Clean up DB interface elements

* `create_db` -> `get_db` or `get_db_connection`
* `gene.database.database` gives `from datetime import datetime vibes`. not desirable.
* Can we rename `DynamoDbDatabase` to `DynamoDb` or `DynamoDatabase`? I think it was done to be consistent with child class names ending in Database, but seems redundant to have db and database in the name
* Change URL environment variable?

Start by locating the database interface definitions and references to `create_db`, `gene.database.database`, `DynamoDbDatabase`, and the URL environment variable. Review how these names are used across the repository before deciding the consistent replacements; the work is done when the agreed naming and environment-variable changes are applied without broken references.

Written by the indexing model from the issue text.