TrEMBL release 23.0
Published March 1, 2003
TrEMBL Release Notes Release 23, March 2003 EMBL Outstation European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Telephone: (+44 1223) 494 444 Fax: (+44 1223) 494 468 Electronic mail address: firstname.lastname@example.org WWW server: http://www.ebi.ac.uk/ Swiss Institute of Bioinformatics (SIB) Centre Medical Universitaire 1, rue Michel Servet 1211 Geneva 4 Switzerland Telephone: (+41 22) 702 50 50 Fax: (+41 22) 702 58 58 Electronic mail address: Amos.Bairoch@isb-sib.ch WWW server: http://www.expasy.org/ Acknowledgements TrEMBL has been prepared by: o Maria Jesus Martin, Claire O'Donovan, Nicola Althorpe, Rolf Apweiler, Daniel Barrell, Kirsty Bates, Paul Browne, Daniel Barrell, Kirill Degtyarenko, Gill Fraser, Alexander Fedetov, Andre Hackmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Ernst Kretschmann, Kati Laiho, Minna Lehvaslaiho, Michele Magrane, Michelle McHale, Virginie Mittard, Nicola Mulder, John F. O'Rourke, Sandra Orchard, Astrid Rakow, Sandra van den Broek, Eleanor Whitfield and Allyson Williams at the EMBL Outstation - European Bioinformatics Institute (EBI) in Hinxton, UK; o Amos Bairoch, Alexandre Gattiker, Karine Michoud, Isabelle Phan and Sandrine Pilbout at the Swiss Institute of Bioinformatics in Geneva, Switzerland. Copyright Notice TrEMBL copyright (c) 2003 EMBL-EBI This manual and the database it accompanies may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy. Citation If you want to cite TrEMBL in a publication please use the following reference: Boeckmann B., Bairoch A., Apweiler R., Blatter M., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Schneider M. (2003) The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370. 1. Introduction TrEMBL is a computer-annotated protein sequence database complementing the Swiss-Prot Protein Knowledgebase. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL/GenBank/DDBJ Nucleotide Sequence Databases and also protein sequences extracted from the literature or submitted to Swiss-Prot, which are not yet integrated into Swiss-Prot. For all TrEMBL entries which should finally be upgraded to the standard Swiss-Prot quality, Swiss-Prot accession numbers have been assigned. 2. Why a complement to Swiss-Prot? The ongoing gene sequencing and mapping projects have dramatically increased the number of protein sequences to be incorporated into Swiss-Prot. We do not want to dilute the quality standards of Swiss-Prot by incorporating sequences without proper sequence analysis and annotation, but we do want to make the sequences available as quickly as possible. TrEMBL achieves this second goal, and is a major step in the process of speeding up subsequent upgrading of annotation to the standard Swiss-Prot quality.To address the problem of redundancy, the translations of all coding sequences (CDS) in the EMBL Nucleotide Sequence Database already included in Swiss-Prot have been removed from TrEMBL. 3. The Release This TrEMBL release has been produced in synch with Swiss-Prot release 41. It was created from the EMBL Nucleotide Sequence Database release 73 and contains 921'952 entries and 40'914'860 amino acids. TrEMBL is split in two main sections: SP-TrEMBL and REM-TrEMBL: SP-TrEMBL (Swiss-Prot TrEMBL) contains the entries (830'525) which should be eventually incorporated into Swiss-Prot. Swiss-Prot accession numbers have been assigned for all SP-TrEMBL entries. SP-TrEMBL is organized in subsections: arc.dat (Archaea): 1736 entries arp.dat (Complete Archaeal proteomes): 31625 entries fun.dat (Fungi): 15977 entries hum.dat (Human): 34880 entries inv.dat (Invertebrates): 79680 entries mam.dat (Other Mammals): 12223 entries mhc.dat (MHC proteins): 8813 entries org.dat (Organelles): 73538 entries phg.dat (Bacteriophages): 6448 entries pln.dat (Plants): 80929 entries pro.dat (Prokaryotes): 79736 entries prp.dat (Complete Prokaryotic Proteomes): 181432 entries rod.dat (Rodents): 40143 entries unc.dat (Unclassified): 331 entries vrl.dat (Viruses): 82490 entries vrt.dat (Other Vertebrates): 14889 entries vrv.dat (Retroviruses): 85655 entries 107'123 new entries have been integrated in SP-TrEMBL. The sequences of 1713 SP-TrEMBL entries have been updated and the annotation has been updated in 252'549 entries. In the document deleteac.txt, you will find a list of all accession numbers which were previously present in TrEMBL, but which have now been deleted from the database. REM-TrEMBL (REMaining TrEMBL) contains the entries (91'427) that we do not want to include in Swiss-Prot. REM-TrEMBL entries do not have Swiss-Prot accession numbers. Instead the stable ID portion of the protein_id present in the source EMBL/DDBJ/GenBank nucleotide sequence database entries is used as the ID and accession number.This section is organized in six subsections: 1) Immunoglobulins and T-cell receptors (Immuno.dat) Most REM-TrEMBL