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There are many reference book, but I mostly mean by that a book that list concepts and organize them like most encyclopedia, but not necessarily an encyclopedia. What do you call the work done to make such reference books? I was thinking research, but research doesn't cover the part of organizing your ideas by theme, or whatever other way of organizing something.

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I think you're right that half this work could be described as "research." The act of bringing it all together could be termed "compilation."

n., the action or process of producing something, especially a list, book, or report, by assembling information collected from other sources.

The verb is "to compile."

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I expect the official title for the person who does this job is the same as for any other book: editor. But this particular action can be variously described as compile, collate, and catalogue, depending on the specifics.

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