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Validation

cy3sbml does not validate SBML. It imports every file that JSBML can read, also files with SBML errors, and converts what it finds. Check your models with an SBML validator before you rely on the import:

  • the online SBML validator of the SBML team,
  • libSBML, for example with python-libsbml,
  • sbmlutils, which reports validation and modeling practice warnings.

Files that cannot be read

If JSBML cannot read a file, for example because the XML is not well-formed or the file is not SBML, the import fails. Cytoscape shows one error message that names the file, a short cause (for XML errors with the line in the file), and the link to the SBML validator. No network is created. If the validator accepts the file, please report the problem with the file attached.

Annotation checks

The info panel checks the annotations of the selected object against the identifiers.org registry. It warns if an identifier does not match the identifier pattern of its data collection, and if a data collection is not in the registry.

Import warnings

Content that cy3sbml cannot convert is skipped with a warning in the log file (~/CytoscapeConfiguration/cy3sbml/cy3sbml-v<version>.log), for example the gene associations of fbc version 1, a layout that cannot be read, or an external file of the comp package that cannot be read. See Supported SBML packages.