Hi @koayst ,
Welcome to Prodigy
For the entity relation extraction (REL) use-case, your first option of
annotating them separately makes sense. This is because for most REL applications, deciding whether something is an entity is unrelated to whether that
entity is a relation, so you have different thought processes in annotating.
If you annotate them at the same time, you might miss out on actual entities that just happened to not belong in a relation--lowering your recall and affect the consistency of the NER data and subsequent models.
I also suggest looking at these discussions for more information: