Restrict owning entity when querying characteristics

[arteymix]

Methods in CharacteristicDao should always take in a collection of owning entity classes to avoid exposing characteristics from unexpected origin.

In particular the following are likely not a good thing to expose since they are generally free-text or not curated:

• cell type annotation
• cell-level characteristics
• biomaterial characteristics (mostly free text from GEO)

I've added the logic for creating a clause, so this is just about applying it consistently.