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I am in the final stage of completing a thesis.

Context: I propose a new knowledge representation to tackle information overload in science (E-Science, scientific communication, linked data). Specifically, I created a knowledge representation of scientific problems.

In the introduction, I motivate the need of the new artefact based on two things: 1. A general need for digital knowledge representations for automatic reasoning, being able to filter out relevant aspects of scientific work to make them findable, 2. The unavailability of a knowledge representation for a specific aspect of scientific work; namely, scientific problems ("challenges", "gaps").

Other approaches that present a digital knowledge representation of aspects of scientific work were included as related work, but they also exemplify that the aspect I focus on is missing.

Do I incorporate this related work in the introduction, or present them in a separate related work section? Would it be better to state "To this day, no representations of scientific problems exist" in the introduction and show the other approaches in a separate related work section, or is it nicer to show these other approaches in the introduction first (by including a subsection with all related work - separate subsections per approach - what would the title of this subsection be?), to then base the motivation of creating this new representation in an "approach" subsection which contains the research questions?

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The structure of your paper should make it attractive to read and easier to understand. So keeping to the common structure in your field is usually helpful, but not a dogma that should be obeyed when it's not useful.

Introduction -> Related Work -> Main Contributions is a pretty common start for CS writing, so making it a separate section would be the default option.

However, if you have to lean heavily on a literature discussion to motivate the need for your work, it can make more sense to pull them together into a single chapter, perhaps with subsections.

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Do I incorporate this related work in the introduction, or present them in a separate related work section?

That's a matter of taste. As a third option, you could include related work in each research chapter.

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