UniProt release 1.1
Published January 16, 2004
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.
Changes concerning keywords
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.