I just wrote a script that retrieves multiple protein networks and converts the database-specific identifiers (like bioGrid-ID, HPRD-ID etc.) to UniProt accession numbers.

The problem is that the databases use different versions of Uniprot in their ID mapping files, many of the Uniprot AC's are obsolete and have since been merged/demerged into other AC's.

What would be the easiest way to convert any obsolete Uniprot-AC into its corresponding new Uniprot-AC?

A text file or web-service that can be accessed in a java program and is always up to date would be perfect.

Uniprot's own ID conversion only seems to work in the browser by uploading a file or copy-paste.

Edit: I'm talking about Accession Numbers (Uniprot-AC), apparently UniProt-ID's are something different

Edit2: I found a solution: http://www.uniprot.org/uniprot/?format=tab&query=replaces:P29358