EMBL Nucleotide Sequence Database Release Notes 
Release 75 June 2003  

 
EMBL Outstation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

Telephone: +44-1223-494400
Telefax  : +44-1223-494468

Email: datalib@ebi.ac.uk
URL:   http://www.ebi.ac.uk 


CONTENTS

   1 RELEASE 75
        
      1.1 Feature Table Definition Document v5 
      1.2 Database Files
        1.2.1 Naming Conventions
        1.2.2 EST Database Files
        1.2.3 GSS Database Files
        1.2.4 INV Database Files
        1.2.5 HUM Database Files
        1.2.6 HTG Database Files
        1.2.7 PAT Database Files
        1.2.8 CON Database Files 
        1.2.9 CRC Values for Distributed Files
      1.3 Cross-Reference Information
        1.3.1 Cross-references to GeneDB
        1.3.2 PUBMED/MEDLINE references 
        1.3.3 Cross-references statistics
      1.4 Sequence Retrieval System (SRS) 
      1.5 EMBL Database FAQ
      1.6 Disclaimer

   2 FORTHCOMING CHANGES
      2.1 Sequence length limit : update
      2.2 New accession number formats 
      2.3 Molecule type information : update
      2.4 New feature : gap
      2.5 New qualifier : /ecotype
      2.6 Line length in the flatfiles
      2.7 Retrofits : /segment and /variety
      2.8 Electronic resources: modification of RL line

   3 SEQUENCE SUBMISSION SYSTEMS
        
   4 CITING THE EMBL NUCLEOTIDE SEQUENCE DATABASE

   5 EBI NETWORK SERVICES
        5.1 Electronic Mail Server
        5.2 Anonymous FTP Server
        5.3 World Wide Web (WWW) Server
	5.4 Sequence Version Archive 
        5.5 Sequence Similarity Search Servers

   6 DISTRIBUTION FILES
        6.1 Release 75 Files
       

   APPENDIX A : DATABASE GROWTH TABLE


 RELEASE 75

The EMBL Nucleotide Sequence Database was frozen to make Release 75 on 
30-MAY-2003. The release contains  25,214,767 sequence entries comprising 
32,195,012,823 nucleotides. This represents an increase of about 10% over 
Release 74. 

A breakdown of Release 75 by division is shown below:

Division	Entries	Nucleotides
Constructed	184	838,699,179 (see Note)
ESTs	16,928,340	8,595,205,394
Fungi	77,835	121,563,447
GSSs	5,360,409	3,158,737,181
HTC	151,653	199,532,408
HTG	68,836	11,785,274,832
Human	248,193	3,969,969,766
Invertebrates	121,828	609,642,910
Other Mammals	48,751	103,252,725
Mus musculus	74,469	1,135,155,874
Organelles	204,489	168,241,510
Patents	1,122,385	616,778,214
Bacteriophage	2,332	8,445,422
Plants	176,501	568,303,125
Prokaryotes	190,734	638,372,821
Rodents	24,936	45,228,463
STSs	165,775	69,132,571
Synthetic	8,750	16,009,034
Unclassified	1,485	2,124,638
Viruses	188,213	167,797,523
Other Vertebrates	48,669	216,244,965
Total	25,214,767	32,195,012,823

EMBL database statistics are available at 
URL: http://www.ebi.ac.uk/embl/Services/DBStats/ 

Note: The nucleotide count for CON(structed) entries is included 
in the table, but not in the total. Starting from 
this release, the nucleotide count for CON entries will not 
be included in the sum, because CON entries don't include 
sequence as such, just assembly information for the segments.
The nucleotide count for the segments of a CON entry is in the 
taxonomic divisions and already included into the total.
 
1.1 Feature Table Definition Document v5     

The last version of the Feature Table Definition Document (FTv5) has been 
implemented on 15-DEC-2002. The document is available from the EBI 
servers at: 

http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/

Next edition of the Feature table document will become available in 
Octover 2003

1.2 Database Files

In order to keep the size of the data files within reasonable limits for 
handling purposes, additional division files will be added in subsequent
releases as appropriate.


1.2.1 Naming Conventions

When a division is split into several files, these are named so that 
they sort sequentially, e.g. est_hum01.dat, est_hum02.dat,......,
est_hum22.dat, est_hum23.dat etc 


1.2.2 EST Database Files

ESTs (single pass cDNA reads) constitute a major source of sequence 
records. 

EST files are split according to taxonomic subdivisions following 
the model of the taxonomic split of all other EMBL database divisions, 
for example files est_fun01.dat - est_fun02.dat contains fungi EST data.
For the full list of distribution files see table in section 6.1
 
1.2.3 GSS Database Files

Genome Survey Sequences (GSS) are of similar nature to EST data, except 
that sequences are genomic rather than cDNA (mRNA). The GSS division 
contains e.g. random `single pass read' genome survey sequences, single 
pass reads from cosmid/BAC/YAC ends, exon trapped genomic sequences and 
Alu PCR sequences.

