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It could make sense to have two configs, one for training and one for the full pipeline. spacy assemble was made for this use case.

On the other hand, if you can include the initialized Entity Ruler at train time, you can just leave it there - if it's not an annotating component (as specified in the config) then the NER component won't see its annotations, so it just won't do anything. You can also mark it as a disabled component during training to keep it from running. This way you can use just one config and just override the disabled_components setting with your training command.

The double NER sample project might be a helpful reference, though it's combining multiple NER components.

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@cuiqui
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@polm
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feat / pipeline Feature: Processing pipeline and components
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