Computing borrowed the word. In knowledge representation, an ontology is an explicit specification of the concepts in a domain and the relationships between them. Engineers have used the idea in many forms: data dictionaries, entity-relationship diagrams, knowledge graphs, semantic layers.
We use the word in the plain enterprise sense. What are the things in this business? How do they relate? What can be done with them, and by whom? Customers, accounts, shipments, machines, patients and contracts are not rows. They are objects with meaning and with rules about how they behave.
The difference between a diagram on a wall and an ontology in production is that the second one is executable. It is stored, versioned and enforced. Applications read from it. Agents act through it. Changes go through review. That is what makes it a layer and not a document.