The EBI provides SOAP interface to their analysis queues at their webservices site. They provide example clients in both Perl and Java code.
A nice project for someone would be to implement Run package modules which provided support for submitting and retrieving analyses through their site. Interpro, BLAST, FASTA, Clustalw, T-Coffee, MUSCLE, EMBOSS analyses are all available services
Currently the Bibliographic data is available through the Bio::Biblio modules in BioPerl.
The sequence data used to be available through a Bio::DB module but that is no longer implemented.