Ontology where the same word has different meaning in different contexts?

Are there any example ontologies where the same word has different meaning in different contexts?

For example, when building an ontology for a large company, it is not uncommon for different departments and systems to have a different definition and understanding of common words like "customer", "account", etc.

Is there a generally accepted way to model this in Protege that preserves the original words in their context, while also introducing a layer of disambiguating words for enterprise use?

This is a problem we encounter often in the biological community. I.e., the concept Eye is very dependent on the context, i.e. human eye vs fish vs spider eye etc. You can see a search for eye on the Ontology Lookup Service (OLS) and the results it return for eye from different ontologies. Disclosure: I am responsible for this tool.

1. Provide an IRI for your concept. This IRI should be similar to a surrogate key for your concept. I.e., instead of giving your Account concept an IRI like http://MyBusiness/someBusinessContex/Account you give it an IRI like http://MyBusiness/someBusinessContex/Context0000001. For the Eye concept the IRI for a human eye is http://purl.obolibrary.org/obo/NCIT_C12401 and for an insect it is http://purl.obolibrary.org/obo/SIBO_0000086.

I explain in this StackOverflow question the reason for using "surrogate keys".

2. Assign a context specific label and definition to your concept. You can use rdfs:label for label and rdfs:comment or skos:definition for definition.

3. You may find that you need alternatives for you concept. I.e. may be you refer to customers also as members. In this case you can use skos:altlabel to provide alternative names for your concept and skos:preflabel to define a preferred label.

So how does this work? For user interfaces you make use of rdfs:label/skos:preflabel and rdfs:comment/skos:definition for display purposes. From a data integration perspective you use the IRI.