bug: unnecessary invalid BiGG identifiers suggested

[edkerk]

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 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.

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Done this analysis in the main branch of the repository
• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue

[mihai-sysbio]

I would suggest looking into an automatic way of keeping annotation updated.