Our Forum is Excruciatingly Slow

Yes.


Not entirely sure how subforums will help you with SEO. Subforum names aren't referenced in the title or url of threads. Prefixes on the other hand are referenced in the thread title, which means they'll show up in Google searches.


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SEO and other stuff aside, look at it from your users point-of-view. 9000+ forums with only a couple posts in them look dead, I'd be moving on. Instead if you have a few forums that extensively use prefixes, it makes the forums more active and you can still drill down by using a prefix (if needed).

I'm pretty sure our subforums are being indexed: site:medisherpa.com/community

Having said that it sounds like the consensus here is to use prefixes instead of subforums.
 

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Prefixes can be categorized and set to specific nodes. A great help documentation about it can be found here. After you have defined the prefixes I would suggest installing this addon. It shows all the prefixes within the node above the thread list. that way a user can click on a prefix and filter them.
 
Is there a live example of a forum using prefixes we can see. We're still a bit confused as to how we should set this up. So we should have a few main categories, and a few main forums, and then replace all the sub-forums with prefixes?
 
Is there a live example of a forum using prefixes we can see. We're still a bit confused as to how we should set this up. So we should have a few main categories, and a few main forums, and then replace all the sub-forums with prefixes?
Here's an example of what XF uses them for.
http://xenforo.com/community/forums/resolved-bugs/

For example on your site I'd create a Drug Reviews forum and then make a prefix for all your subforums in that category (ie. ADHD, Cancer, Pain, etc).
http://www.medisherpa.com/community/#drug-reviews.9473

For your procedures I'd create a forum called Procedures and have broad prefixes (ie. Oncology, Fertility, Dental, Cardiology, Cosmetic, etc). Once these prefixes take off you could move the threads/prefixes off into their own subforum.
 
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