The pathway names from HUMAnN 2.0 are too long...

[liaom...@gmail.com]

Hello, all

I find the pathway names obtained from HUMANN2 were too long, and then try to figure out if there is another way to show them. Then I found out:

There is a classification hierarchy for metabolic pathways

http://metacyc.org/META/class-tree?object=Pathways

Does anyone try to download this classification hierarchy and map to the pathway names obtained from HUMANN2 ? I do not know how to do it. Thanks

Best,

Ming

[Eric Franzosa]

Hi Ming,

I have experimented with parsing this hierarchy. You can find the resulting file here:

https://www.dropbox.com/s/ytk9v2sryxhelis/map_metacyc-pwy_lineage.tsv

This file is not officially supported by HUMAnN2 yet, but it does provide the mapping of individual MetaCyc pathways to their higher level categories. Perhaps it will be of some use to you?

Thanks,

Eric

[liaom...@gmail.com]

Thanks, Eric,

This is the information I am looking for, but it seems a slightly different from what we observe in the website. Probably it has been updated.

For example, one specific pathway I am interested in was GLUCONEO-PWY. In the output of Humann2, it is GLUCONEO-PWY : gluconeogenesis I

As shown in your file, it is

GLUCONEO-PWY Biosynthesis|Carbohydrates-Biosynthesis|CARBO-BIOSYNTHESIS|Gluconeogenesis

but in the website <http://metacyc.org/META/class-tree?object=Pathways>, it is

GLUCONEO-PWY Biosynthesis|Carbohydrates-Biosynthesis|Sugar Biosynthesis|gluconeognesis I



There is another pathway I obtained from Humann2, it is originally named " GLYCOLYSIS : glycolysis I (from glucose 6-phosphate)", but actually I cannot find it in your file.



Best,


Ming