I'd like to add this model of Methylococcus capsulatus Bath to BiGG which I built as part of my Ph.D. a while ago.
We encourage contributions of models to BiGG. The following are the minimal requirements for acceptance into the knowledge base:
A genome-scale metabolic network reconstruction that has been published in a peer-reviewed journal
The accession ID for a NCBI RefSeq genome annotation. In some cases, we can accept genome annotations in Genbank format, but we prefer annotations from a well-known genome repository.
Reactions, metabolites, and compartments using the BiGG Models namespace
To my knowledge, this is the case. When building the model I did stumble over a few ambiguous reaction IDs i.e. IDs with suffixes (x, y, i) etc. which might have lead to me picking wrong IDs to some reactions in the model. In addition, I had to create IDs for some metabolites and reactions which I could not identify to already exist in BiGG. According to the memote snapshot report, however, both metabolite and reaction IDs mostly match the BiGG namespace.
Gene identifiers that match locus tags from the genome annotation
All gene IDs are within the MCA[0-9] scheme and match the Genbank locus tags.
Hi there SBRG BiGG team,
I'd like to add this model of Methylococcus capsulatus Bath to BiGG which I built as part of my Ph.D. a while ago.
The model has been published in Frontiers in Microbiology
Is available here: https://github.com/ChristianLieven/memote-m-capsulatus/tree/master/ModelFiles
Unfortunately, only Genbank is available: https://www.ncbi.nlm.nih.gov/nuccore/AE017282.2
To my knowledge, this is the case. When building the model I did stumble over a few ambiguous reaction IDs i.e. IDs with suffixes (x, y, i) etc. which might have lead to me picking wrong IDs to some reactions in the model. In addition, I had to create IDs for some metabolites and reactions which I could not identify to already exist in BiGG. According to the memote snapshot report, however, both metabolite and reaction IDs mostly match the BiGG namespace.
All gene IDs are within the
MCA[0-9]
scheme and match the Genbank locus tags.Let me know if you have any further questions!