GSS division files are also split according to taxonomic subdivisions.
Example: gss_hum01.dat - gss_hum09.dat contain human GSS data
For the full list of distribution files see table in section 6.1
 
1.2.4 INV Database Files

The INV division has been split into 3 files (inv01.dat - inv03.dat).
 
1.2.5 HUM Database Files 

The HUM division has been split into 25 files (hum01.dat-hum25.dat).


1.2.6 HTG Database Files

'Unfinished' DNA sequences generated by the high-throughput sequencing 
centres are represented in the HTG division and are rapidly made 
available
to the scientific community for homology searches.  Entries in this 
division all contain keywords to indicate the status of the sequencing 
(e.g., HTGS_PHASE1). A single accession number is assigned to one clone,
and as sequencing progresses and the entry passes from one phase to 
another, it will retain the same accession number.  Once 'finished', HTG 
sequences are moved into the appropriate primary EMBL taxonomic division.

HTGS_PHASE0 entries typically consist of one-to-few pass reads of a single
clone, have not been assembled into contigs and are unoriented, unordered,
unannotated and contain gaps of unknown length.
Low-pass sequence sampling is useful for identifying clones that may be 
gene-rich. Phase0 sequences are used to check whether another centre is 
already sequencing this clone. If not, it will be sequenced through phase
1 and phase 2. When records are updated, the accession numbers will be 
preserved.

HTG division files are split according to taxonomic subdivisions. 
Example: htg_hum01.dat - htg_hum05.dat - Human HTG data
For the full list of distribution files see table in section 6.1

1.2.7 PAT Database Files 

PAT files include sequence data incorporated from the European patent 
literature (EPO) and complemented by American and Japanese patent 
data integrated from NCBI(USA)and DDBJ(Japan). 
The Patent division has been split into 6 files (pat01.dat - pat06.dat)

1.2.8 CON Database File

CON files include construct information for building contig sequences 
of chromosomes, genomes and other long DNA sequences. CON entries in 
file 'embl.con' do not contain sequence data per se. CON division
data is included in file embl.con 

1.2.9 CRC values for distributed files

To help users verify the integrity of release data files, we supply files
containing 32-bit checksum Cyclic Redundancy Check (CRC) values, plus byte
counts, for both compressed and uncompressed release files.

CRC values are calculated based on the IEEE Std 1003.2-1992 (POSIX 1003.2)
and X/Open CAE specifications. These values are generated by default by 
the 'cksum' command on Irix, RedHat Linux, SunOS, Solaris. On Tru64 unix, 
the environment variable CMD_ENV needs to be set to xpg4.

File: crc_gz.txt      for compressed data files 
File: crc.txt         for uncompressed data files 

Example from crc.txt 
1820298576 265044866 est_fun01.dat

This output shows that the checksum of the file est_fun01.dat is 
1820298576 and the file contains 265044866 bytes.  


1.3 Cross-Reference Information

1.3.1 Cross-references to GeneDB

Cross-references to GeneDB database were added to EMBL records.
GeneDB  is a curated database resource mainly for three organisms: 
Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei.
Cross-linking to GeneDB was done via protein_id and corresponding 
Swiss-Prot record. 

1.3.2 PUBMED/MEDLINE references 

PubMed, a service of the National Library of Medicine, provides access 
to over 12 million MEDLINE citations. In release 75, 152,598 
PUBMED/MEDLINE references have been included into EMBL database entries.
Example (entry AJ269470): 
RX   PUBMED; 12000641.


1.3.3 Cross-references statistics

Links to external databases allow integration with specialised data 
collections, such as protein databases, species-specific databases, 
taxonomy databases etc. The WWW-based sequence retrieval system SRS 
enables users to easily navigate between cross-referenced database 
entries.

EMBL Release 75 includes 32563155 cross-references to related 
databases. 2228238 of these are also referring to individual 
features e.g. CDS (coding sequences) via the /db_xref feature qualifier 
in EMBL entries. 

EMBL cross-references to other databases:

 
1.4 Sequence Retrieval System (SRS) 

EBI's SRS server is available at URL http://srs.ebi.ac.uk 
All external services are available via the 'Toolbox' tab  
on EBI's Web pages. If you have any comments and/or suggestions 
please send these to support@ebi.ac.uk


1.5 EMBL Database FAQ

EMBL Database FAQ are available from the EBI at URL 
http://www.ebi.ac.uk/embl/Documentation/FAQ/

1.6 Disclaimer

No guarantee is given and no legal liability or responsibility is assumed
for the completeness and accuracy of the database entries, in particular
the conformity of sequence data in the database with the journal 
publication where the sequence is also disclosed.
 
