Databases and Systems

223
other databanks, and define specific views on application results. For example: the
default view for a BLAST search links all BLAST hits to the databank searched (e.g.
SWISS-PROT), and displays the description field from there. Since application
results from further application launches are accumulated, one can answer questions
such as “Which hits were reported by the last search but not by the previous search?”,
or “In the last three searches, which hits had a bit-score above 30?” The comparison
is done using a link operation. This method can also be used to collate different
algorithms’ performance on a particular problem (e.g., a specific search by both
BLAST and FASTA, or the effects of different parameters settings on an algorithm’s
performance).
As soon as the application program has finished running, its results are thus ‘just
another databank’, which are consequently parsed and indexed. Each application
therefore has an associated SRS databank parser, database structure description and
documentation. This documentation is augmented by the help text for application
parameters.
SRS Views
In the past within SRS, the retrieved information was always a set of entries each
from a single databank. The specification of views was added so that the user can
define virtual entries that may include information from many sources. Views can be
used to treat the sum of all installed databanks as a single structure where user
defined entities can freely span databank boundaries.
SRS regards an entry as a list of data-fields. The simplest form of a view acts as a
filter and allows only selected fields to be displayed. For instance, a view could be
defined to display only the ID, the description and the line containing the sequence
length for SWISS-PROT entries as shown in figure 4. This type of view, the ‘list-
view’, displays the selected data-fields in the order they occur within the entry and in
their original format which includes line codes or field labels. It is mostly useful for
‘turning off undesired information during browsing large sets of entries.
ID ACHA_HUMAN STANDARD; PRT; 402 AA.
DE ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN PRECURSOR.
SQ SEQUENCE 482 AA; 54545 MW; E050B513 CRC32;
Figure 4. A SWISS-PROT entry displayed by a list-view.
The table-view provides more sophistication and possibilities. The entry in the