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draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
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Adding Subsystem Annotation for models without Model BiGGId in BiGG #97

Closed mephenor closed 4 years ago

mephenor commented 4 years ago

As discussed in https://github.com/SBRG/bigg_models/issues/362, this would be a nice feature to have and could be implemented easily. Using only reaction BiGGIds, unique subsystems or those with multiple entries differing only in case could be added as groups to models without model BiGGId. This way the majority of subsystem information could be added, if a valid reaction BiGGId is present or can be retrieved. This would still require manual validation of resulting subsystem information by the user, as subsystem information might be missing in the resulting model due to ambiguity of the information in BiGG or might not be applicable to the model in question.

Should this be something ModelPolisher does by default or should this behavior be toggled by another flag?

mephenor commented 4 years ago

This behavior is now implemented in the 2.1 branch and prints a warning message to check the obtained subsystems.