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Language Explorer supports lexical relations on lexical entries and senses.

In the screenshot, we are about to insert a synonym relation to the first sense of zazisa.
Screenshot of Lexicon Edit view

This brings up the following dialog, which lets us identify the entry and sense which is the synonym.

Screenshot of Lexical Relation Dialog

The lexical relation is added to both entries/senses, so if we now jump to the entry zaza we will find that the relation has been added there as well.

Screenshot of Lexical Relation Dialog

There are seven built-in relation types, and you can add your own.