Release 3.5

UniProtKB News

Extension of the Swiss-Prot entry name format

We endeavor to assign meaningful entry names that facilitate the identification of the proteins and the species of origin. Swiss-Prot uses a general purpose naming convention that can be symbolized as X_Y, where X is a mnemonic code of alphanumeric characters representing the protein name, the '_' sign serves as a separator, and the Y is a mnemonic species identification code of at most 5 alphanumeric characters representing the biological source of the protein.

The entry name used to consist of up to ten uppercase alphanumeric characters. We now elongated the mnemonic code for the protein name from up to 4 characters to up to 5 characters, thus entry names can from now on consist of up to 11 characters.

As this modification might have an impact on many programs, we introduced in this release only one Swiss-Prot entry with an entry name in the new format: TINA1_DROME (Q9W0Y1). With UniProtKB release 4.0 at the beginning of February, we will change the entry names of many Swiss-Prot entries.

We strongly advise users to cite Swiss-Prot entries by their unique and stable identifer, which is the first (primary) accession number of an entry. It happens occasionally that entries are only referred to by the entry name. As we will soon change the entry names of thousands of entries, we provide the tool IDtracker, which allows users of the Swiss-Prot protein knowledgebase to trace the identifiers (ID) of protein entries.

Cross-references to Ensembl

Cross-references have been added to the Ensembl database, a bioinformatics project that organizes biological information around the sequences of large genomes. Ensembl is available at http://www.ensembl.org.

The format for the explicit links are:

O43462: 
DR   Ensembl; ENSG00000012174; Homo sapiens.