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Q1. What is meant by a two-dimensional matrix? Does it involve only the ontologies or actually involve an alignment?
A1. This is matrix with classes from each of two ontologies running along each side. Potential overlap between the the two can be displayed as intersections in the matrix. This display will be based on an alignment between two ontologies.
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Q3. Can you clarify or give an example about the “definition of context”?
A3. The equivalence between two concepts, or otherwise their relation, may depend on a context. Is "Person" the same as "Employee"? Probably yes in the context of payroll, but not otherwise. Especially in an iterative environment, it would be good to have some way to specify assumptions (or limits of validity) for a mapping.
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Q4. To clarify, does this request indicate the need for partial mappings to be provided externally rather than being automatically calculated by the alignment algorithm?
A4. Ref 3.1.1, this indicates the need for the tool to be able to consume reference mappings that can be sourced externally. This is in contrast with a tool that can only generate mappings, but not make use of mapping already existing. For instance, the tool could be used to visualise overlap or edit/annotate externally provided mappings.