Swiss-Prot Protein Knowledgebase
TrEMBL Protein Database
Release 2013_11 of 13-Nov-2013
Also read about recent changes, and recent and forthcoming changes for the XML version of the UniProt Knowledgebase.
Table of contents
|Extension of the UniProtKB accession number format|
Not before: 19-Feb-2014
UniProtKB accession numbers currently consist of 6 alphanumerical characters in the format:
1 2 3 4 5 6 [O,P,Q] [0-9] [A-Z,0-9] [A-Z,0-9] [A-Z,0-9] [0-9] [A-N,R-Z] [0-9] [A-Z] [A-Z,0-9] [A-Z,0-9] [0-9]
With our projected growth of UniProtKB, we expect to use up all accession numbers of this format in 2014. We will therefore extend the format to 10 alphanumerical characters:
1 2 3 4 5 6 7 8 9 10 [O,P,Q] [0-9] [A-Z,0-9] [A-Z,0-9] [A-Z,0-9] [0-9] [A-N,R-Z] [0-9] [A-Z] [A-Z,0-9] [A-Z,0-9] [0-9] [A-N,R-Z] [0-9] [A-Z] [A-Z,0-9] [A-Z,0-9] [0-9] [A-Z] [A-Z,0-9] [A-Z,0-9] [0-9]
|Removal of the cross-references to IPI|
Not before: 22-Jan-2014
Cross-references to IPI will be removed.
IPI has closed in 2011. The last release is archived at ftp://ftp.ebi.ac.uk/pub/databases/IPI.
Complete proteome data is available from UniProtKB.
If you have IPI identifiers which you need to map to UniProtKB, we recommend to convert these identifiers as soon as possible. You can use UniProt's ID mapping service, or query UniProtKB programmatically with queries like this:
More information about programmatic access can be found here.
You can also download (until the removal of the cross-references) a mapping table between UniProtKB and IPI:
Once the cross-reference is removed, an archive of the last mapping table between UniProtKB and IPI will be archived at:
|Format change in the cross-references to PROSITE and HAMAP|
Not before: 22-Jan-2014
Changes for PROSITE:
The optional qualifiers 'UNKNOWN', 'FALSE_NEG' and 'PARTIAL' will be removed. Only matches above the threshold will be kept, i.e. cross-references with a 'FALSE_NEG' or 'PARTIAL' qualifier will be removed.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; UNKNOWN_1. DR PROSITE; PS00922; TRANSGLYCOSYLASE; FALSE_NEG.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.O02781:
DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; PARTIAL. DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1.
DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1.
Changes for HAMAP:
The optional field that describes the nature of signature hits ('atypical', 'fused' or 'atypical/fused') will be removed. Only matches above the threshold will be kept, i.e. 'atypical' and 'atypical/fused' cross-references will be removed if their match score is below the threshold.
DR HAMAP; MF_00006; Arg_succ_lyase; 1; fused. DR HAMAP; MF_01105; N-acetyl_glu_synth; 1; atypical/fused.
DR HAMAP; MF_00006; Arg_succ_lyase; 1.
|Cross-references for isoform sequences|
Not before: 19-Mar-2014
Some of the resources to which we link contain information that is specific to an isoform sequence. Where applicable, we are going to indicate this in UniProtKB by an optional field at the end of the DR line that shows the UniProtKB isoform sequence identifier in square brackets:
DR ResourceAbbreviation; ResourceIdentifier(; AdditionalField)+. [IsoId]