You can check this tutorial on ontologies in GATE.
As stated in the pdf:
- Link annotations to concepts in a knowledge base.
- The annotated text is a “Mention” of a concept in the KB
- We can use the knowledge associated with Mentions in our IE pipeline: e.g. Persons have JobTitles, Cities have zip codes
- We can use the knowledge associated with Mentions for “Semantic Search”
- We can use semantically annotated documents to add new facts to our knowledge base
In the process of annotation, ontology data (instances, classes, relations, etc.) can be used by JAPE for smarter matching, i.e. matching a mention with class "engineer", knowing that "engineer" is a subclass of a "person". Also there are ontology-aware gazetteers which can create annotations based on instances and put the right class and uri for the created annotations.
The last two questions are too generic but I'll try...
After following the tutorial, you'll know exactly how to use ontologies for annotation, hence you'll know if you need to create a custom ontology for your task.
ANNIE is an example of a pipeline and a good place to start studying GATE and writing your own application.