From owner-bionews@hgmp.mrc.ac.uk Tue Oct 30 01:25:06 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CEA1417A63 for ; Tue, 30 Oct 2001 01:24:58 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1D49017BEA for ; Tue, 30 Oct 2001 01:24:53 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6022) id 5F4D717AB4; Tue, 30 Oct 2001 01:24:43 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CF4BF17B28 for ; Wed, 24 Oct 2001 08:58:32 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id B71CB17B69; Wed, 24 Oct 2001 08:57:44 +0100 (BST) To: bionet-announce@net.bio.net From: Elisabeth.Gasteiger@isb-sib.ch (Elisabeth Gasteiger) Newsgroups: bionet.announce Subject: SWISS-PROT release 40 available Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <3BD67458.7F40213F@isb-sib.ch> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6A76D17A81 for ; Wed, 24 Oct 2001 08:57:37 +0100 (BST) X-Received: from isb-sib.ch (expasy-e.unige.ch [192.33.215.141]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 722A717B69 for ; Wed, 24 Oct 2001 08:57:16 +0100 (BST) X-Received: from isb-sib.ch ([192.33.215.130]) by isb-sib.ch (8.9.3/8.9.3) with ESMTP id JAA22629; Wed, 24 Oct 2001 09:56:47 +0200 (MET DST) X-Reply-To: Elisabeth.Gasteiger@isb-sib.ch X-Mailer: Mozilla 4.77 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: en X-To: bionews@net.bio.net Date: Tue, 30 Oct 2001 01:24:43 +0000 (GMT) Sender: owner-bionews@hgmp.mrc.ac.uk Precedence: bulk (I) DATABASE AVAILABILITY ANNOUNCEMENT Name : SWISS-PROT Description : Protein sequence database. Release : 40.0 of October 2001 Statistics : 101'602 fully annotated sequences , 37'315'215 amino acids, 91'880 references. Citation : Bairoch A., Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28:45-48(2000). Availability: FTP: ftp://ftp.expasy.org/databases/swiss-prot ftp://ftp.ebi.ac.uk/pub/databases/swissprot WWW: http://www.expasy.org/sprot/ http://www.ebi.ac.uk/swissprot/ Name : ENZYME Description : Enzyme nomenclature database. Release : 27.0 of October 2001 Statistics : 3'870 enzymes described. Citation : Bairoch A. The ENZYME database in 2000. Nucleic Acids Res. 28:304-305(2000). Availability: FTP: ftp://ftp.expasy.org/databases/enzyme ftp://ftp.ebi.ac.uk/pub/databases/enzyme WWW: http://www.expasy.org/enzyme/ --------------------------------------------------------------------- (II) SUMMARY OF CURRENT CHANGES AND FUTURE DEVELOPMENTS IN SWISS-PROT, PROSITE AND ENZYME Note: a much more complete description of the changes and future developments that are listed below is available from the release notes. The release notes can be accessed from the WWW at the address: http://www.expasy.org/sprot/relnotes/ or downloaded by FTP from: ftp://ftp.expasy.org/databases/swiss-prot/release/relnotes.txt ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release/relnotes.txt A) Summary of the changes in SWISS-PROT release 40 and ENZYME release 27. In SWISS-PROT: - The name of the database changed from 'SWISS-PROT protein sequence database' to 'SWISS-PROT knowledgebase' to emphasize the fact that SWISS-PROT collects, by far, more than just information on protein sequences and that it is a central linking and linked database which connects the various findings in the diverse fields of proteomics research. - Release 40.0 of SWISS-PROT contains 101'602 sequence entries, comprising 37'315'215 amino acids abstracted from 91'880 references. 15'184 sequences have been added since release 39, the sequence data of 2'908 existing entries has been updated and the annotations of 44'684 entries have been revised. With this release SWISS-PROT has passed the symbolic mark of 100 thousand entries. - In order to handle the large amount of "raw" data coming from the microbial genomic sequencing, the High quality Automated Microbial Annotation of Proteomes (HAMAP) project was initiated. The latter aims to automatically annotate a significant percentage of proteins which originate from microbial genome sequencing projects. See: http://www.expasy.org/sprot/hamap/ - The Human Proteomics Initiative (HPI) project is progressing. There are currently 7'471 annotated human sequences in