Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries

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 form the text considerably more information than is immediately apparent due to his extended biological background knowledge and logical reasoning. 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(annotator) program, is described and the results of its application to sequence attribute assignment and sequence domain annotation of SWISS-PROT entries, are presented. The current software version assigns useful subcellular localization qualifiers to similar to 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: The software is available form Frank.Eisenhaber@embl-heidelberg.de. Results of the cellular localization assignment can be viewed at the ULR http://www.bork.embl-heidelberg.de/CELL_LOC/CELL_LOC.html. Contact: Frank.Eisengaber@EMBL-Geidelberg.DE.