querying user bookmarks from a large number of bookmarks

It looks like the default get_bookmarks()

http://codex.wordpress.org/Function_Reference/get_bookmarks

is using this query:

SELECT * FROM wp_links  WHERE 1=1 AND link_visible="Y" ORDER BY link_name ASC;

You can check the function in /wp-includes/bookmark.php.

The get_bookmarks() function has limit and order parameters that you might find helpful.

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The option get_bookmarks("limit=5")

gives this query:

SELECT * FROM wp_links  WHERE 1=1 AND link_visible="Y" ORDER BY link_name ASC LIMIT 5

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The category parameter get_bookmarks("category=1")
gives you this one with JOIN:

SELECT * FROM wp_links  
INNER JOIN wp_term_relationships AS tr ON (wp_links.link_id = tr.object_id) 
INNER JOIN wp_term_taxonomy as tt ON tt.term_taxonomy_id = tr.term_taxonomy_id 
WHERE 1=1 AND link_visible="Y"  AND ( tt.term_id = 1 ) AND taxonomy = 'link_category'       
ORDER BY link_name ASC;

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So if you don’t use the category parameters, these are just plain SELECT queries that use the $wpdb Database Object.

Edit: If you want to search for a special link_owner you can use this example:

global $wpdb;
$link_owner=1; // EDIT this value
$sql="SELECT * FROM wp_links  WHERE link_visible="Y" AND link_owner = %d ORDER BY link_name ASC;";
$results = $wpdb->get_results($wpdb->prepare($sql,$link_owner));