Roche Biochemical Pathways charts – navigable and annotated | Hacker News Reader

Roche Biochemical Pathways charts – navigable and annotated

roche.com

72 pointsmfringel17 comments

The Roche Biochemical Pathways charts were the inspiration for the MetaCyc family of pathway/genome databases, all enabled by the Pathway Tools software (itself written with 400,000+ lines of Common Lisp):

Example pathway: Super-Pathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass

http://www.metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=GL...

MetaCyc has an order of magnitude more information integrated into it than most wall charts. Plus, you can get true interactive metabolic overview maps, where you can click on the enzymes and compounds (example from the E. coli database):

http://www.ecocyc.org/overviewsWeb/celOv.shtml (be sure to zoom in and click on things!)

The Pathway Tools software, and the metabolic networks, are freely available for academic use, and you can use it to construct your own metabolic networks.

Full disclosure: I'm a former full-time bioinformaticist on the project.

I have been looking for this for years. It used to be from Boeringer Mannheim, you could jsut write a letter and they would send a copy for free (I was a biochem major and kept a copy on my wall). After a year of biochem, I could recognize most the elements and had memorized a significant fraction of the chart. This chart represent a collection of monumental knowledge and achievement in biochemistry over the past 100 years.

KEGG is what you're looking for. The Roche charts are beautiful but not really that great in terms of navigability. KEGG annotates organisms over the 'full chart' so you can see which pathways are thought to be active in that organism based on sequencing results. E.G. for humans -

http://www.kegg.jp/kegg-bin/show_pathway?hsa00360

If you need the full pathway map, you can see them e.g.:

http://www.kegg.jp/kegg-bin/show_pathway?hsa01100

No. I mean I've been looking for that poster online, for the nostalgia.

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.

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/

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.

just use the contact form and they will send you a real poster for free

http://lifescience.roche.com/shop/en/us/store/contact-us?mes...

Apparently, not for medical students. This is what their service rep responded:

>For life science research only. Not for use in diagnostic procedures.

I'm not sure how you'd use them for diagnosis. Maybe to check someone's eyesight?

Yup! When I was in college I ordered 3 for me and my biochemistry-majoring roommates. We mounted one of them on the wall right across the toilet.

Wow, 49 years of refinement - there's an intellectual legacy to be proud of. I know virtually nothing of biochemistry but resources like this are wonderful for gaining a sense of what there is to learn and how fundamental things relate to each other. It's rare to see such a comprehensive and beautifully curated map.

Sure, this chart[1] may look impressive, but trust me, we don't understand nearly enough about human metabolism to create a product like Soylent. /s

1: http://biochemical-pathways.com/#/map/1

The size of a chart, and a quantity of the unknown (the knowledge needed to safely produce a dietary replacement) is a pretty silly comparison, ignoring the intended snark.

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