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Upload a list of reactions

Options


Mapping option
Mapping option medium

Instructions

What Comment
Mapping This service provides two options to map a set of reactions to the MNXref namespace
  • no - keep the user reactions as they are
  • medium - utilize identifiers of chemical compounds and cellular compartments for the mapping (do NOT map regular names)
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
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 +
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