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I created a protein tag for those of us in protein/enzyme/peptide engineering but when I tried to add synonyms, it wouldn't let me as I do not have sufficient rep/score in the protein tag or for another reason.

Whilst we are a small niche, we still use TeX and friends extensively and lots of my questions on my profile concern it or ancillary purposes. Proteins, enzymes and peptides are composed of amino acids, the main difference being that peptides are less than ~20 amino acids in length, proteins don't typically possess catalytic activity whilsts enzymes do. All 3 possess amino acids as their main structure (ribozymes comprises nucleotides for catalytic activity, it is for the ribozyme engineers to proposes that!).

I want to help this site with our biochemical stuff to help future readers, I am working on a package called aminosymb and aminosymb-lua for my protein/enzyme packages I have created for my PhD, but I was wondering on how this site feels about making peptide(s), enzyme(s) and protein(s) synonyms to each other?

The conventional Chemistry packages, whilst incorporating some of our material in protein engineering, don't quite make it specific enough. I am aware a serious developer of Chemistry packages, Joseph Wright, is active so hopefully the difference is understood by our little niche that does this. For instance, the enzyme is:question search yields 43 results, protein is:question yields 162 results and peptides is:question yields 7 results for 212 questions that could potentially be similar.

What are the thoughts on these synonyms please and what next steps could be taken? I have never proposed a synonym before so not sure how this site works for it, forgive me if this post is unnecessary.

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If the candidate synonyms don't currently exist as tags, there's probably limited benefit to creating a synonym, the bar for creating a tag is not high so no suggests very few would use it if it existed (directly or as a synonym), although it's possible the tag has frequently popped in and out of existence in the past.

Just because a synonym could exist doesn't make it valuable, questions which already exist are findable if appearing in a search for enzyme, can be added to where appropriate, and wouldn't benefit from a tag synonym. Not that most of the existing questions from protein is:question should be retagged, most of them wouldn't lose meaning if you replaced the instances of protein(s) with lorem ipsum.

I'm also unsure (not a chemist/biochemist) that, if they both existed, would be an exact synonym of , they might co-exist frequently (which isn't a problem for tags), but looking at the questions returned by enzymes is:question score:2, they all seem to me to either be enzyme/catalyst-specific (Drawing enzyme with TikZ, Easy way to write below arrow (\arrow{-U>}) in chemfig? and Anchor point seems incorrect for Chemfig package) or incidental to proteins/enzymes altogether (How do I align these inline bullet points?, How do I align these inline bullet points?, How can I change a sentence based upon input to a command? and Bioinfo.cls leads to strange ignoring of header). So while a synonym may aid discovery of a tag, I would be concerned about automatic retagging losing some of the meaning the user wants from an tag.

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  • Thank you for the answer, what you write makes sense, appreciate the feedback!
    – JamesT
    Sep 1, 2023 at 18:13

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