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Howdy,
I'm currently writing my thesis in English and several times I've come across the problem of choosing the right word without repeating the same one for the third time. The problem is that whenever I open my Collins Thesaurus and look up a word, it gives me several similar ones but I'm never sure if they are 100% interchangeable... For instance, if I look up the word "desolate" here's what I get:

1) bare
2) bleak
3) desert
4) dreary
5) godforsaken
6) ruined
7) solitary
8) uninhabited
9) devastated
10) abandoned

While some of those synonyms are not quite what I'm looking for, some make me confused. For instance nr\umber 9) devastated. Is there any way of dealing with synonyms?

Thanks
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A thesaurus presents a plethora of synonyms for many possible meanings and contexts of the base word. None are 10% interchangeable. Thesauri, unfortunately, are essentially for those who already have a pretty good vocabulary and are just stymied or blank for the moment about word choice. If you are not already reasonably familiar with the choices offered you (in regard particularly to register and collocation), then there is little you can do beyond searching corpora to observe the use of your various options in order to determine whether they might be appropriate alternatives.
Comments  
Trust me, this is a problem that afflicts native speakers as well! For instance, having just completed my first grant, I can tell you that there are very, very few synonyms for the word "community." Emotion: smile

Have you tried the Visual Thesaurus? I think there might be an annual fee to use it, but you can try it out for free. Its structure is more helpful than a list.

http://www.visualthesaurus.com /
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 Mister Micawber's reply was promoted to an answer.
then how do I learn the differences between two or three similar words? for instance: "a desolated city" VS "an empty city" ?
Search corpora ([url=http://www.americancorpus.org /]HERE'S[/url] one) or do a Google search to observe the use of your various options in order to determine whether they might be appropriate alternatives. Look carefully at the dictionary definitions and the sample collocations provided.
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another example - do understanding, comprehension and apprehension mean the same thing?