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UniProt release 14.8

Published February 10, 2009

Headlines

The UniProtKB/Swiss-Prot bronze medal is awarded to the plant Arabidopsis thaliana

With 7'764 manually annotated entries, Arabidopsis thaliana is now the third most represented species in UniProtKB/Swiss-Prot, behind Homo sapiens (human) and Mus musculus (mouse). This corresponds to about 25% of the complete proteome of A.thaliana, which can be retrieved from UniProtKB using the keyword 'Complete proteome'.

The members of the Plant Proteome Annotation Program (PPAP) are very proud of this third position. As shown in a study on Olympic medalists by Medvec et al. (1995), competitors who won the bronze medal are significantly happier with their award than those who won the silver medal. The silver medalists tend to be frustrated at having missed out on the gold, while the bronze medalists are simply happy to have received any honor at all.

UniProtKB News

Cross-references to Plant Ontology (PO) in the tisslist.txt file

Cross-references to Plant Ontology (PO) have been added in the tisslist.txt file. Each term in this tissue list can be mapped to the corresponding eVOC term and, as of this release, also to a Plant Ontology (PO) term.

Examples:

ID   Aleurone.
AC   TS-0027
SY   Aleurone layer.
DR   PO; PO:0005360; aleurone layer.
//
ID   Embryo.
AC   TS-0229
SY   Embryonic; Embryonic tissue; Whole embryo; Parthenogenote.
DR   eVOC; EV:0300001; development-stage: embryo.
DR   PO; PO:0009009; embryo.
//

Cross-references to IPI

Cross-references have been added to the International Protein Index IPI. IPI maintains a database of cross-references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins and maintains stable identifiers for proteomes of higher eukaryotic organisms.

IPI is available at http://www.ebi.ac.uk/IPI/IPIhelp.html.

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

Resource abbreviation IPI
Resource identifier IPI unique identifier.
Examples 
Q8NFR9:
DR   IPI; IPI00168887; -.
DR   IPI; IPI00177866; -.
DR   IPI; IPI00747706; -.
DR   IPI; IPI00789075; -.
DR   IPI; IPI00876915; -.

P03898:
DR   IPI; IPI00716083; -.

Cross-references to Bgee

Cross-references have been added to Bgee, a database for Gene Expression Evolution. Bgee is a database that allows to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix and in situ hybridization data) on anatomical and developmental ontologies.

Bgee is available at http://bgee.unil.ch/bgee/bgee.

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

Resource abbreviation Bgee
Resource identifier UniProtKB accession number.
Examples 
Q9Z351:
DR   Bgee; Q9Z351; -.

P62835:
DR   Bgee; P62835; -.

Changes in subcellular location controlled vocabulary

New subcellular locations:

  • Membrane raft
  • Perispore
  • Prospore
  • Prospore membrane
  • Spore coat
  • Spore core membrane
  • Spore cortex
  • Spore outer membrane

Deleted subcellular locations:

  • Endospore
  • Endospore coat
  • Endospore cortex
  • Endospore exosporium
  • Endospore intermembrane
  • Endospore outer membrane

Changes in PTM controlled vocabulary

New PTMs:

  • (3R,4R)-4,5-dihydroxyisoleucine
  • (3R,4S)-4-hydroxyisoleucine
  • (3S,4R)-3,4-dihydroxyisoleucine
  • 2'-cysteinyl-6'-hydroxytryptophan sulfoxide (Trp-Cys)
  • 2-oxazoline-4-carboxylic acid (Cys-Ser)
  • 3-hydroxy-5-methylproline
  • 3-hydroxyphenylalanine
  • 3-hydroxyvaline
  • 5-amino-piperideine-2,5-dicarboxylic acid (Ser-Cys) (with S-...)
  • 5-amino-piperideine-2,5-dicarboxylic acid (Ser-Ser) (with C-...)
  • 5-methoxythiazole-4-carboxylic acid (Val-Cys)
  • 5-methyloxazole (Ser-Thr)
  • 5-methylthiazole-4-carboxylic acid (Asn-Cys)
  • Cyclopeptide (Ile-Pro)
  • Cyclopeptide (Leu-Leu)
  • Decarboxylated threonine
  • N6-(ADP-ribosyl)lysine
  • O-methylthreonine
  • Pyridine-2,5-dicarboxylic acid (Ser-Cys) (with S-...)
  • Pyridine-2,5-dicarboxylic acid (Ser-Ser) (with C-...)
  • Thiazole-4-carboxylic acid (Asn-Cys)
  • Thiazole-4-carboxylic acid (Cys-Cys)
  • Thiazole-4-carboxylic acid (Ile-Cys)
  • Thiazole-4-carboxylic acid (Phe-Cys)
  • Thiazole-4-carboxylic acid (Pro-Cys)
  • Thiazole-4-carboxylic acid (Ser-Cys)
  • Thiazole-4-carboxylic acid (Thr-Cys)
  • Thiazole-4-carboxylic acid (Val-Cys)
  • Thiazoline-4-carboxylic acid (Phe-Cys)
  • Thiazoline-4-carboxylic acid (Thr-Cys)