I am a bit confused on the difference between the BioMart Perl API and the Ensembl Perl API, are they the same thing? What are the differences in the data available to either API?
They are not the same thing. Simply put, the Ensembl API gives programmatic access to the Ensembl data and the BioMart API provides access to the data that you can access through BioMart. Certainly, there will be some overlap between the data you can access through these methods, but the Ensembl API will provide a richer set of methods to work with the data. I could be wrong, but it is my understanding that the BioMart Perl API is no longer being developed and supported. It is probably better to access BioMart through something like R or one of the other supported methods. If you have a more specific question about what you can do with these APIs, please clarify and we can provide more information.
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version 2.3.6
That was it, however I was not aware that BioMart does not provide access to all ensembl date. I guess then my question would be what is missing from the BioMart subset of the Ensembl data? I will not likely use Perl or R for biomart, generating XML files for requests seems like a better option.