If you have a web service and a standalone app calling the same bean, I would recommend you to move the functionality in a separate stateless bean and create remote and local interfaces to it. This way you can inject local bean into you web service bean, and call the remote one with jndi.
More about accessing Java EE beans here.
Alternatively, your client java code can call the web service to get all the data. Refer to this question about ways to connect to a RESTful service.