entries are immunoglobulins and T-cell receptors. We stopped entering immunoglobulins and T-cell receptors into Swiss-Prot, because we only want to keep the germ line gene derived translations of these proteins in Swiss-Prot and not all known somatic recombinated variations of these proteins. We would like to create a specialized database dealing with these sequences as a further supplement to Swiss-Prot and keep only a representative cross-section of these proteins in Swiss-Prot. 2) Synthetic sequences (Synth.dat) Another category of data, which will not be included in Swiss-Prot are synthetic sequences. Again, we do not want to leave these entries in TrEMBL. Ideally one should build a specialized database for artificial sequences as a further supplement to Swiss-Prot. 3) Patent application sequences (Patent.dat) A third subsection consists of coding sequences captured from patent applications. A thorough survey of these entries have shown that apart from a rather small minority (which in most cases have already been integrated in Swiss-Prot), most of these sequences contain either erroneous data or concern artificially generated sequences outside the scope of Swiss-Prot. 4) Small fragments (Smalls.dat) Another subsection consists of fragments with less than eight amino acids. 5) CDS not coding for real proteins (Pseudo.dat) This subsection consists of CDS translations where we have strong evidence to believe that these CDS are not coding for real proteins. 6) Truncated proteins (Truncated.dat) The last subsection consists of truncated proteins which result from events like mutations introducing a stop codon leading to the truncation of the protein product. 4. Format Differences Between Swiss-Prot and TrEMBL The format and conventions used by TrEMBL follow as closely as possible that of Swiss-Prot. Hence, it is not necessary to produce an additional user manual and extensive release notes for TrEMBL. The information given in the Swiss-Prot release notes and user manual are in general valid for TrEMBL. The differences are mentioned below. The general structure of an entry is identical in Swiss-Prot and TrEMBL. The data class used in TrEMBL (in the ID line) is always 'PRELIMINARY', whereas in Swiss-Prot it is always 'STANDARD'. Differences in line types present in Swiss-Prot and TrEMBL: The ID line (IDentification): The entry name used in SP-TrEMBL is the same as the Accession Number of the entry. The entry name used in REM-TrEMBL is the stable part of the protein_id tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database. 'protein_id' stands for the "Protein Identification" number. It is a number that you will find in the feature table of the EMBL nucleotide sequence entries in a qualifier called "/protein_id" which is tagged to every CDS. Example: FT CDS 339..1514 FT /codon_start=1 FT /db_xref="PID:g1256015" FT /product="dystrobrevin-epsilon" FT /protein_id="AAC50431.1" The protein_id is defined as follows in the The DDBJ/EMBL/GenBank Feature Table Definition documentation Qualifier /protein_id Definition Protein Identifier, issued by International collaborators. This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. Value format Example /protein_id="AAA12345.1" Comment When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented. The stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein. This qualifier is valid only on CDS features which translate into a valid protein. The DT line (DaTe) The format of the DT lines that serve to indicate when an entry was created and updated are identical to that defined in Swiss-Prot; but the DT lines in TrEMBL refer to the TrEMBL release. The difference is shown in the example below. DT lines in a Swiss-Prot entry: DT 01-JAN-1988 (Rel. 06, Created) DT 01-JUL-1989 (Rel. 11, Last sequence update) DT 01-AUG-1992 (Rel. 23, Last annotation update) DT lines in a TrEMBL entry: DT 01-NOV-1996 (TrEMBLrel. 01, Created) DT 01-NOV-1999 (TrEMBLrel. 12, Last sequence update) DT 28-FEB-2003 (TrEMBLrel. 23, Last annotation update) 5. Weekly updates of TrEMBL and non-redundant data sets 5.1 TrEMBL updates Weekly cumulative updates of TrEMBL are available by anonymous FTP and from the EBI SRS server. 5.2 SPTr We also produce every week a complete non-redundant protein sequence collection by providing three compressed files (these are in the directory /pub/databases/sp_tr_nrdb on the EBI FTP server and in databases/sp_tr_nrdb on the ExPASy server): sprot.dat.gz, trembl.dat.gz and trembl_new.dat.gz. This set of non-redundant files is especially important for two types of users: (i) Managers of similarity search services. They can now provide what is currently the most comprehensive and non-redundant data set of protein sequences. (ii) Anybody wanting to update their full copy of Swiss-Prot + TrEMBL to their own schedule without having to wait for full releases of Swiss-Prot or TrEMBL. 