 FORTHCOMING CHANGES

2.1 Sequence length limit

Currently sequence length in database entries is limited to 350kb. 
The size restriction is going to be to removed completely in 1 years
time (June 2004).
This will allow representation of complete genomic units 
(such as complete chromosomes) in one entry. 
The practical size limit for sequences in EMBL entries will 
be defined by the size of the longest sequenced chromosome. 
Introduction of "gap" feature (see below) will allow representation
of sequences with gaps in a single entry.  

2.2 New accession number formats  

Two new accession number formats will be introduced for 
WGS (whole genome shotgun) data entries in June 2004. 
WGS data will be included from the June 2004 release onwards.

Formats: 
4 letters + 2 digits for assembly number + 6 digits 
and 
4 letters + 2 digits for assembly number + 7 digits 

Examples: AABA01000001 or BBAC010000001

2.3 Molecule type information : update

From 01-JUL-2003 /mol_type will be a mandatory qualifier to the "source" 
feature key and will consistently display the in vivo molecule type of 
the sequence.
The qualifier will be mandatory in all source features in the next 
release (Sep 2003)
List of mol_type values:
"genomic DNA", "genomic RNA", "mRNA" (incl. EST), "tRNA",
"rRNA", "snoRNA", "snRNA", "scRNA", "pre-mRNA", 
"other RNA" (incl. synthetic),"other DNA" (incl. synthetic), 
"unassigned DNA" (incl. unknown),"unassigned RNA" (incl. unknown)

Molecule type in ID lines:
Starting from the next release (Sep 2003), molecule type information in
the flatfile ID line will corresponding to the value from the
/mol_type qualifier. 
Examples: 
ID   AB016606   standard; circular genomic DNA; ORG; 17407 BP.
ID   TRBG361    standard; mRNA; PLN; 1859 BP.
   
2.4 New feature : gap

At the recent collaborative meeting it was agreed that a new "gap" 
feature will be introduced with the next edition of the Feature 
Table document (Oct 2003).
The purpose of the feature is to distinguish the ambigious sequence from 
gap in the sequence. The format of the feature is

Feature Key         gap

Qualifiers          /gap_length=number
		    /gap_type=

Where the length gap_type qualifier value format could be 
"estimated" or "arbitrary".

Example: 

FT   gap             101..200
FT                   /gap_length=30000
FT                   /gap_type=estimated

This feature describes a gap of estimated length of 3000 bp, 
represented in the sequence itself by a run of "NNN" from position 
101 to position 200. 

2.5 New qualifier : /ecotype
New qualifier /ecotype is going to be introduced into the next edition of
the Feature Table Document (Oct 2003). 

Description of the feature: 
Qualifier:	/ecotype
Definition:	A distinct population of organisms of a widespread 
                species that has adapted genetically to its own local
                habitat. Nevertheless they can still reproduce with 
                members of other ecotypes of the same species.
Value Format:	"text"
Example:	/ecotype="Columbia"
Comment: 	'Ecotype' is often applied to standard genetic stocks 
                of Arabidopsis thaliana, but it can be applied to any 
                organism, especially sessile organisms like plants.

2.6 Line length in the flatfiles

The 80 characters length limit is relaxed for some of the lines in the 
flatfile. The lines affected are SQ line and in the future the ID line.
The change is due to the very long sequences that are now being stored 
in the database. 

2.7 Retrofits : /segment and /variety

The retrofit of old entries to the current standard of annotation for  
"source" feature qualifiers /segment and /variety is now finished.  
/segment qualifier is used to store the name of viral or phage 
segment sequenced. Example: 
/segment="6"
/variety is used to store variety (= varietas, a formal Linnaean rank) 
of organism from which sequence was derived. Example: 
/variety="insularis"

2.8 Electronic resources: modification of RL line

From December 2003, a new publication type will become legal in 
EMBL. The new format will be used specifically to 
describe a publication in an electronic resource (such as e-journal). 

The new format 
RL   (er) Free text

("RL" followed by three spaces, followed by "(er)" for 
electronic resource, followed by space, followed by the
free-text reference). 

The format will be used in the case of an electronic journal 
where the citation information doesn't have the same format 
as for "normal" journals (with journal abbreviation, volume, 
issue, page numbers and year). 
Many electronic journals in practice follow the same
conventions as for paper publication, and these citations will not 
contain the "(er)"

Example: 
RL   (er) Microbial Ecology DOI: 10.1007/s00248-002-2038-4

 
 SEQUENCE SUBMISSION SYSTEM

Information on submission of sequence data to the EMBL Nucleotide 
Sequence Database is available at:
http://www.ebi.ac.uk/embl/Submission/

For further information on submission of sequence data to the 
EMBL Nucleotide 
Sequence Database please contact database staff at:

EMBL Nucleotide Sequence Submissions
e-mail: datasubs@ebi.ac.uk
telephone: +44-1223-494499
telefax: +44-1223-494472


 CITING THE EMBL NUCLEOTIDE SEQUENCE DATABASE

We encourage authors to include a reference to the EMBL Database in 
publications related to their research.

