differences between the various metacyc pathway files

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Billy Taj

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Oct 24, 2019, 5:56:41 PM10/24/19
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Hi, I'm trying to figure out what the differences are between:
- metacyc_pathways (mp)
- metacyc_pathways_structured (mps)
- metacyc_pathways_structured_filtered (mpsf)

what I think I know:
- (mpsf) is supposed to be pathways with more than 4 quantifiable reactions 
- (mp) is supposed to be a manifest of all constituent reactions within the pathway
- (mps) is supposed to be (mp), but structured for minpath, as it contains brackets and rules meant for pathway modelling

However: 
- (mps) seems to have more lines than (mp).  and more reactions.  

What were the purposes of these files? 
How were these files made?

Eric Franzosa

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Oct 25, 2019, 4:51:07 PM10/25/19
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Hi Billy,

"mp" is a legacy file intended to maintain compatibility with certain aspects of HUMAnN1. It is not used in the default HUMAnN2 workflows. Your understanding of "mps" and "mpsf" is otherwise correct, and "mpfs" is the default set of pathway definitions used by HUMAnN2 to quantify MetaCyc pathways from gene/reaction abundances.

These files are generated by parsing database files available with a MetaCyc account. The code responsible for this step is not a part of the HUMAnN2 distribution.

Thanks,
Eric



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