Step 1: First blank.
“Ontologies are ________ equated” — the word must indicate frequency. “Often” is the most natural choice, fitting better than “frequently” in this academic tone.
Step 2: Second blank.
The correct phrase is “the subsumption relation,” because we are pointing to a specific, known relation in ontology. “A subsumption relation” would be less precise.
Step 3: Third blank.
We need a conjunction to contrast. “But” signals contrast perfectly: although ontologies are equated with certain taxonomic structures, they are not confined to them.
Step 4: Fourth blank.
The phrase “these forms” fits, since it refers back to the “taxonomic hierarchies, class definitions, and the subsumption relation.” “Such forms” would also make sense, but “these forms” explicitly points back to the listed elements.
\[
\boxed{\text{often, the, but, these}}
\]