OBO-Edit:Reasoner Repair Mode

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Repair mode is a conservative way of using the reasoner. It is to be contrasted with reasoner-dependency mode, in which the EDITOR'S version of the ontology must be edited with the reasoner on. This is the case for SO and for fly_anatomy.

In repair mode, links that can be implied by the reasoner from cross-products are asserted in the ontology. This means the reasoner will think these are redundant (in reasoner dependency mode, these links are never asserted. The editor lets the reasoner do everything). The reasoner can be periodically invoked by the editor to find missing links. These links can then be semi-automatically asserted (see the Edit menu option, "assert implied links") into the ontology, post-approval.

Repair mode is compatible with a workflow in which xps are maintained externally to the core ontology. For example, two files:

  • gene_ontology_write.obo
  • go_xp_regulation.obo

(for more see XP:biological_process_xp_regulation)

The editor has the option of loading just the core, or the core + xps.

If they do the latter then they have the additional burden of configuring OE to save the xps into the separate file.

This can be done in such a way that OE1 is used to edit/examine the core and OE2 is used to load both and use the reasoner to assert implied links