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UniProt release 7.2

Published March 7, 2006

Headlines

The most frequently updated entry

The most obvious way to quantify the work done by UniProtKB/Swiss-Prot is to count the increase in new entries. However, the integration of new entries is only part of the annotation work. Providing the scientific community with high quality data also - and maybe mostly - involves time-consuming updates of older entries. Thanks to the introduction of sequence and annotation version numbers and to the creation of the UniProtKB Sequence/Annotation Version Database, it is now possible to know when and how a UniProtKB/Swiss-Prot entry has been updated.

Sequences shown at the bottom of each entry are relatively stable. In 83% of entries, the sequence has not been updated since its integration in the knowledgebase, in 15% of the entries, it has been updated once. So far, the maximal number of sequence updates is 6 times and this is observed only in 8 entries. By contrast, the annotation has to be constantly reviewed.

Currently the average UniProtKB/Swiss-Prot entry has been updated more than 50 times. The most frequently updated entry is human coagulation factor IX which has been reviewed 103 times while its sequence has been updated only once. The human coagulation factor IX entry was created in the first UniProtKB/Swiss-Prot release in July 1986. Since then, over 50 references have been added, mostly dealing with polymorphisms and disease-causing mutations. This is also reflected at the level of the feature table, where the number of described variants had risen from 1 to 145, most of them associated with hemophilia. While the presence of gamma-carboxyglutamate was already well-established 20 years ago and the sites of N-glycosylation suspected, other post-translational modifications, such as sites of O-glycosylation, phosphorylation and sulfation were described, and thus annotated, later. Information on secondary structure was added to the entry in 1994, as well as the first link to the 3D structure submitted to PDB. Today 7 cross-references to PDB are provided.

Science is going forward and we, at Swiss-Prot, are doing our best to keep pace. Nevertheless, we need the user community to help us in this task. All our entries are equipped with a "Submit update" button and we greatly encourage you to use it every time your favourite protein is not up-to-date in UniProtKB/Swiss-Prot, or if it is not yet integrated.


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Cross-references to GenomeReviews

Cross-references have been added to GenomeReviews, a genome annotation database which provides up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes.

The format of the explicit links in the flat file is:

Resource abbreviation GenomeReviews
Resource identifier GenomeReviews accession number.
Optional information 1 Ordered locus name, or, if it does not exist, gene name.
Examples
P08409:
DR GenomeReviews; U00096_GR; b0016.
DR GenomeReviews; U00096_GR; b0582.
DR GenomeReviews; U00096_GR; b2394.

Q92YD2: 
DR GenomeReviews; AE006469_GR; betB2.

Changes concerning keywords