kozo2 / f1000keggscape Goto Github PK

Matthew DeJongh

• the authors do not cite the origin of the gene expression dataset they use in their example.

Egon Willighagen

• One thing that strikes me is the lack of references to related work. For example, it mentions "most biological pathway databases" without citing or even naming them, which I find suboptimal as they critique those databases and to which the authors contrast their solution. Unlike the Introduction currently seems to suggest, KGML is not the only pathway format that tracks graphical information (e.g. GPML used by PathVisio).