Bioinformatics, Vol 15, 528-535, Copyright © 1999 by Oxford University Press
F Eisenhaber and P Bork
MOTIVATION: Computer-based selection of entries from sequence databases
with respect to a related functional description, e.g. with respect to a
common cellular localization or contributing to the same phenotypic
function, is a difficult task. Automatic semantic analysis of annotations
is not only hampered by incomplete functional assignments. A major problem
is that annotations are written in a rich, non- formalized language and are
meant for reading by a human expert. This person can extract from the text
considerably more information than is immediately apparent due to his
extended biological background knowledge and logical reasoning. APPROACH: A
technique of automated annotation evaluation based on a combination of
lexical analysis and the usage of biological rule libraries has been
developed. The proposed algorithm generates new functional descriptors from
the annotation of a given entry using the semantic units of the annotation
as prepositions for implications executed in accordance with the rule
library. RESULTS: The prototype of a software system, the Meta_A(nnotator)
program, is described and the results of its application to sequence
attribute assignment and sequence selection problems, such as cellular
localization and sequence domain annotation of SWISS-PROT entries, are
presented. The current software version assigns useful subcellular
localization qualifiers to approximately 88% of all SWISS-PROT entries. As
shown by demonstrative examples, the combination of sequence and annotation
analysis is a powerful approach for the detection of mutual
annotation/sequence inconsistencies. AVAILABILITY: Results for the cellular
localization assignment can be viewed at the URL http://www.bork.
embl-heidelberg.de/CELL_LOC/CELL_LOC.html.
ARTICLES
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries
Max-Delbruck-Centrum fur Molekulare Medizin, Robert-Rossle-Strasse 10, 13122 Berlin-Buch, Germany. Frank.Eisenhaber@embl-heidelberg.de
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