SWISS-PROT. These entries are associated with 19'922 literature references, 18'974 experimental or predicted PTM's, 1'697 splice variants and 12'061 polymorphisms. See: http://www.expasy.org/sprot/hpi/ - There can now be more than one AC (ACcession) line per SWISS-PROT entry. - The OX (Organism taXonomy cross-reference) line has been introduced to indicate the identifier to a specific organism in a taxonomic database. - The RX line format changed, and it now provides identifiers not only to Medline but also to PubMed. - We have introduced two new 'topics' for the comments (CC) line type: o The topic 'BIOTECHNOLOGY' has been introduced to describe the use of a specific protein in the biotechnological industry. o The topic 'PHARMACEUTICAL' has been introduced to describe the use of a specific protein as a pharmaceutical drug. - We are continuing a major overhaul of various comment line topics. A special effort has been done in making the ALTERNATIVE PRODUCTS and SIMILARITY topics more standardized. - We have added cross-references from SWISS-PROT to the following databases: ANU-2DPAGE, COMPLUYEAST-2DPAGE, GlycoSuiteDB, Leproma, MEROPS, MypuList, PHCI-2DPAGE, PMMA-2DPAGE, ProDom, Siena-2DPAGE and SMART. - A new FT key: SE_CYS was introduced to describe selenocysteine residues. - We have introduced feature identifiers (FTId) to the feature keys CARBOHYD and VARIANT. These stable feature identifiers allow to construct links directly from position-specific annotation in the feature table to specialized protein-related databases. - We are gradually converting SWISS-PROT entries from all 'UPPER CASE' to 'MiXeD CaSe'. The line-types that have been converted between release 38 and 40 are: DE (DEscription), most RC (Reference Comment) topics (SPECIES, TISSUE, PLASMID and TRANSPOSON) and DR (Database cross- Reference). The new OX line and the new CC topics PHARMACEUTICAL and BIOTECHNOLOGY have been introduced in mixed case. The CC topic MASS SPECTROMETRY has been converted to mixed case. - The SQ line syntax was changed to replace the 32-bit CRC (Cyclic Redundancy Check) value by a 64-bit CRC. - Many new documents were introduced such as DBXREF.TXT (list of databases cross-referenced in SWISS-PROT), HUMCHR01.TXT to HUMCHR15.TXT, INTEIN.TXT (Index of intein-containing entries referenced in SWISS-PROT), or PLASMID.TXT (List of plasmids). - The ExPASy WWW server was the target of many improvements that are all described at the address: http://www.expasy.org/history.html In ENZYME: - Many new enzymes were added to the database. The description of many more was updated. In PROSITE: - A new release of PROSITE will be announced in a few weeks. B) Future developments Here is what was announced as planned changes for release 41: - We are planning to elongate the mnemonic code for the protein name in the ID line from up to 4 characters to up to 5 characters. - Starting with release 41, there can be more than one RP (Reference Position) line per reference in a SWISS-PROT entry. - We are in the process of cleaning up the CC comments topics PATHWAY and COFACTOR. - Conversion to mixed case will continue and will affect the GN (Gene Name) line, the RC (Reference Comment) line topic STRAIN, and the CC (Comment) line topics CATALYTIC ACTIVITY and PATHWAY. Of course the above list is far from being definitive, we await your suggestions! ---------------------------------------------------------------------------- SWISS-PROT is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL Outstation - the European Bioinformatics Institute. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement. For information about the licensing scheme see: http://www.isb-sib.ch/announce/ or send an email to license@isb-sib.ch. ---------------------------------------------------------------------------- -- ----------------------------------------------------------------- Elisabeth Gasteiger Swiss Institute of Bioinformatics CMU - 1, rue Michel Servet Tel. (+41 22) 702 58 75 CH - 1211 Geneva 4 Switzerland Fax (+41 22) 702 58 58 Elisabeth.Gasteiger@isb-sib.ch http://www.expasy.org/ ----------------------------------------------------------------- --- .