which are used to compute a stacking order for the pathways. Layouts are determined by a global layout of the union of all pathway graphs using a variant of the proven Sugiyama approach for layered graph drawing. Our variant layout approach allows edges to cross if they appear in different graphs.
##### Subject (DDC)
004 Computer Science
##### Published in
Journal of Integrative Bioinformatics ; 1 (2004), 1. - 2
##### Cite This
ISO 690BRANDES, Ulrik, Tim DWYER, Falk SCHREIBER, 2004. Visual Understanding of Metabolic Pathways Across Organisms using Layout in Two and a Half Dimensions. In: Journal of Integrative Bioinformatics. 1(1), 2. Available under: doi: 10.2390/biecoll-jib-2004-2
BibTex
@article{Brandes2004Visua-5694,
year={2004},
doi={10.2390/biecoll-jib-2004-2},
title={Visual Understanding of Metabolic Pathways Across Organisms using Layout in Two and a Half Dimensions},
number={1},
volume={1},
journal={Journal of Integrative Bioinformatics},
author={Brandes, Ulrik and Dwyer, Tim and Schreiber, Falk},
note={Article Number: 2}
}

RDF
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:void="http://rdfs.org/ns/void#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#" >
<rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/5694">
<dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
<bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/5694"/>
<dc:rights>Attribution-NonCommercial-NoDerivs 2.0 Generic</dc:rights>
<dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/5694/1/metabolic.pdf"/>
<dcterms:bibliographicCitation>First publ. in: Journal of Integrative Bioinformatics 1 (2004), 1, Article 2</dcterms:bibliographicCitation>
<foaf:homepage rdf:resource="http://localhost:8080/"/>
<dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
<dc:creator>Brandes, Ulrik</dc:creator>
<dcterms:title>Visual Understanding of Metabolic Pathways Across Organisms using Layout in Two and a Half Dimensions</dcterms:title>
<dcterms:issued>2004</dcterms:issued>
<dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/5694/1/metabolic.pdf"/>
<dc:contributor>Dwyer, Tim</dc:contributor>
<dc:format>application/pdf</dc:format>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2011-03-24T15:59:25Z</dc:date>
<void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
<dc:creator>Dwyer, Tim</dc:creator>
<dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2011-03-24T15:59:25Z</dcterms:available>
<dc:contributor>Brandes, Ulrik</dc:contributor>
<dcterms:abstract xml:lang="eng">We propose a method for visualizing a set of related metabolic pathways across organisms using 2 1/2 dimensional graph visualization. Interdependent,two-dimensional layouts of each pathway are stacked on top of each other so that biologists get a full picture of subtle and significant differences among the pathways. The (dis)similarities between pathways are expressed by the Hamming distances of the underlying graphs which are used to compute a stacking order for the pathways. Layouts are determined by a global layout of the union of all pathway graphs using a variant of the proven Sugiyama approach for layered graph drawing. Our variant layout approach allows edges to cross if they appear in different graphs.</dcterms:abstract>
<dcterms:rights rdf:resource="http://creativecommons.org/licenses/by-nc-nd/2.0/"/>
<dc:contributor>Schreiber, Falk</dc:contributor>
<dc:language>eng</dc:language>
<dc:creator>Schreiber, Falk</dc:creator>
</rdf:Description>
</rdf:RDF>

Yes