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Comment by dnautics | Hacker News Reader

I love the Roche charts, but I also always wanted a more rational organization to them, perhaps at least regionally organized such that on one axis number of carbons and on another axis net oxidation state of total carbon.

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Using Pathway Tools, the pathways are automatically laid out for you in a rational manner, organizing pathways and super-pathways based on a manually-curated ontology. For example, all biosynthetic pathways are displayed side by side. Wall charts dazzle with their complexity, but it isn't the best layout for organizing information.

One of my professors (in medical school) pointed out that these posters are great for learning the chemistry, but aren't very useful to us students because they don't show you what cells/tissues these processes are happening in.

A problem with these wall charts and the KEGG diagrams is that not only do you not know which enzymes or pathways are active in which tissues within a single multi-cellular organism, you don't know which organisms they come from. These pathway charts are actually mosaic pathways, trying to show a summary of metabolism across all domains of life. This can be misleading, in that no one organism contains all parts as displayed.

KEGG filters for organism, although it's automated and not 100% correct.

There's also a lot that's not on either map, like specialized secondary metabolite synthesis pathways (although kegg has select secondary pathways).

KEGG filters at the MAP or MODULE level, but it merely highlights the enzymes of the mosaic MAP/MODULE that it inferred is present in the organism, rather than display the subset of the network that is actually present.

I agree with you regarding their mutual incompleteness. There's plenty more literature to curate! See my systematic omparison of KEGG and MetaCyc for more details:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665663/

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