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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
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.
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).
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
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.
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