| What |
Comment |
| Mapping |
Independent of the selected option, the following identifiers will be recognized and mapped to the MNXref namespace in any case
- The special identifiers: BIOMASS, MNXDX and BOUNDARY
- Identifiers for chemical compounds, i.e. metabolites with prefix MNXM (e.g. MNXM3)
- Identifiers for cellular compartments with prefix MNXC (e.g. MNXC2); and with prefix MNXD for generic compartments
- Identifiers of the form database:entry will be mapped to the MNXref namespace, if possible (e.g. CHEBI:15422)
but
- Identifiers with prefix 'my_ or user_ will never be mapped to the MNXref namespace
- Chemical compounds or cellular compartments not participating in any reaction will be removed automatically
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| Format |
- Each line represents a biochemical reaction
- Comments start with # ignoring anything following on the considered line
- Identifiers for chemical compounds consist of alphanumeric characters and underscores:
- Chemical compounds with prefix MNXM are mapped to the corresponding entry in the MNXref namespace
- The special identifier BIOMASS marks the biomass reaction
- Identifiers of the form database:entry are mapped to the MNXref namespace, if possible (e.g. CHEBI:15422)
- Identifiers for cellular compartments consist of alphanumeric characters and underscores:
- Cellular compartments with prefix MNXC are mapped to the corresponding entry in the MNXref namespace
- The special identifier BOUNDARY represents the model boundary
- Chemical reactions are defined as:
- A set of substrates and a set of products separated by a reaction-arrow indicating the reaction's direction (-->, <--, <==>)
- Reactants may be associated with compartments if the identifiers for chemical compounds are joined by @ with the identifiers of cellular compartments (e.g. MNXM3@MNXC2 represents cytosolic ATP)
- Each reactant may be associated with a stoichiometric coefficient with or without parentheses separated by whitespace (e.g. 2 MNXM1 or 1.5 MNXM1); if no stoichiometric coefficient is supplied, the coefficient 1 is used per default; for polymerisation reaction non-numeric coefficients are supported if placed in parentheses, e.g. (n) and (n+1)
- Each set of reactants with or without stoichiometric coefficients (substrates or products) are separated by +
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| Nota bene |
This service is provided to ease the upload of a set of reactions.
Please consider the model upload service for uploading more complete and diverse information pertaining to metabolic networks. |
| Disclaimer |
MetaNetX is not responsible for syntax errors and will not offer user support on these issues |
