ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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incorrect KEGG Compound identifiers #4419

Closed egonw closed 1 year ago

egonw commented 1 year ago

In BridgeDb I get a warning that the following KEGG Compound identifiers have an unexpected format. I tried two, and indeed neither worked. The full list is:

$ head -1 ~/Downloads/chebi_database_accession.tsv
ID      COMPOUND_ID     SOURCE  TYPE    ACCESSION_NUMBER
$ grep "C-" ~/Downloads/chebi_database_accession.tsv  | grep "KEGG COMPOUND"
1057058 169879  KEGG COMPOUND   KEGG COMPOUND accession C-1079
1066416 173370  KEGG COMPOUND   KEGG COMPOUND accession C-1041
1066419 173371  KEGG COMPOUND   KEGG COMPOUND accession C-5141
1076346 177030  KEGG COMPOUND   KEGG COMPOUND accession C-8853
1076129 176967  KEGG COMPOUND   KEGG COMPOUND accession C-4569
1073463 176440  KEGG COMPOUND   KEGG COMPOUND accession C-4561
1077513 177494  KEGG COMPOUND   KEGG COMPOUND accession C-8875
1078805 177923  KEGG COMPOUND   KEGG COMPOUND accession C-8514
1088629 182011  KEGG COMPOUND   KEGG COMPOUND accession C-4179
1081362 179151  KEGG COMPOUND   KEGG COMPOUND accession C-1689
1081564 179249  KEGG COMPOUND   KEGG COMPOUND accession C-5011
1087520 180996  KEGG COMPOUND   KEGG COMPOUND accession C-1031
1083262 179946  KEGG COMPOUND   KEGG COMPOUND accession C-5116
1088057 181462  KEGG COMPOUND   KEGG COMPOUND accession C-1160
1090745 183289  KEGG COMPOUND   KEGG COMPOUND accession C-5733
1085610 180552  KEGG COMPOUND   KEGG COMPOUND accession C-6045
1106176 191088  KEGG COMPOUND   KEGG COMPOUND accession C-9227
1102416 189210  KEGG COMPOUND   KEGG COMPOUND accession C-8660
1115526 194669  KEGG COMPOUND   KEGG COMPOUND accession C-5242
amalik01 commented 1 year ago

These KEGG accessions came from the MetaboLights database. I have now removed all of the above KEGG accessions. Thank you.

egonw commented 1 year ago

thank!