Canonical to PDF
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See Tip #2 from Tom Anthony...
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This Moz post gives advanced directions on HTTP headers (for using rel=canonical in non-HTML files) and cited this and this information from Google.
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Hi there,
Do you know if the PDF files are currently being indexed/ranked in the search engines? Do the PDFs provide any additional content than the HTML version? I have never been a big fan of PDFs in the search results (especially as a user!), so I try to limit this from happening with my own sites by not making the PDFs accessible to the search engines in the first place. Obviously there are reasons why you would want PDFs available to view for your users but if the content is the exact same as the HTML version, then there really is no need for them to be indexed by search engines.
One way to address this issue is to move the PDFs to a different directory and restricting search engines from accessing that directory. Then you can simply 301 redirect the old PDF urls to the HTML version urls so that the search engines know to only index the HTML version without the need for the canonical tags.
For more information on how to resolve this issue, I wrote a couple of blog posts that go into more detail about why I don't like PDFs and how to 301 redirect them -
http://streamlinemetrics.com/blog/seo-for-pdfs-optimizing-pdf-files-for-search-engines.php
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Hi Egol. thanks for your reply

I tried to sort this out but I couldn't. It still doesn’t work. In the post you recommended, advices are given on how to install canonical on PDFs in Lynunx (.htaccess). Do you know how to do it in Windows (web.config)? Cheers
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**Do you know how to do it in Windows (web.config)? **
Sorry. I only know about .htaccess.
When I purchase hosting I always look for those that can handle .htaccess - because it is so frequently used on my sites.