How does SEOMoz get ranking data? is it automated queries to Google?
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Google's terms don't allow automated queries without Google's permission. https://support.google.com/webmasters/bin/answer.py?hl=en&answer=66357
How does SEOMoz get ranking data then? Is it sending automated queries with or without Google's permission? is it violating Google's guideline? Will it affect my site performance as far as rankings?
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Well i can tell you that Gooogle are quite aware of SEOMoz so one would assume they have permission to do what they do,and no it would not affect your rankings, if there was any problem it would be with the appKey holder.
notice that rankings are done on the first 50 results, you can do that with Bing and Goolge API in one query, i think what they do not like is continuis queries untill you find your result that may never happen.
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Yeah, no worries! It won't affect your site. Imagine if it did, all our competitors would run a bot on each other to wipe everyone out.
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You've touched on a tricky and delicate issue. As you've noted, Google's TOS specifically forbid automated queries, but rank checking services all over the world need to collect this data.
Although I can't tell you exactly how SEOmoz does it (it's part of the secret sauce), I can tell you it's done in a manner that's as Google friendly as possible - we want to stay on their good side.

Rest assured that the rank checking SEOmoz does will not effect your site in anyway. In fact, because SEOmoz is checking keywords (some you don't even rank for) and not your site specifically, there is no way to associate the queries with your website. This is one of the advantages of using a 3rd party rank checker.
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What about now since Google has revoked SEOMoz's AdWords API?