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UniProt release 13.5

Published June 10, 2008

Headlines

Over 100 cross-references in UniProtKB/Swiss-Prot

UniProtKB/Swiss-Prot was the first biomolecular database to include cross- references in its entries. As of this release, we provide our users with 101 explicit links (stored in the various distributed file formats, flat text, XML and RDF/XML) and 23 implicit links (available only from web servers, such as UniProt and ExPASy). Most cross-references can be found in the 'Cross-references' section of the entry (see for example Q9FK25), some are in the 'Sequence annotation' section (the Feature table in the flat file) (see for example cross-references to dbSNP in Q969T7). The dbxref.txt document provides a list of the databases cross-referenced in UniProtKB/Swiss-Prot. This document is available on the UniProt website and by ftp.

Additional links pepper almost every section of a UniProtKB/Swiss-Prot entry. They include cross-references to PubMed which are located in the 'References' section (see for example P0A790) and cross-references to the ENZYME database available through the EC numbers in the 'Names and origin' section (see for example Q00955). Moreover the 'Web resources' section is dedicated to databases or web pages that are specific for a single protein (see for example P04637). Note that the dbxref.txt document does not list these 'special' links.

Historically, a 'hundred' was a geographic division referring to the amount of land sufficient to sustain one hundred families. With over 120 cross-references, we hope to sustain many more research groups in quest of protein information.

UniProtKB News

Cross-references to HOGENOM

Cross-references have been added to HOGENOM, a database of homologous genes from fully sequenced organisms. HOGENOM allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is as well possible to search for orthologous genes in a wide range of taxons. Thus HOGENOM is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generaly, HOGENOM gives an overall view of what is known about a peculiar gene family.

The HOGENOM database is available at http://pbil.univ-lyon1.fr/databases/hogenom.php.

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

Resource abbreviation HOGENOM
Resource identifier UniProtKB accession number.
Examples
P0A9I1:
DR   HOGENOM; P0A9I1; -.

P49642:
DR   HOGENOM; P49642; -.

Cross-references to HOVERGEN

Cross-references have been added to HOVERGEN, a database of homologous vertebrate genes. HOVERGEN allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. Thus HOVERGEN is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generaly, HOVERGEN gives an overall view of what is known about a peculiar gene family.

The HOVERGEN database is available at http://pbil.univ-lyon1.fr/databases/hovergen.php.

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

Resource abbreviation HOVERGEN
Resource identifier UniProtKB accession number.
Examples
P31946:
DR   HOVERGEN; P31946; -.

Q91ZB4:
DR   HOVERGEN; Q91ZB4; -.

Changes concerning keywords

New keywords: