user62: It seems many SE sites have some sort of concept of what I call "sub-tags", but it seems to be slightly different for this site as one tag literally is a subset of another. Granted, I know that there are 'ribozymes' that are enzymes made from RNA, but >99% of all enzymes are proteins to my knowledge. Since enzymes are almost an exact subset of proteins, should all enzyme questions be tagged proteins as well?
Perhaps a better solution to avoid this redundancy would be to only tag proteins if the question actually relates strongly to what proteins are and not just what certain enzymes do. However, it can be nice to have all protein related questions under one tag to make them easily searchable. 
What are your thoughts on this? How should "sub-tags" be used on this site?

related question from meta.stackoverflow about sub-tags
Example question on this site: How does ATP-Synthase work?

user66: Even thout you are correct that enzymes are in 99% proteins, the reverse is not always true. 
Enzymes are the proteins that server as biological catalysts, helping to mediate the chemical reactions. This is very important funtion of proteins, but not the only one.
Besides the enzymatic function proteins also have the structural (being building blocks), informational (convey information about something, for example MHC-proteins) and in some cases even the energetic ones (rare). 
So, to put it in a nutshell: every enzyme is a protein, but not every protein is an enzyme.

user69: I can see this happening for a number of tags actually.
photosynthesis will likely nine times out of ten be a subset of botany or plant-physiology (N.b. what do people thing about whether or not those two tags are actually distinct)?
genetics has some children in the form of introns and splicing etc.
And as the site has so far a quite an anthropocentric feel tags such as neuroscience, immunology, endocrinology and hematology will quite often be used as a subset of human-biology.
I personally am in favour of using a super-tag wherever and whenever appropriate, editing them in if missed by the OP.  I realise that this will lead to some large tag sizes for a few tags however hopefully this will not have too great a detrimental effect on the tags usefulness.  We will also have to be careful of the occasions where the sub-tag does not actually belong to its usual super-tag  - e.g. this immunology tagged question would not fit human-biology.
Looking through the neuroscience tag in particular, I see a lot of questions that have not been tagged in this sub/super tag style that I believe would benefit from it.  If the change is to be made, it probably is a good idea to tackle it now whilst the problem is manageable.  

62: <p>It seems many SE sites have some sort of concept of what I call "sub-tags", but it seems to be slightly different for this site as one tag literally is a subset of another. Granted, I know that there are 'ribozymes' that are enzymes made from RNA, but >99% of all enzymes are proteins to my knowledge. Since enzymes are almost an exact subset of proteins, should all enzyme questions be tagged <a href="https://biology.stackexchange.com/questions/tagged/proteins" class="post-tag" title="show questions tagged &#39;proteins&#39;" rel="tag">proteins</a> as well?</p>

<p>Perhaps a better solution to avoid this redundancy would be to only tag <a href="https://biology.stackexchange.com/questions/tagged/proteins" class="post-tag" title="show questions tagged &#39;proteins&#39;" rel="tag">proteins</a> if the question actually relates strongly to what proteins are and not just what certain enzymes do. However, it can be nice to have all protein related questions under one tag to make them easily searchable. </p>

<p>What are your thoughts on this? How should "sub-tags" be used on this site?</p>

<hr>

<p><a href="https://meta.stackexchange.com/questions/41206/should-questions-be-tagged-with-both-a-tag-and-a-sub-tag">related question from meta.stackoverflow about sub-tags</a></p>

<p>Example question on this site: <a href="https://biology.stackexchange.com/questions/800/how-does-the-enzyme-atp-synthase-use-a-proton-concentration-gradient-to-make-atp">How does ATP-Synthase work?</a></p>
 66: <p>Even thout you are correct that <a href="https://biology.stackexchange.com/questions/tagged/enzymes" class="post-tag" title="show questions tagged &#39;enzymes&#39;" rel="tag">enzymes</a> are in 99% <a href="https://biology.stackexchange.com/questions/tagged/proteins" class="post-tag" title="show questions tagged &#39;proteins&#39;" rel="tag">proteins</a>, the reverse is not always true. </p>

