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Annotation score

The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score cannot be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.

The annotation score is computed in the following way:

  • The score of an individual entry is the sum of the scores of its annotations.
  • The score of a proteome is the sum of the scores of the entries that are part of the proteome.

The open-ended interval obtained for these absolute numbers is translated into a 5-point-system by splitting it into 5 sub-intervals. Scores in the first interval are represented by “1 point out of 5” , those in the second by “2 points out of 5”, etc. An annotation score of 5 points is therefore associated with the best-annotated entries, and a 1-point-score denotes an entry with rather basic annotation.

There are several contexts in which annotation scores can be used:

The annotation scores can help you to get a quick idea of the relative level of annotation of the entries in your search results. Please note that search results are not ranked by the annotation score, but by a query score that considers not only the annotation scores of the entries that match your query, but also how often (and where) your query term(s) appear in a matching entry and across the whole database, and the importance of a term according to the total number of terms. For this reason, the best ranked entries are not necessarily those with the highest annotation scores.

UniProt is using annotation scores to select the representative member of a UniRef cluster.

UniProt is using annotation scores to assist the selection of reference proteomes.

Please note that the annotation score cannot be used as a measure of the accuracy of the annotation – as we cannot define the ‘correct annotation’ for any given protein.

See also:
Introducing Annotation Scores in UniProt

UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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