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Adding model of Methylococcus capsulatus Bath to BiGG #361

Open ChristianLieven opened 4 years ago

ChristianLieven commented 4 years ago

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.

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 model has been published in Frontiers in Microbiology

A COBRApy-compatible file (SBML, MAT, or JSON) representing all model content, ideally included as a supplementary file to the original publication

Is available here: https://github.com/ChristianLieven/memote-m-capsulatus/tree/master/ModelFiles

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.

Unfortunately, only Genbank is available: https://www.ncbi.nlm.nih.gov/nuccore/AE017282.2

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.

Let me know if you have any further questions!