This service provides three options to map a model to the MNXref namespace
Independent of the selected option, the following identifiers are recognized and mapped to the MNXref namespace
- no - keeps the model as is; however some functionalities of the web site are unavailable
- medium - uses identifiers of chemical compounds and cellular compartments for the mapping (without using additional information that is available in the descriptions and notes)
- all - uses identifiers, descriptions and notes for the mapping (which is slightly more risky
- the special identifiers: BIOMASS, MNXDX and BOUNDARY
- the identifiers describing chemical compounds, i.e. metabolites with the prefix MNXM (e.g. MNXM10)
- the identifiers describing cellular compartments with the prefix MNXC (e.g. MNXC3); and with the prefix MNXD for the generic compartments
- the identifiers of the form database:entry are mapped to the MNXref namespace if possible, e.g. CHEBI:15422. Note that this feature is not supported for SBML model
- identifiers with the prefixes my_ or user_ are never be mapped to the MNXref namespace
- chemical compounds or cellular compartments not participating in any reaction are automatically removed
||The following file formats are supported
The syntax for text files / Excel spreadsheet is given in the model internals documentation.
- TAB-delimted files within a compressed archive .tar.gz with the proper filenames
- Excel Spreadsheet .xls with the proper sheet names
- SBML file .xml, version 2 and 3 are supported
Regarding the SBML file, cross references can be supplied using MIRIAM-compliant annotations or using XML notes and can be used to establish the mapping to MNXref.
Since, metabolic networks are complex objects combining biochemical, genetic, and genomic information, we recommend new MetaNetX users to practice the following steps
- Pick a model from the repository (e.g. bigg_iAF1260)
- Export it as an SBML file, or as a compressed text file, or as an Excel spreadsheet (recommended for this exercise)
- Introduce a small modification in the downloaded model, for example, modify the flux constraints on a single boundary (external) reaction
- Upload the modified model under a new name
- Use MetaNetX.org to compare the original model with the modified one
||MetaNetX is not responsible for malformed file or syntax errors and will not offer user support on these issues.
We are unfortunately aware that some public genome-scale metabolic networks distributed in SBML format are not 100% compliant with the SBML specifications. As a consequence, their import might be problematic. We recommend to check if a version of such model already exists in the MetaNetX repository.