All Classes and Interfaces

Class	Description
BasePlugin	Helper base class for ROBOT commands.
DefaultSpeciesSubsetter	The “default” strategy to create a taxon-specific subset.
EquivalenceSetMerger	A helper class to merge classes that are inferred to be equivalent.
InferenceDiffCommand	A command to produce a report on the consequences of logical changes between two versions of the same ontology.
ISpeciesSubsetStrategy	Represents a strategy to create a taxon-specific subset of an ontology.
MergeEquivalentSetsCommand	A command to merge sets of equivalent classes across ontologies.
MergeSpeciesCommand	A command to fold species-specific classes to form a “composite” ontology.
PreciseSpeciesSubsetter	A “precise” strategy to create a taxon-specific subset, as an alternative to the strategy implemented in DefaultSpeciesSubsetter.
ReasoningException	This exception may be thrown by other classes in this package if an error occurs when reasoning over an ontology (for example, if the ontology is unexpectedly inconsistent).
SpeciesMerger	This class may be used to create multi-species ontologies following the "composite/merger" strategy described in Uberon's wiki.
SpeciesMerger.GCAMergeMode	Mode of operation for general class axioms.
SpeciesSubsetCommand	A command to create a taxon-specific subset of an ontology, that is a subset containing only the classes that are valid for a given taxon.