How to abbreviate species name?
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7.0 years ago
Cacau ▴ 520

I want to abbreviate species name based on the following rule, that is, if the species name is Saccharomyces cerevisiae, then it will be abbreviated as Scer. Now I have a species named as Saccharomyces sp. 126, what should the abbreviation be? Should it be Ssp.126 or Ssp. 126 or anything else?

gene • 2.5k views
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This question surprises me a lot. Obviously, how you like to abbreviate something is completely arbitrary and based on subjective preference; unless there are some domain specific constraints. I assume that you want to use species name in some context or with some software, but you forgot to mention that.

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Thank you. I want to make the format consistent but Saccharomyces sp. 126 obviously cannot be named as Ssp. because other species can be abbreviated as so if their species names are something like Sccharomyces sp. XXXX.

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I usually use NCBI Taxonomy id's. They are numbers but can be tracked easily.

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Good idea. But I want to make it more readable so i want to use species names.

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Keep in mind that not all organisms have a TAXID and multiple entries can have an identical TAXID.

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Are you limiting yourself to 4 (or a certain number of characters)? Ssp.126 does not indicate in any way that it stands for Saccharomyces species 126.

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I intended to make the format consistent as there is not much space for the full species name.

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I like this: Sspp126.

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Thanks a lot. BTW, could Ssp126 be fine?

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Like M. Dondrup mentioned, it's completely arbitrary.

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You are inventing your own abbreviations, so there is no use in asking us for advice in your own scheme. For all I care you could call abbreviate Saccharomyces sp. 126 to 126ScS. But if you are looking for something unambiguous you may have to think harder, or not abbreviate at all.

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7.0 years ago
Michael 54k

Consistent for what? For a paper: use the full scientific name once Exemplum horribile sp. 666, then E. horribile sp. 666 or leave the sp. part if it is the only exemplar. For a phylogenetics program using e.g. phylyp format use the longest possible abbreviation length (~10) internally (Ehorribi666) or replace the sequence ids by integers 1..N and restore the original name afterwards. When changing fasta Ids, make sure they are unique, so you won't get errors from the downstream software.

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Upvote! Upvote! Upvote!

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