Handle user provided ontology file

**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](https://github.com/asyml/forte/pull/692/), 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.

Start by studying the existing implementation in PR 692, then trace the `is_subclass` and `is_annotation` checks. Verify that top-level types such as `Annotation` and `Entry` are recognized correctly and that `Entry(pack)` can be initialized; the work is done when these ontology-file use cases function without generated classes.

Written by the indexing model from the issue text.