Hi there! Kristina from Moz's Help Team here.
When you run a search on a URL in Open Site Explorer, if you set the target to the entire root domain, we will display all links for that domain that we have included in our Mozscape Index: https://www.screencast.com/t/ylFWSmQMr
However, when it comes to downloading/exporting this data, there is a limitation of our API is that we can only export the top 25 links from each linking root domain. This means that, if the majority of your links are coming from a small number of domains, we would only be able to export a small percentage of your links. This includes internal links as well as external links. For example, moz.com has 61k internal links, but we would still only be able to export the top 25 of those internal links.
The reason why is that if someone has 500,000 links and most of them are from the same domain, then we wouldn't want to fill up all 10,000 links with the same domain information and leave out important links from other domains. Instead, we'll only show the top 25 based on Page Authority so that we can show links from other sites without the same domain taking up all 10,000 spaces. In other words - we want to show link diversity.
The advanced reports have the same limitations on the number of links per linking root domain, and can only give links from an increased number of root domains.
If you want to obtain more than 25 links from a particular domain (we export only 25/per domain) to a target, this is only achievable through the Mozscape API directly.
For example, if you want to find the number of pages that link to the yahoo.com root domain from the wikipedia.org root domain, you could issue the following query:
http://lsapi.seomoz.com/linkscape/links/yahoo.com?Scope=page_to_domain&SourceDomain=wikipedia.org&SourceCols=4&Limit=50&Offset=0
This will return the source URL of the first 50 pages from anywhere in the wikipedia.org root domain to anywhere in the yahoo.com root domain. Then, you can set the Offset parameter to 50 and run the same call, and so on, always incrementing Offset by 50. As soon as you get a number of links back that's less than 50, you know you've reached the end of the links we have that fit your parameters. Just add up all the links you've seen, and you've got your count!
Please note the limit for free users will be 1000 links total. There is no limit with a paid subscription, however higher offsets take longer to process and may time-out.
I hope this helps but please let us know if there's more information we can provide. And as always, the best way to reach our team is to contact us directly by emailing [email protected].
Thank you!
-Kristina