Starting from a list of MicroCyc pathways predicted by the Pathway Tools software,
users are able to curate the prediction for a given organism by assigning different status.
Distinct pathway status are:
- predicted: predicted by the BioCyc pathologic algorithm (default one)
- validated: curated as a functional pathway (all the reactions of the pathway are supposed to exist in the organism)
- variant needed: the predicted pathway is not completely correct for the organism
(i.e. some reactions may not be present in the organism but no better pathway definition exists in MetaCyc). Thus, a new pathway variant definition is needed.
- unknown: not enough evidence to declare the pathway as functional (i.e. validated status)
- non functional: the pathway has been lost in the organism and is no more functional (i.e. due to gene loss or pseudogenisation events)
- deleted: curated as a false positive prediction