Database configuration and access is mainly determined by the database manager. There are several factors that determine the allotted API usage, and the database manager will likely be the best source for API help.
At times, having your database manager reconfigure the database to allow a user more API usage can be enough to solve this problem. Other times, creating a persistent cache to store data rather than querying the database every time a job runs can also save API usage. Lastly, creating file extracts of the tables you are using can sometimes serve as a way to query data storage without using APIs against the database.