<p>Enzymes are the proteins that server as biological catalysts, helping to mediate the chemical reactions. This is very important funtion of proteins, but not the only one.</p>

<p>Besides the enzymatic function proteins also have the structural (being building blocks), informational (convey information about something, for example MHC-proteins) and in some cases even the energetic ones (rare). </p>

<p>So, to put it in a nutshell: <strong>every enzyme is a protein, but not every protein is an enzyme.</strong></p>
 69: <p>I can see this happening for a number of tags actually.</p>

<p><a href="https://biology.stackexchange.com/questions/tagged/photosynthesis" class="post-tag" title="show questions tagged &#39;photosynthesis&#39;" rel="tag">photosynthesis</a> will likely nine times out of ten be a subset of <a href="https://biology.stackexchange.com/questions/tagged/botany" class="post-tag" title="show questions tagged &#39;botany&#39;" rel="tag">botany</a> or <a href="https://biology.stackexchange.com/questions/tagged/plant-physiology" class="post-tag" title="show questions tagged &#39;plant-physiology&#39;" rel="tag">plant-physiology</a> <br /><em>(N.b. what do people thing about whether or not those two tags are actually distinct)</em>?</p>

<p><a href="https://biology.stackexchange.com/questions/tagged/genetics" class="post-tag" title="show questions tagged &#39;genetics&#39;" rel="tag">genetics</a> has some children in the form of <a href="https://biology.stackexchange.com/questions/tagged/introns" class="post-tag" title="show questions tagged &#39;introns&#39;" rel="tag">introns</a> and <a href="https://biology.stackexchange.com/questions/tagged/splicing" class="post-tag" title="show questions tagged &#39;splicing&#39;" rel="tag">splicing</a> <em>etc</em>.</p>

<p>And as the site has <strong>so far</strong> a quite an anthropocentric feel tags such as <a href="https://biology.stackexchange.com/questions/tagged/neuroscience" class="post-tag" title="show questions tagged &#39;neuroscience&#39;" rel="tag">neuroscience</a>, <a href="https://biology.stackexchange.com/questions/tagged/immunology" class="post-tag" title="show questions tagged &#39;immunology&#39;" rel="tag">immunology</a>, <a href="https://biology.stackexchange.com/questions/tagged/endocrinology" class="post-tag" title="show questions tagged &#39;endocrinology&#39;" rel="tag">endocrinology</a> and <a href="https://biology.stackexchange.com/questions/tagged/hematology" class="post-tag" title="show questions tagged &#39;hematology&#39;" rel="tag">hematology</a> will quite often be used as a subset of <a href="https://biology.stackexchange.com/questions/tagged/human-biology" class="post-tag" title="show questions tagged &#39;human-biology&#39;" rel="tag">human-biology</a>.</p>

<p>I personally am in favour of using a super-tag wherever and whenever appropriate, editing them in if missed by the OP.  I realise that this will lead to some large tag sizes for a few tags however hopefully this will not have too great a detrimental effect on the tags usefulness.  We will also have to be careful of the occasions where the sub-tag does not actually belong to its <em>usual</em> super-tag  - e.g. <a href="https://biology.stackexchange.com/questions/524/do-antigens-protrude-through-the-capsule-slime-layer-in-prokaryotic-organisms-wh">this</a> immunology tagged question would not fit human-biology.</p>

<p>Looking through the <a href="https://biology.stackexchange.com/questions/tagged/neuroscience" class="post-tag" title="show questions tagged &#39;neuroscience&#39;" rel="tag">neuroscience</a> tag in particular, I see a lot of questions that have not been tagged in this sub/super tag style that I believe would benefit from it.  If the change is to be made, it probably is a good idea to tackle it now whilst the problem is manageable.  </p>
