Handle user provided ontology file

[hunterhector]

Is your feature request related to a problem? Please describe.
Without having to generate and without having all the classes ready, one can also use the data store with simply the ontology configuration file. This is currently developed here, but not finished

Describe the solution you'd like

1. Study the existing PR and fix is necessary
2. Make sure top-level types like "Annotation", and "Entry" is correctly used
   • can be found in is_subclass, is_annotation check
   • these types should also be intializable (i.e. entry = Entry(pack))

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context

• This is part of the data efficiency project
• This PR should be made to the master branch.
• After the data tuple class is finished, we may switch to a new branch for integration.