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lozuponelab / AMON

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data
MIT License
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AMON is getting no reactions from the KOs... #19

Closed sterrettJD closed 8 months ago

sterrettJD commented 8 months ago

This is a new issue...

With polyomic dataset

Total number of KOs: 12707 Total number of reactions: 0 ... Number of cos produced across samples: 0

Previously was:

Total number of KOs: 717 Total number of reactions: 1019 ... Number of cos produced across samples: 796

REACTION was added 2 weeks ago the to KEGG_Parser KO not captured fields - I wonder if something is going on there. If it isn't there, the parser errors with "What is REACTION in ?"

sterrettJD commented 8 months ago

Seems like KEGG moved RN from DBLINKS to its own field named REACTION! KEGG_Parser needs to be updated to address this.

Used to look like:

ENTRY       K00006                      KO
SYMBOL      GPD1
NAME        glycerol-3-phosphate dehydrogenase (NAD+) [EC:1.1.1.8]
PATHWAY     map00564  Glycerophospholipid metabolism
            map01110  Biosynthesis of secondary metabolites
            map04011  MAPK signaling pathway - yeast
DISEASE     H00728  Brugada syndrome
BRITE       KEGG Orthology (KO) [BR:ko00001]
             09100 Metabolism
              09103 Lipid metabolism
               00564 Glycerophospholipid metabolism
                K00006  GPD1; glycerol-3-phosphate dehydrogenase (NAD+)
             09130 Environmental Information Processing
              09132 Signal transduction
               04011 MAPK signaling pathway - yeast
                K00006  GPD1; glycerol-3-phosphate dehydrogenase (NAD+)
            Enzymes [BR:ko01000]
             1. Oxidoreductases
              1.1  Acting on the CH-OH group of donors
               1.1.1  With NAD+ or NADP+ as acceptor
                1.1.1.8  glycerol-3-phosphate dehydrogenase (NAD+)
                 K00006  GPD1; glycerol-3-phosphate dehydrogenase (NAD+)
DBLINKS     COG: COG0240
            GO: 0004367
            RN: R00842

Now this is the format:

ENTRY       K00006                      KO
SYMBOL      GPD1
NAME        glycerol-3-phosphate dehydrogenase (NAD+) [EC:1.1.1.8]
PATHWAY     map00564  Glycerophospholipid metabolism
            map01110  Biosynthesis of secondary metabolites
            map04011  MAPK signaling pathway - yeast
REACTION    R00842  sn-glycerol-3-phosphate:NAD+ 2-oxidoreductase
DISEASE     H00728  Brugada syndrome
BRITE       KEGG Orthology (KO) [BR:ko00001]
             09100 Metabolism
              09103 Lipid metabolism
               00564 Glycerophospholipid metabolism
                K00006  GPD1; glycerol-3-phosphate dehydrogenase (NAD+)
             09130 Environmental Information Processing
              09132 Signal transduction
               04011 MAPK signaling pathway - yeast
                K00006  GPD1; glycerol-3-phosphate dehydrogenase (NAD+)
            Enzymes [BR:ko01000]
             1. Oxidoreductases
              1.1  Acting on the CH-OH group of donors
               1.1.1  With NAD+ or NADP+ as acceptor
                1.1.1.8  glycerol-3-phosphate dehydrogenase (NAD+)
                 K00006  GPD1; glycerol-3-phosphate dehydrogenase (NAD+)
DBLINKS     COG: COG0240
            GO: 0004367
sterrettJD commented 8 months ago

Addressed in https://github.com/lozuponelab/AMON/pull/20