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UniProt release 15.0

Published March 24, 2009

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A UniProtKB major release (15.0)

UniProt Knowledgebase release 15.0 includes Swiss-Prot release 57.0 and TrEMBL release 40.0.

Release 57.0 of 24-Mar-09 of UniProtKB/Swiss-Prot contains 428'650 sequence entries, comprising 154'416'236 amino acids abstracted from 177'584 references. 36'053 sequences have been added since release 56.0, the sequence data of 2'010 existing entries have been manually updated and the annotations of 368'500 entries have been revised.

Release 40.0 of 24-Mar-2009 of UniProtKB/TrEMBL contains 7'537'442 sequence entries, comprising 2'459'135'421 amino acids. 1'700'878 sequences have been added since release 39.0, the sequence data of 24'829 existing entries has been updated and the annotations of 4'218'268 entries have been revised. This represents an increase of 31%.

The following improvements were carried out in the last 8 months:

  • We have structured the 'Pathway' subsection of the 'General annotation (Comments)' section (comment line (CC) topic PATHWAY in the flat file), using the controlled vocabulary provided by the UniPathway resource, in order to improve the consistency of annotation and to allow to parse its content. To accompany this change, we have created a new document: pathlist.txt which describes the controlled vocabulary used in the 'Pathway' subsection of the 'General annotation (Comments)' section.
  • We have enriched the controlled vocabulary for subcellular location description with 14 new terms. 6 have been deleted.
  • We have enriched the controlled vocabulary for post-translational modification description with 30 new terms: 9 for the subsection 'Modified residue' of the 'Sequence annotation (Features)' section (FT 'MOD_RES' in the flat file) and 21 for the subsection 'Cross-link' (FT 'CROSSLNK' in the flat file).
  • We have added cross-references to 9 new databases, bringing the total number of explicit cross-references to 111: Bgee, GeneCards, IPI, NextBio, Pathway_Interaction_DB, PRIDE, TCDB, Xenbase and to Plant Ontology (PO) in the tisslist.txt file. Cross-references to StyGene have been removed.
  • We have added 17 new keywords and 1 has been deleted. 10 of the newly created keywords are medical ones.

UniProtKB News

Change in the 'Encoded on' subsection (OG line in the flat file): from 'Chromatophore' to 'Organellar chromatophore'

After discussion with experts in the field and consultation with the Gene Ontology experts we have changed the OG line describing proteins encoded by the chromatophore of Paulinella chromatophora from:

      OG   Plastid; Chromatophore.
to: 
      OG   Plastid; Organellar chromatophore.

Changes concerning cross-references to StyGene

Cross-references to StyGene have been removed.

Removal of the 'salty.txt' document

The document salty.txt, listing Salmonella typhimurium strain LT2 entries, gene names and cross-references to StyGene, has been removed.

Changes concerning keywords

New keywords:

Modified keyword:

Changes in subcellular location controlled vocabulary

New subcellular location:

  • Pollen coat

Modified subcellular locations:

  • Chromatophore -> Organellar chromatophore
  • Chromatophore inner membrane -> Organellar chromatophore inner membrane
  • Chromatophore intermembrane space -> Organellar chromatophore intermembrane space
  • Chromatophore membrane -> Organellar chromatophore membrane
  • Chromatophore outer membrane -> Organellar chromatophore outer membrane
  • Chromatophore stroma -> Organellar chromatophore stroma
  • Chromatophore thylakoid -> Organellar chromatophore thylakoid
  • Chromatophore thylakoid lumen -> Organellar chromatophore thylakoid lumen
  • Chromatophore thylakoid membrane -> Organellar chromatophore thylakoid membrane