Abstract
In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape ( http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a variety of Cytoscape apps. From the analyzed data, users can create complex and interactive visualizations which cannot be done in the KEGG PATHWAY web application. Experimental data with Affymetrix E. coli chips are used as an example to demonstrate how users can integrate pathways, annotations, and experimental data sets to create complex visualizations that clarify biological systems using KEGGscape and other Cytoscape apps.
Highlights
Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg)[1] is a widely used biological database of high-level biological functions
Most biological pathway databases store data as machinereadable graph topologies, which leave much of the details about how the diagrams were drawn excluded from the data files
The KEGG PATHWAY database stores graphics information in machine-readable KEGG Markup Language (KGML, http://www.kegg.jp/kegg/xml) format. In these pathway diagrams, biological entities, such as enzymes or compounds, are manually laid-out and the diagrams are easy to understand for biologists
Summary
The Introduction sufficiently explains the setting of the plugin. One thing that strikes me is the lack of references to related work. Given the enormous impact of KEGG it can be wondered why this kind of integration with KEGG has not been done yet, because people have done this for other data sets for years (both open source and proprietary). The first data-loss clearly indicates a problem with the reader These things must be discussed in the Limitations subsection, in my opinion (and/or returned to in the Future Plan at the end). I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, I have significant reservations, as outlined above
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