To meet our internal requirements, we are storing models as TAB-delimited files according to the following specifications. Apart from the header lines, the Excel spreadsheets we are providing follow exactly the same syntax.
SBML files are also available and should allow data exchanges with other Web sites and tools.
|File/Sheet name||Column content|
When feasible, we strongly advise the users to utilize the same identifiers as defined in the MetaNetX repository. The special identifier BIOMASS must be used to specify the biomass.
When feasible, we strongly advise the users to utilize the same identifiers as already defined in the MetaNetX repository. The special identifier MNXDX must be used when the compartment is not known. The identifier BOUNDARY is reserved to specify the model boundary.
|enzymes||Additional information about the reactions are given here. It could be the description of the protein complex that catalyzes the reaction, if known. Also, the lower and upper bounds for the flow on the reaction can be specified. The direction can be B, LR or RL for bidirectional, left to right or right to left respectively.|
|peptides||Additional information about the peptides used to form enzymes are given here, if known.|
|properties||The results of the different model-specific analysis.|
Additional information about the reaction stoichiometries to ease parsing.
|ID||A reference identifier that satisfies the following requirements
In addition, the following recommendations holds
|EXT_ID||An external resource identifier. It is usually made of a database identifier, followed by ':', followed by an entry identifier or an accession number. For example: chebi:1234|
The equation of a compartmentalized reaction, written according to the following rules:
|ENZS||A list of enzymes able to perform a given reaction. Enzymes are separated by ';' and within an enzyme, proteins that form that enzyme are separated by '+'. The number of subunits of each protein is indicated by an integer followed by '*'. Nota bene: The syntax of this field is likely to be updated in the near future!|
|STRING||A string of characters, that does not contain TAB, CR or LF|
|REAL||A real number|
|INTEGER||An integer number (possibly negative)|