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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: datalib@ebi.ac.uk
    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.