5.3 XML A version of Swiss-Prot and TrEMBL in XML format has been developed and is provided with this release. More information is available at http://www.ebi.ac.uk/swissprot/SP-ML <http://www.ebi.ac.uk/swissprot/SP-ML/> and the data can be downloaded from ftp://ftp.ebi.ac.uk/pub/databases/trembl/xml <ftp://ftp.ebi.ac.uk/pub/databases/trembl/xml/> and ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/xml <ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/xml/> We would welcome any feedback from the user community. 5.4 Varsplic Expand We also provide Varsplic Expand which is a program to generate "expanded" sequences from Swiss-Prot and TrEMBL records i.e. sequences including the variants specified by the varsplic, variant and conflict annotations. New records are produced in either pseudo-Swiss-Prot or FASTA format for each specified variant. More information and the data is available at ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/ 6. Access/Data Distribution FTP server: ftp.ebi.ac.uk/pub/databases/trembl <ftp.ebi.ac.uk/pub/databases/trembl/> SRS server: http://srs.ebi.ac.uk/ TrEMBL is also available on the Swiss-Prot CD-ROM. Swiss-Prot + TrEMBL is searchable on the following servers at the EBI: FASTA3 (http://www.ebi.ac.uk/fasta33/) BLAST2 (http://www.ebi.ac.uk/blast2/) Scanps (http://www.ebi.ac.uk/scanps/) MPSrch (http://www.ebi.ac.uk/MPsrch/) For each TrEMBL release, a synchronized version of the concurrent Swiss-Prot release is distributed at ftp.ebi.ac.uk/pub/databases/trembl/swissprot/ 7. Description of changes made to TrEMBL since release 22. 7.1 Changes concerning cross-references (DR line) We have added cross-references from TrEMBL to a number of new databases. 7.1.1 Schizosaccharomyces pombe GeneDB Prototype We have added cross-references to the Schizosaccharomyces pombe GeneDB Prototype (available at http://www.genedb.org/genedb/pombe/index.jsp) 7.1.2 Genew We have added cross-references to the Human Gene Nomenclature Database Genew (available at http://www.gene.ucl.ac.uk/nomenclature/searchgenes.pl). 7.2 Changes concerning the Organelle (OG) line The term Nucleomorph has been added which is the residual nucleus of an algal endosymbiont that resides inside its host cell. 8. Planned changes 8.1 Evidence tags We are continuing with the introduction of evidence tags to Swiss-Prot and TrEMBL entries. The aim of this is to allow users to see where data items came from and to enable Swiss-Prot staff to automatically update data if the underlying evidence changes. This is ongoing internally and the evidence tags are visible in the XML version of Swiss-Prot and TrEMBL. For more information, please see http://www.ebi.ac.uk/swissprot/SP-ML/evidence.html We would welcome any feedback from the user community. 8.2 Conversion of TrEMBL to mixed case Most of the DE (DEscription), GN (Gene Name), RC (Reference Comment) and CC (Comment) lines have been converted to mixed case internally. The conversion is ongoing and will be made public as the conversion of each line type reaches a satisfactory stage. A mixed case version of the DE line was made public in release 21. The RC line is mixed case in this release. 8.3 Version of SPTr in XML format: We intend to provide an XML version of SPTr updated monthly 8.4 Reference Comment (RC) line topics may span lines The RC (Reference Comment) line store comments relevant to the reference cited, in currently 5 distinct topics: PLASMID, SPECIES, STRAIN, TISSUE and TRANSPOSON. It is not always possible to list all information within one line. Therefore we will allow multiple RC lines, in which one topic might span over a line. Example: RC STRAIN=Various strains; could become RC STRAIN=AZ.026, DC.005, GA.039, GA2181, IL.014, IN.018, KY.172, KY2.37, RC LA.013, MN.001, MNb027, MS.040, NY.016, OH.036, TN.173, TN2.38, RC UT.002, AL.012, AZ.180, MI.035, VA.015, and IL2.17; 8.5 New format of comment line (CC) topics We are continuing a major overhaul of various comment line topics. We would like the majority of the information stored to be usable by computer programs (while remaining human-readable). We are therefore standardizing the format of the topics. Please see Swiss-Prot release 41 relnotes for further details. 8.6 Modifications concerning the feature table (FT line) We are investigating a major effort in the annotation of posttranslational modifications, which has an effect on various feature keys and feature descriptions. Please see Swiss-Prot release 41 relnotes for further details. 8.7 Extension of the entry name format Currently TrEMBL has it's accession number as the entry name. It is intended to extend this to have the accession number as the protein name component of the entry name (having elongated the mnemonic code from 4 characters to 6) and to assign the mnemonic species identification code of at most 5 alphanumeric characters as Swiss-Prot currently does.