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bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement
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How to obtain parent taxonomy level for metabolic pathways? #61

Closed roman-spanek closed 5 years ago

roman-spanek commented 5 years ago

Dear Jeff, thank you very much for Paprica, it is a great software. May I ask you, I was wondering if there is an easy (semi/automated) way how to group identified pathways into a higher level. I mean in your paper Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula you have a nice figure 6. Metabolic pathways differentially present between summer surface samples and winter and deep samples. where you did group pathways into higher taxonomic level – e.g. Anaerobic metabolism, Nitrogen degradation etc.

Thank you very much.

Roman

bowmanjeffs commented 5 years ago

We don't have a built-in way to do this as many pathways can be assigned to multiple higher level "taxonomies". The best thing to do is use BioCyc to create your own hierarchy for pathways of interest.