With the expansion of proteome projects, new and more effective techniques are being used to study proteins, such as microsequencing, amino acid composition or mass spectrometry. These techniques are often combined with two-dimensional gel electrophoresis (2-DE), in order to identify and characterize hundreds or thousands of proteins that are detectable on 2-DE maps.
Many laboratories are producing increasingly larger volumes of 2-DE related data which they are willing to share with other research teams, both in academia and in industry. Exchanging pieces of data from heterogeneous databases usually requires a detailed data exchange standard. Defining a standard that has to be widely accepted among researchers in the 2-DE community could be a difficult and cumbersome task.
The concept of federated 2-DE databases recently arose and is being adopted by an increasing number of proteome laboratories as a means of exchanging 2-DE maps and data. Utilizing the World-Wide Web (WWW), it lets producers of 2-DE databases publish their data on Internet without having to convert them using new and complex data interchange standards. The federated 2-DE databases concept defines a framework with five simple rules. The first two rules guarantee that 2-DE data may be queried over the Internet. Rule 3 lets users efficiently retrieve related data from other proteome and genome databases, such as SWISS-2DPAGE, SWISS-PROT, EMBL/GenBank, OMIM, etc. With Rule 4, one can access data graphically through clickable images. Finally, Rule 5 defines the framework for 2-DE analysis software to access proteome databases directly over the Internet. Using computer systems such as the Melanie II 2-DE analysis package, one may analyse proteins on various 2-DE gel images, then automatically compare these with reference 2-DE maps available on the Internet, select one protein spot and, provided the latter has been identified in one of the federated 2-DE databases, retrieve all currently available related data over the net.
Several laboratories have already published their 2-DE data on the Internet using the concept of federated 2-DE databases and have assessed its two main advantages: its efficiency for exchanging and interconnecting data and interactive analysis programs, and its simplicity of implementation.
Federated 2-DE databases are described and referenced in http://expasy.hcuge.ch/ch2d/2d-index.html