.. How do I open the box with the animals?

You can't mess with the animal box on the bookcase until Melina tells you to.

Where is the filing cabinet key?

The goal here is to move each animal to the symbol of the Greek god it's associated with. Read to the end of this hint for the right arrangement.

You should have a book on "Greek Gods" in your inventory; if not, go ask Niobe about mythology, and she'll give it to you.

Now read through the descriptions, looking for the animals and symbols of the different gods. Some will be obvious --

-- like Hera, who is associated with both cows and peacock feathers --

-- and some will be obscure, like the dolphin, which goes not to Poseidon (who isn't represented here) but Apollo, who once turned into a dolphin. Fine, whatever.

Here's a halfway hint: the seven gods you're looking for are --

-- Aphrodite, Apollo, Ares, Artemis, Athena, Hera, and Zeus. But not in that order.

Here's the final layout, in case you're sick of the whole thing:

Animal Figurine Puzzle