When citing data in the EMBL Database, we suggest to give the
primary accession number and the publication in which the sequence first 
appeared. For unpublished data, we suggest to contact the original 
submitters for recent publication information or revisions of the data.

We suggest to also provide a reference for the EMBL Database itself. Our 
recent publication describing the EMBL database should be cited:

Stoesser G., Baker W., van den Broek A., Garcia-Pastor M., Kanz C., 
Kulikova T., Leinonen R., Lin Q., Lombard V., Lopez R., Mancuso R., 
Nardone F., Stoehr P., Tuli M., Tzouvara K. and Vaughan R. (2003) 
"The EMBL Nucleotide Sequence Database: major new developments"
Nucleic Acids Research 31(1): 17-22 (2003).

Example: The numbers in parentheses refer to the reference citation in 
the EMBL database entry, and to the EMBL citation above.

"Sequence entry X56734 (1) has been retrieved from the EMBL Database (2) 
and showed significant sequence similarity to ..."

(1) Oxtoby, E., et al., Plant Mol. Biol. 17:209-219(1991).
(2) Stoesser G. et al., Nucleic Acids Res 31:17-22(2003).
 

 EBI NETWORK SERVICES

5.1 Electronic Mail Server

Copies of database entries and other information could be obtained by 
sending commands via email to a server running at EBI. New and updated 
EMBL nucleotide sequence entries are made available on the server on a 
daily basis.

Send file server commands to the address 
netserv@ebi.ac.uk. Each line of the mail message should consist of a 
single file server request.

The most important file server request, to get started, is:

HELP

If the file server receives this command, it will return a helpfile to 
the sender, explaining in some detail how to use the facility. For 
example, to request a copy of the nucleotide sequence with accession 
number X55652, use the command:

GET NUC:X55652

The file server offers various other services, (eg., access to nucleotide 
and protein sequence data, protein structure data, software), details of 
which are provided in the HELP file.


5.2 Anonymous FTP Server

An alternative method of accessing the EBI archives is to use the file 
transfer protocol (ftp). Researchers with direct access to the Internet 
can use the FTP program on their local machine to connect to the host 
FTP.EBI.AC.UK and enter the username "anonymous" and their email address 
as password. 
The directory pub/help contains detailed information about the data 
available from the EBI anonymous FTP server which includes the complete 
EMBL Nucleotide Sequence Database releases as well as daily and weekly 
updates and a cumulative update file (gzip compressed format) in the 
following directories:

EMBL quarterly release:   pub/databases/embl/release
EMBL updates:             pub/databases/embl/new


5.3 World Wide Web (WWW) Server

The EBI operates a WWW server at URL http://www.ebi.ac.uk/ 
providing information about the EBI and it's products and services. 

Data Retrieval: 

Nucleotide sequences can be retrieved by a simple query by 
accession number at http://www.ebi.ac.uk/cgi-bin/emblfetch

More  complex queries can be constructed using the SRS 
databank browser at http://srs.ebi.ac.uk 

Data Submission: Nucleotide sequences can be submitted to the 
database using the interactive submission system Webin at
http://www.ebi.ac.uk/embl/Submission/webin.html 


5.4 Sequence Version Archive 

The EMBL Sequence Version Archive (SVA) is a new publicly available 
database containing all versions of any entry which has ever appeared
in the EMBL database.

The archive can be accessed programmatically via 
dbfetch at http://www.ebi.ac.uk/cgi-bin/dbfetch or interactively via a Web interface at 
http://www.ebi.ac.uk/embl/sva/

5.5 Sequence Similarity Search Servers

The EBI offers two network servers for sequence similarity searches via 
electronic mail or interactive WWW forms:
      
FASTA based on W. Pearson's FASTA algorithm. Allows local 
similarity searches of protein and nucleotide sequence databases. 
Send "help" to fasta@ebi.ac.uk or use URL http://www.ebi.ac.uk/fasta33/      
Complete genomes (and proteomes) could be searched at the following URL: 
http://www.ebi.ac.uk/fasta33/genomes.html 
Alternatively, send "help" command to gpfasta@ebi.ac.uk

BLAST based on the NCBI and WU-BLAST software 
Send "help" to blast@ebi.ac.uk or use URL http://www.ebi.ac.uk/blast2/ 
         
 DISTRIBUTION FILES

6.1 Release 75 Files

The release contains the files shown below.

 
APPENDIX A

DATABASE GROWTH TABLE

The following table shows the growth of the EMBL Nucleotide Sequence Database
at each release.