Annotation changes in how an ontology is marked up for use by GEEM in the last month will require updates to GEEM code to be compatible, so right now the GEEM scripts can only work on the FoodOn and GenEpiO ontology files from before April 25th. We will document the changes shortly. Suffice to say, GEEM was making reference too-directly to ontology contents using the "has component" relation, leading to contradictions when reasoners evaluated GEEM annotations in conjunction with umbrella ontology (e.g. BFO.owl) disjointWith clauses. That is resolved on the ontology side now.
Annotation changes in how an ontology is marked up for use by GEEM in the last month will require updates to GEEM code to be compatible, so right now the GEEM scripts can only work on the FoodOn and GenEpiO ontology files from before April 25th. We will document the changes shortly. Suffice to say, GEEM was making reference too-directly to ontology contents using the "has component" relation, leading to contradictions when reasoners evaluated GEEM annotations in conjunction with umbrella ontology (e.g. BFO.owl) disjointWith clauses. That is resolved on the ontology side now.