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I wrote:

In most treebanks, sentences are annotated either (by or with ?) dependency structure or phrase structure depending on the syntax properties of the language.

The dependency structure is not the doer of the annotation, can I still use "by"? Should I only use "by" for the actor of the action?

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    First off, "by" (or whatnot) needs to precede "either". And actually I find that most often the preposition "with" is used with the verb "annotate". – Victor Bazarov Oct 21 '15 at 21:12
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You don't have to reserve "by" for the actor. For instance, Legos can be sorted by color.

My mind does make a very subtle distinction between the connotations of "annotated by" versus "annotated with", but it's hard to express, and I'd really need a larger segment of context to be sure that "by" is acceptable. So I'd stay safe and stick with "with".

EDIT: Your comment has sharpened my thinking on this. I think that when you could use "based on" you can use "by". For instance, Legos can be sorted based on color. I.e. when you're making a distinction based on some criteria then you could use "by".

  • Thanks, then when we are not sure if "by" is applicable, we'd better use "with" or "using"? – Ahmad Oct 21 '15 at 21:31
  • "Annotated by" is used when something or someone does the annotation or when talking about some process the result of which is the annotation. If I annotate your text, your text would be "annotated by Victor". Similar verb: "decorate". – Victor Bazarov Oct 23 '15 at 17:48

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