Biomedical Engineering Reference
In-Depth Information
Entrez is an example of a portal—a pre-linked gateway to databases selected by the portal designer.
Sequence Retrieval Service (SRS), and BioKRIS (as well as Entrez) are examples of portals that
provide access to link-integrated databases through a variety of special support tools. For example,
SRS allows users to search multiple databases simultaneously because of a powerful and unique set
of link operators that dynamically link multiple databases. Portals can make better use of intelligent
agents because the search engine designer can design the heuristics to fit the databases included in
the portal, as opposed to working with every database on the Internet. Similarly, special operators
can be defined to facilitate working with the databases encompassed by the portal.
For example, SRS uses two link operators "<" and ">" to combine two sets from different databases
in the portal system, such as SWISS-PROT and PDB. The statement SWISS-PROT > PDB gives those
entries in the PDB database of solved tertiary protein structures that are referenced by or linked to
entries in SWISS-PROT. Conversely, the statement SWISS-PROT < PDB gives those entries in SWISS-
PROT that reference or are linked to entries in PDB. As a result, the statement [swissprot-def:kinase]
> PDB retrieves all kinase sequences from the SWISS-PROT protein sequence database, which are
then linked to the PDB. The result is a set of all the PDB entries with atomic coordinates for all
kinases for which the tertiary structure has been determined.
The SRS portal supports linking from any database to any other database in the system. If two
databases are not directly connected by a link, then a series of intermediary links is created. As
illustrated in
Figure 4-6
, SRS attempts to find the shortest possible way for linking two databases.
Ideally this is the direct link as between EMBL and SWISS-PROT However, with a link request such as
EMBL > PDB, when there are no nucleotide sequences in EMBL that are referenced by the PDB
database of tertiary protein structures, then SRS automatically links the two databases through a
SWISS-PROT intermediary, which relates both databases.
Figure 4-6. SRS Database Linking. When instructed to link databases
without relevant references, SRS identifies the best intermediary database
to support the link. In this example, a link between EMBL and PDB is
automatically facilitated by SRS-directed links through the SWISS-PROT
database.
