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opencobra / cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.
http://opencobra.github.io/cobrapy/
GNU General Public License v2.0
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Metabolite ID conversion #952

Closed greenetarget closed 4 years ago

greenetarget commented 4 years ago

I've downloaded a model (in xml) made by others, metabolites are in SEED ID (eg. dATP is id="M_cpd00115_c0" name="dATP[c0]"),

Is there a way I can convert these IDs into "datp_c" style that is commonly used in many E coli models? from which database?

(I'm very new to this, any help will be much appreciated! thank you!)

Midnighter commented 4 years ago

Hi there,

The kind of identifier that you are looking for comes from BiGG. It is certainly possible to map SEED identifiers to BiGG ones but it may require a substantial amount of manual work since the identifiers do not always map 1:1.

A good starting point for attempting such a mapping is MetaNetX.