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kozo2/KEGGscape.md

Last active August 29, 2015 14:09
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KEGGscape.md

Matthew DeJongh

However, the example presented in the paper does not contain sufficient information to enable a reader to duplicate the process.

  • the authors do not cite the origin of the gene expression dataset they use in their example.
  • as far as I can tell, there is no tutorial provided with KEGGscape. At a minimum, the authors should provide instructions for opening a KGML file and loading a dataset.

Egon Willighagen

Melissa Cline

There are only two changes I would ask for:

  • First, the authors should mention that KGML files are currently freely available on the KEGG website. This will be news to some readers of this paper, since KEGG has gone through various distribution and licensing models.
  • Second, the authors should expand their discussion of merging gene expression data with KGML diagrams. The power of network visualization is in pathway data integration. If there are special challenges in integrating with KEGG pathways, these should be brought forth. The mention of custom python scripts and fuzzy ID matching suggests that this integration task can involve special challenges.
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