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CobraBabel: COBRA Model Translator

Project description

Metabolic models are available from many sources and different sources use different ID namespaces. That makes combining and comparing models from different sources difficult. CobraBabel provides functions to translate between ID namespaces and convert metabolic models to a common ID namespace. CobraBabel supports the following namespaces:

  1. ModelSEED
  2. Virtual Metabolic Human (VMH)
  3. Biochemical, Genetic and Genomic knowledge base (BiGG)
  4. MetaNetX
  5. Kyoto Encyclopedia of Genes and Genomes (KEGG)

Features include:

  1. Take a list of models, open all of them, create a universal model with all unique reactions and metabolites.
  2. Download specific files, can get the whole BiGG database, VMH mapping file, MetaNetX translation file.
  3. Function to convert compartment suffixes.
  4. Import from a Excel file or csv file.
  5. ID match without special characters

VMH Notes

VMH provides a SEED2VMH_translation.csv file which is not current with the translation table in Supplementary Table 15 in the AGORA paper. Supplementary Table 15 is provided as an Excel workbook which was parsed into two files: (1) vmh_metabolite_xref.tsv and (2) vmh_reaction_xref.tsv which are provided in the “data” folder.

BiGG Notes

Universal metabolites can have more than one formula if different models use a different formula for a metabolite with the same ID (same situation can occur with charge). Currently, CobraBabel blindly picks the first formula in the list of formulae for a universal metabolite.

Universal metabolites have a list of all the compartments where the metabolite is used. Currently, CobraBabel assumes that all compartment IDs are defined the same across all models. For example, compartment ID “c” means “cytosol” in all BiGG models. The first instance of the compartment in a metabolite is the one that sets the name.

MetaNetX Notes

Some reactions are defined with unspecified stoichiometry coefficients, for example: (2n) MNXM1471 + 1 MNXM3341 = (2n) MNXM1 + 1 MNXM4074 + (2n) MNXM537. Currently, CobraBabel does not include these reactions when creating an universal model.

There are some reactions where there is a BIOMASS metabolite in the reaction definition. But the BIOMASS metabolite is not defined so any reactions with the BIOMASS metabolite are not included in the universal model.

If a reaction has a value in the Source field, there is only one source in the format: source:id. Sources include Rhea (rhea), KEGG (kegg), MetaCyc (metacyc), UniPathway (upa), The Seed (seed), BiGG (bigg), BioPath (biopath), and Reactome (reactome). Set the verbose parameter when calling create_metanetx_universal_model() to show a warning for reactions with an invalid format in the Source field.

There are no compartments so metabolites are defined without a compartment. Still not sure how exchange and transport reactions are defined.

All reactions are defined as bi-directional so the lower and upper bounds are set to the default values (-1000.0, 1000.0) for all reactions.

KEGG Notes

There are some limitations on the KEGG API, most importantly:

Restrictions: KEGG API is provided for academic use by academic users belonging to academic institutions. This service should not be used for bulk data downloads. Please obtain KEGG FTP academic subscription for downloading KEGG data.

When setting OTU representatives in the organism database, there can be variability in which organism is selected when there are multiple good matches. For example, in the KEGG database there are two Mycobacterium tuberculosis H37Rv organisms, one with ID “T00015” and one with ID “T02178”. It is random as to which one gets picked as the OTU representative.

References

BiGG

MetaNetX.org: a website and repository for accessing, analyzing and manipulating metabolic networks. Bioinformatics (2013)

VMH

Project details


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