[Bioperl-l] EUtilities policy change

Chris Fields cjfields at illinois.edu
Thu Jan 28 14:00:26 EST 2010


Per NCBI's recent change in eutils user policy (effective June 1):


Both the tool and email parameters ('-tool', '-email') are now required
when making requests.  Note this will significantly break all modules
requiring remote access to eutils (Bio::DB::GenBank/GenPept, some Biblio
and Taxonomy stuff as well, IIRC).  This also applies to web services
(SOAP-based access).  Mark, not sure how this affects your SOAP-based

I have reconfigured Bio::DB::EUtilities to follow this policy; the
default tool setting has been 'bioperl' and will remain that way.
However, there has been no default email, therefore setting this is now
required for future requests unless we (the bioperl devs) decide there
is a safe default email to utilize.  My gut tells me, however, that
falling back to a default email opens up a can of worms for the devs and
is very likely a 'BAD IDEA'(TM).  

Regardless, be aware that, after June 1, NCBI will very likely exclude
requests with no email and will notify users who are considered to be
violating their policies.

I will likely make further changes to Bio::DB::EUtilities in the
meantime to ensure that using the tools by default will not violate
NCBI's policy (e.g. override this at your own risk).  


More information about the Bioperl-l mailing list