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saezlab / cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
https://saezlab.github.io/cosmosR/
GNU General Public License v3.0
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metabolic IDs seem to be inconsistent #21

Closed gabora closed 4 months ago

gabora commented 2 years ago

Hi @adugourd ,

I found Metab__HMDB0001514_c and also Metab__439213_c in the PKN, but based on this: https://hmdb.ca/metabolites/HMDB0001514 they both encode "D-Glucosamine".

Unfortunately, in the PKN, they have different reaction partners, so they are not representing the same metabolite:

interactions based on HMBD: > meta_network[meta_network$source=="Metab__HMDB0001514_c",]

                source interaction                   target

48415 MetabHMDB0001514_c -1 IL1B 81712 Metab__HMDB0001514_c 1 Gene9119GCK 81714 MetabHMDB0001514_c 1 Gene9119HK2 81716 MetabHMDB0001514_c 1 Gene9119HK1 81718 MetabHMDB0001514_c 1 Gene9119HKDC1 81720 MetabHMDB0001514_c 1 Gene9119HK3 83913 MetabHMDB0001514_c 1 Gene9717HK1 83917 MetabHMDB0001514_c 1 Gene9717HK2 83921 MetabHMDB0001514_c 1 Gene9717HK3 83925 MetabHMDB0001514_c 1 Gene9718HK1 83929 MetabHMDB0001514_c 1 Gene9718HK2 83933 MetabHMDB0001514_c 1 Gene9718HK3 93661 MetabHMDB0001514_c 1 Gene8990__SLC2A1_reverse 93663 MetabHMDB0001514_c 1 Gene8990SLC2A4_reverse 93665 Metab__HMDB0001514_c 1 Gene8990SLC2A2_reverse

interactions based on PubChem id:

> meta_network[meta_network$source=="Metab__439213_c",] source interaction target 35844 Metab__439213_c -1 MMP9 47070 Metab__439213_c -1 NFKB2

This seems to be inconsistent. How could be this solved? thanks Attila

adugourd commented 2 years ago

ah I see, thanks for noticing this. The second one comes from STITCH db and the first one from HMDB. In theory I should have translated the 49213 to hmdb format as well, dont know what happened here. I will double check the STITCH part of the code ASAP !