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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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Directionality on reactions for enrichm pathway/explore? #74

Closed TYMichaelsen closed 5 years ago

TYMichaelsen commented 5 years ago

Hi Joel,

Since you're doing a major upgrade - could you make the network being generated from the enrichm pathway and explore functions directional? This information would be very helpful for generating meaningful de-novo metabolic networks and is available in the KEGG database.

Best, Thomas

geronimp commented 5 years ago

Hi Thomas,

I'd love to include directionality but its not easy to do currently. The KEGG database provides directionality in its pathway maps, but the information is not easily accessed. You can find directionality if you parse pathway kgml files directly. However I suspect not providing the information openly is intentional, because the directionality of a reaction can depend on a lot of things and is rarely a "right" or "left" situation. The other choice would be to use KEGG's rpair database but to my knowledge support for that has been discontinued and they are no longer releasing updates. For now I'll add this as an enhancement and I'll look into it, but its unlikely to be in the next release as my thesis is looming and this is not a straight forward addition.

Thanks for the great suggestion though, I agree that it would be helpful

Thanks, Joel

TYMichaelsen commented 5 years ago

Hi Joel,

Thanks for the response. I see and you are right - the computationally generated reaction maps are far from (likely) what happens in the real world!

Good luck with your thesis and looking forward to a new release of enrichm!

Best, Thomas