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Following APA style, "if you are citing a work written in a non-Latin script (e.g., Chinese, Greek, Japanese, Russian), the reference must be transliterated into the English alphabet."

Sometimes, for a given language, e.g, Persian, there are more than one system for transliteration and the researcher needs to choose one of them. In such cases, shall we tell our audience what system have been used for transliteration? If yes, where is the best section to put it in an academic journal? In the methods?

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It is unlikely that you need to specify in your references which system of transliteration was used. The purpose of the references is for the reader to be able to look up the paper, and this should be possible regardless of the system used.

If you do need to to specify the system anyway for some reason I am unaware of, a footnote attached to the reference(s) in question would be a good place.

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  • Footnotes are not allowed in most science journals. Jan 5, 2022 at 19:42
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    @FelipeG.Nievinski That is probably field dependent. I have seen plenty of footnotes in science journals.
    – Louic
    Jan 5, 2022 at 19:57
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It depends on the journal style, so only the editorial office can give a definite answer. I'd suggest using the Acknowledgements section, which often sits between Conclusions and References.

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  • This is a very bad place to put the information: it is the last place anyone would look to find it.
    – Louic
    Jan 5, 2022 at 18:32
  • "Acknowledgements in scientific articles can be described as miscellaneous" journals.plos.org/plosone/article?id=10.1371/… Jan 5, 2022 at 19:46
  • If you actually read that (fairly poor) article, you would notice that nearly all of the classifications mentioned are stating appreciation for help with various parts of the research, in other words: that article states that acknowledgements are used for acknowledging people for their help - that is precisely what they are for, and nothing else.
    – Louic
    Jan 5, 2022 at 20:02
  • you're interpreting "acknowledgements" literally, that's a misunderstanding of scientific publishing. it's an umbrella section that often contains myriad statements, such as author contributions, data availability, competing interests, and any additional information. Jan 8, 2022 at 18:47

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