The variety of identifiers used to refer to the same biological object, such as a protein, is a recurrent source of problems. When different aliases are used for the same protein, bringing together data or data sets requires a substantial amount of time and effort.

Aliases have various origins: systematic names defined by sequencing projects, accession numbers used by public database, protein names used by the biologists, etc. While the designation of a universally-accepted unique identifier would theoretically solve the problem, this has absolutely no chance of happening given the multiplication and growth of molecular biology databases.

Therefore, solutions must be proposed to help in the handling of the diversity of aliases. In this respect, species oriented databases like SGD for Saccharomyces cerevisiae, that collect and centralize aliases, are very helpful. However, the help provided by such resources is limited for different reasons: they are specialized to a given species, they are not designed to easily incorporate new alias definitions, and they do not offer to users and programs dedicated "alias management services" such as the translation of identifiers from one type to another, like systematic names into accession numbers.

AliasServer was developped in an attempt to overcome these limits. The system is designed to load and store aliases attached to the proteomes of an extendable list of organisms and to provide services through both an interactive web interface and a SOAP based API.