Release 1.1

Published January 16, 2004

Headlines

10,000 different citations for JBC in Swiss-Prot

The Journal of Biological Chemistry (generally known as JBC) has always been a gold mine for publications directly relevant to the scope of Swiss-Prot. Starting with the first release in 1986 and up to now it has always been the most cited journal in Swiss-Prot. We are now citing about 10,000 different JBC papers in Swiss-Prot. This is almost twice the value for the next most cited journal, PNAS (Proceedings of the National Academy of Sciences of the U.S.A.).

It is also noteworthy that JBC was the first major life science journal to be available as full text on the WWW. It is therefore a good opportunity to thank the JBC editorial board and its staff for the great service they are providing to the Life Sciences community.

UniProtKB news

Changes concerning keywords

New keywords:

Deleted keywords:

Liver
Muscle
Nerve
Neurone

New documentation file strains.txt

The strain information is usually given in the RC line of the reference block, but can also be indicated in the Organism (OS) line of a database entry. Strains are controlled vocabulary and we created a list of the strains and their synonyms. This information is now made available in the documentation file strains.txt, together with the mnemonic species identification code representing the biological source of the protein in the knowledgebase.

New format of the documentation file keywlist.txt

Keywords are controlled vocabulary and the annotation follows strict rules. As biological terms can have several meanings, we added to the list of keywords the definition of their usage in the knowledgebase and further information such as synonyms or relevant GO terms.

Please note that the file header changed and the format for each keyword entry looks as follows:

Line code  Content                         Occurrence in an entry

ID         Identifier (keyword)            Once; starts an entry
AC         Accession (KW-xxxx)             Once
DE         Definition                      Once or more
SY         Synonyms                        Optional; Once or more
GO         Gene ontology (GO) mapping      Optional; Once or more
HI         Hierarchy                       Optional; Once or more
WW         Interesting WWW site            Optional; Once or more
CA         Category                        Once
//         Terminator                      Once; ends an entry

Example of a keyword definition entry:

ID   Acetoin catabolism.
AC   KW-0006
DE   Protein involved in the degradation of acetoin (3-hydroxy-2-butanone).
DE   Acetoin is a component of the butanediol cycle (butanediol
DE   fermentation) in microorganisms.
SY   Acetoin degradation.
GO   GO:0045150; acetoin catabolism
CA   Biological process; Pathway.
//

Change in the name of the files containing deleted AC numbers

As UniProt knowledgebase documentation now comprises both Swiss-Prot and TrEMBL, we changed the name of the files "deleteac.txt" containing deleted AC numbers to

"delac_sp.txt" (for deleted Swiss-Prot ACs)
"delac_tr.txt" (for deleted TrEMBL ACs).

Discontinuation of the embltosp.txt index file

The embltosp.txt file, which contained an index of EMBL Nucleotide Sequence Database entries referenced in Swiss-Prot, is no longer available.