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Guidelines for building a federated 2-DE database

A federated 2-DE database has to comply with the following five rules (for a complete reference, see Appel et al., Electrophoresis 17, 1996, 540-546, 1996):

Rule 1

Individual entries in the database must be remotely accessible by keyword search. Other query methods are possible but not required, such as full text search, for example.

Rule 2

The database must be linked to other databases through active hypertext cross-references, that is through a simple mouse click on a cross-reference, the user automatically gets connected to the corresponding WWW site, and the cross-referenced document is then retrieved and displayed. This simple mechanism links together all related databases and combines them into one large virtual database. Database entries must have such a cross-reference to at least the main index (see Rule 3).

Rule 3

In addition to individually searchable databases, a main index has to be supplied that provides a means of querying all databases through one unique entry point. Bidirectional cross-references must exist between the main index and the other databases. Currently, the main index is the Swiss-Prot/UniProtKB protein knowledgebase.

Rule 4

Individual protein entries must be accessible through clickable images. That is, 2-DE images must be provided on the WWW server and, as a response to a mouse click on any identified spot on the image, the user must obtain the database entry for the corresponding protein. This method allows a user to easily identify proteins on a 2-DE image.

Rule 5

2-DE analysis software, that have been designed for use with federated databases, must be able to directly access individual entries in any federated 2-DE database. For example, when displaying a 2-DE reference map with a 2-DE computer program, the user must be able to select a spot and remotely obtain the corresponding entry from the given database.

A 2-DE computer analysis software may comply with Rule 5 by remote-controlling a WWW browser and requesting the following document for any given protein:


where host is the name of the server on which the remote database is located, database is the selected database on that server, and ID is the entry's unique identification. For example, in order to retrieve the Alpha-1 antitrypsin entry from the SWISS-2DPAGE database on the Expasy server, the following document has to be requested by the WWW browser: