Filtering erroneous protein annotation

Bioinformatics. 2004 Aug 4;20 Suppl 1:i342-7. doi: 10.1093/bioinformatics/bth938.


Motivation: Automatically generated annotation on protein data of UniProt (Universal Protein Resource) is planned to be publicly available on the UniProt web pages in April 2004. It is expected that the data content of over 500,000 protein entries in the TrEMBL section will be enhanced by the output of an automated annotation pipeline. However, a part of the automatically added data will be erroneous, as are parts of the information coming from other sources. We present a post-processing system called Xanthippe that is based on a simple exclusion mechanism and a decision tree approach using the C4.5 data-mining algorithm.

Results: It is shown that Xanthippe detects and flags a large part of the annotation errors and considerably increases the reliability of both automatically generated data and annotation from other sources. As a cross-validation to Swiss-Prot shows, errors in protein descriptions, comments and keywords are successfully filtered out. Xanthippe is a contradictive application that can be combined seamlessly with predictive systems. It can be used either to improve the precision of automated annotation at a constant level of recall or increase the recall at a constant level of precision.

Availability: The application of the Xanthippe rules can be browsed at

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Databases, Protein*
  • Documentation / methods*
  • Information Storage and Retrieval / methods*
  • Molecular Sequence Data
  • Proteins / chemistry*
  • Proteins / classification*
  • Sequence Analysis, Protein / methods*
  • Software


  • Proteins