Disallow inferred equivalencies when reasoning. #56
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Make ROBOT fail when the reasoner finds inferred equivalent classes.
As recommended by Chris Mungall (rationale) and Nico Matentzoglu on Slack.
As for the other FlyBase ontologies:
assert-only
CL:0000003
(cell
) andGO:0005623
) (obsolete GO term forcell
); that equivalence is brought in by CARO, whose termCARO:0000013
still refers toGO:0005623
even though it has been obsoleted (Remove GO:cell obophenotype/caro#23); if we can get that fixed in CARO, then we should be able to switch theallow_equivalents
setting in DPO fromall
toassert-only
.