Link path abundance to MetaCyc Superclasses

[Matteo Sange]

Hi, 

I have a question. I obtained the tratified output (i.e. _contrib.tsv) for EC, KO and path_abundance tables. Since I have very different microbiomes (gut, oral, milk and vaginal) at different timepoints, I want to explore the data as “classes of pathways” and get a sort of bird eye view, rather than analysing one single pathway at a time.

 

In stratified output there are columns function and taxon. The taxon is feature ID of ASV which I believe I can link to taxonomic nomenclature using the original .biom table that I provided as input (which I created via QIIME2)

 

Specifically I am interested in the column function of the pathway abundance file (path_abun_contrib.tsv). As I understand, the ID/acronyms are MetaCyc database ID. I would like to do two things:

1. Link the ID/acronyms to a human-readable name for that pathway
   
2. Very much like the taxonomic nomenclature, the pathways in MetaCyc are hierarchically organized. In the webpage it is visible under the section “Superclasses”. I would like to be able to retrieve this information and add it to my the path_abun_contrib.tsv file as (one or more) column “Superclass”.
   

 

In this way I believe I can merge pathways (row entry in path_abun_contrib.tsv file) to their common “Superclass” and analyse the relative contributions of organisms to that “Superclass of pathways”.

It is relatively simple if I had a “table” to link the acronyms to the pathway name or superclass. However, I never worked with MetaCyc before, and I wonder if there is a “table” or (more likely) a way to do that accessing the MetaCyc database.

 

I thank you in advance

[Gavin Douglas]

Hey there,

You can find a mapfile of pathway ids to descriptions here: https://github.com/picrust/picrust2/blob/master/picrust2/default_files/description_mapfiles/metacyc_pathways_info.txt.gz

Is this the kind of thing you were looking for?

Cheers,

Gavin

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[Matteo Sange]

Dear Gavin,

 Thank you. Yes, for the point 1 in my previous post, the table you provide is what I was looking for. But is there something similar for point 2? Basically a table that matches the pathway ID to “Superclasses” hierarchical order in which they are organized in MetaCyc.

The information is visible and accessible on a click-based format in the MetaCyc webpage, but I do not know how to retrieve, if there is already a way to download that information from somewhere. Here as example (https://metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5143) I click on “Fatty acids and Lipid Biosynthesis” (https://metacyc.org/META/NEW-IMAGE?type=ECOCYC-CLASS&object=Lipid-Biosynthesis).

The hierarchical order, I think, would help to isolate pathways as higher order groups. In my case I plan to combine my data with metabolomics as well. Then it would be much easier to select and compare, for example, “Fatty acids and Lipids metabolism” related data for the two omic datasets.

Best

Matteo

[Gavin Douglas]

Hi Matteo,

I don’t have a mapfile like that handy and I haven’t retrieved files from the MetaCyc website myself, sorry! Hopefully you can figure out a way to download that file. I agree that analyzing them as hierarchical groups makes sense.

Cheers,

Gavin

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[Matteo Sange]

Dear Gavin,

do you have any tip or direction where I may find it?
Thanks and best

Matteo

[Gavin Douglas]

Sorry I haven't looked at that website in a long time. You may be able to create a smart table with the subset of all superpathways, but I would have to play around with it myself to know the specifics.

Cheers,

Gavin

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[Matteo Sange]

Thanks, I did not knew that it was possible. I then I will have a look at the website and try to do that.

Best

Matteo

[Matteo Sange]

I found the solution. I post here in case someone elses has the same issue in future.

One can find "SmartTable" in MetaCyc --> https://metacyc.org/smarttables?tab=PUBLIC

There is already a "SmartTable" of pathways, that transform "Ontology -- all ancestors of entity" --> https://metacyc.org/group?id=biocyc14-463-3861279617  

This yield a full list of classes and superclasses for each pathway.  The table will act as a dictionary to reconstruct the pathway class hierarchy.

Best and thank you again Gavin,

Matteo

[Gavin Douglas]

Good to hear, and thanks for the info!

Gavin

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