The list of replacement BiGG identifiers (rxns, mets) contain new BiGG-style identifiers when no official BiGG identifier could be found. However, these files contain entries where valid BiGG IDs do exist.
Expected feature/value/output:
E.g. r_0005 and r_0006 refer to 1,3-beta-glucan synthase and 1,6-beta-glucan synthase. In BiGG, these are 13GS and 16GS.
Current feature/value/output:
Suggested replacement BiGG IDs are: 13BETGLUSYN and 16BETGLUSYN
Solution:
More thoroughly curate the list where no BiGG ID was found. For instance, the earliest S. cerevisiae models (iND750, iMM904) actually used BiGG identifiers. Matching these to the yeast-net style identifiers (s_0001 and r_0001) is not that straightforward, as these yeast-net identifiers were reassigned in earlier releases. So r_0006 in Yeast7 is not the same as r_0006 in Yeast4.
Description of the issue:
The list of replacement BiGG identifiers (rxns, mets) contain new BiGG-style identifiers when no official BiGG identifier could be found. However, these files contain entries where valid BiGG IDs do exist.
Expected feature/value/output:
E.g.
r_0005
andr_0006
refer to 1,3-beta-glucan synthase and 1,6-beta-glucan synthase. In BiGG, these are 13GS and 16GS.Current feature/value/output:
Suggested replacement BiGG IDs are:
13BETGLUSYN
and16BETGLUSYN
Solution:
More thoroughly curate the list where no BiGG ID was found. For instance, the earliest S. cerevisiae models (iND750, iMM904) actually used BiGG identifiers. Matching these to the yeast-net style identifiers (
s_0001
andr_0001
) is not that straightforward, as these yeast-net identifiers were reassigned in earlier releases. Sor_0006
in Yeast7 is not the same asr_0006
in Yeast4.I hereby confirm that I have:
main
branch of the repository