J2EE Specification has various APIs each having its own functionality to cater for. While developing an Application using these, each API may or may not need others. Following is a usage/interaction level diagram that shows how they can be positioned wrt each other.
Looking from Web Application development based on J2EE compliant server, the EJB container and Web Container APIs are mandatory. Rest of the APIs such as - JMS, JPA, JTA etc are all going to be used based on the services that they offer.
Hence the Container APIs are placed at the center and rest of the APIs are surrounding them.
Note on Terminology:
Container APIs are generally called as Component APIs
Rest of the Service providing APIs - JMS, JAX-WS, JPA, Security - are termed as Resource APIs or Service APIs.
Overview of how Server Runs:
J2EE App Server runs using J2SE Platform APIs and both run in Java Runtime Environment(JRE) on Java Virtual Machine(JVM)
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