I am using Biomart package, when I searched for miRNA information by listFilters(mart), I found a lot of filter options, does anyone know what do they mean especially the difference between with_mirbase versus other?
The two filters that start with_ are boolean filters, meaning that take either TRUE or FALSE. You can use these to return only the entries stored in Ensembl that have a particular type of ID. So if you want the list of all entries that have a mirbase ID you would use the with_mirbase filter and a value of TRUE. Similarly you could exclude anything with a mirebase ID (but it doesn't sound like you want to do that).
The other filters are more specific and let you search for one or more values that you're interest in. So if you you wanted to find out more information about hsa-let-7a-1 then you could use the mirbase_id filter to search for that particular term, and then provide the names of the other attributes you're interested in.