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How does it work? (How does an ontology make the data queryable)

The ontology in is made up of medical concepts. The ontology is visible to researchers through the webclient, and each medical concept in the ontology includes specific code(s) that match medical observation facts (such as diagnoses, medications, procedures, etc). A researcher can select concepts they are interested in to build a query, and medical data that matches those concepts' codes will be counted.

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The ontology you choose to use depends on your local goals and local data. As long as your primary purpose is to understand and show how the i2b2 webclient works, the i2b2 demo ontology is sufficient. If your goal is to set up i2b2 for research use, one of the ACT ontologies will be more useful. In general, to set up an i2b2 instance to support  support research, start with the ACT Ontology. This Ontology includes a wide range of terminologies that should cover most code-sets you'll find in your EMR data. OMOP refers to a data architecture, so if you are using this format locally, then ACT on OMOP will be the most relevant.

Are the ontology and data stored separately? How to they connect and where are the data?

You just mentioned Domains. What do you mean by that?

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Yes! Here is a Glossary that provides explainers for many of the key terms related to i2b2 ontologies and the i2b2 architecture.

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What's the relationship between the metadata and the data?

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