March2011 Annotation Advocacy Report

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Standardizing use of database cross-references in column 8 ('with')

UniProtKB-GOA have been contacting each MOD to work on standardizing the content of the 'with' field. UniProtKB-GOA have created a set of regular expressions (RegExps) which have been checked with the appropriate group for validation. Any values in the 'with' column that do not conform to these RegExps have been manually checked by GOA and either additional RegExps have been created where necessary, or the group supplying the annotations have been contacted with a request to adjust the values to match the RegExp. Most groups have responded in a positive way to this quality check and are interested in receiving regular checks on this field to help them improve the consistency within their gene association files.

Annotation call

The annotation call was held on Tuesday 22nd March. Agenda The topics covered included;

Loading PAINT annotations

Initially, UniProtKB-GOA incorporated PAINT files for human, chicken and other (non-MOD) species. As some groups do not have the resources to incorporate these annotations at the present time, GOA has asked all groups whether they would be happy for us to take the MOD PAINT files directly from the GOC site for upload into our UniProtKB GO annotation dataset, from where individual MODs can retrieve their own PAINT annotations.

GOA now incorporates PAINT annotation files for the following groups;

  • FlyBase
  • WormBase
  • DictyBase
  • EcoCyc
  • RGD

Technical priorities for Annotation Groups

See Draft page