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How would I indicate, for example, that I am going to use "toms" to mean "tomatoes". Something like:

Tomatoes (toms) are red. This is false as some toms are green. I like toms.

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up vote 7 down vote accepted

I have often seen it in brackets, as in your example, with quotation marks and a capital:

Tomatoes ("Toms") are red. This is false, as some Toms are green. I like Toms.

I suppose the capital is not always necessary if the thing referred to isn't a name or a proper noun; however, it is easier to spot that this thing is special later if you use a capital throughout.

In legal texts, they use hereafter or hereinafter:

Tomatoes, hereafter called "Toms", are red. This is false, as some Toms are green. I like Toms.

But this is not recommended in academic writing. You could simply use in this paper and explain what you're going to do:

Tomatoes, which will be referred to as "Toms" in this paper, are red. This is false, as some Toms are green. I like Toms.

Tomatoes, which we will refer to as "Toms" in this paper, are red. This is false, as some Toms are green. I like Toms.

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