EMBL Release 53

The EMBL Nucleotide Sequence Database was frozen to make Release 53 on the 16th December 1997. The release contains 1,917,868 sequence entries comprising 1,281,391,651 nucleotides. This represents an increase of about 8% over Release 52. A breakdown of Release 53 by division is shown below:

Division Entries Nucleotides Bacteriophage ESTs Fungi GSSs HTG Human Invertebrates Organelles Other Mammals Other Vertebrates Plants Patent Prokaryotes Rodents STSs Synthetic Unclassified Viruses 1388 1343796 18137 100154 1868 74384 28126 24715 14429 13145 22136 91221 42666 37043 51172 2424 2380 48684 2188305 496603984 44602064 49099107 102763872 139022655 107524431 22870076 13785092 14653255 37736590 29511807 102750354 46489741 17685717 5377292 2387088 46340221 Total 1917868 1281391651

EST Database Files

In order to keep the size of the data files within reasonable limits for handling purposes, we have split the EST division into several files. At this release we have created one extra files of EST data named EST14.DAT. Additional files will be added in subsequent releases as appropriate.

Feature Table Qualifiers

New SOURCE Qualifier /specimen_voucher

/specimen__voucher="text"

This is an identifier of the individual or collection of the source organism and the place where it is currently stored, usually an institution. Example:

/specimen__voucher="Smith s. n. 4-IV-1995 (U. S. Natl. Herbarium)"

New /focus

/focus

This qualifier defines the preferred source feature for records that have more than one source feature. Example:

/focus

This qualifier is to be used only if there is more than one source feature. The preferred source feature is  used to determine which organism is displayed in the SOURCE and ORGANISM lines and to determine the EMBL division in which it is placed.
For sequences derived from more than one organism, and therefore containing more than one 'source' feature key, the /focus qualifier will be attached to the source key which represents the major organism, that which was the focus of the sequencing effort. If no translation table is specified, the organism with /focus will define the translation table.

Forthcoming changes

Nucleotide And Protein Identifiers

Nucleotide Indentifiers

NI g21954

It has become clear from users and other database groups that confusion has been created about the relationship between these identifiers and the GenBank 'gi' numbers.
It has been decided therefore to introduce a new system of nucleotide identifiers of the form 'accession.version', eg: X12345.3, where the accession number part will be stable, but the version part will be incremented if the sequence changes.
Subject to synchronisation of this change with GenBank and DDBJ, we plan to  implement this new form of nucleotide identifier during 1998.

/db_xref="PID:e123456789"

As for nucleotide identifier values (above), confusion resulted amongst users concerning the relationship of these to GenBank 'gi' numbers also assigned to CDS features. To clarify this, and to adopt a comparable scheme of identifiers for both nucleotides and proteins, the collaborating databases have decided to create a new feature table qualifier /protein_id, eg:

/protein_id="AAA12345.1"

This form of identifier also allows easier tracking of changing protein identifiers by external databases than the previous PIDs.
This qualifier consists of a stable ID portion (3+5 format with 3 positions letters and 5 numbers) plus a version number after a decimal point. The version number will change only when the protein sequence coded by the CDS changes, while the stable part will remain unchanged. This qualifier will be valid only on CDS features which translate into a valid protein.
Subject to synchronisation of this change with GenBank and DDBJ, we plan to implement this new form of protein identifier during 1998.

Feature Table Qualifiers

New /protein_id

/protein_id="<identifier>"

This is a Protein Identifier, issued by International collaborators. This qualifier consists of a stable ID portion (3+5 format  with 3 positions letters and 5 numbers) plus a version number as the decimal point. Example:

/protein_id="AAA12345.1"

Only when the protein sequence coded by the CDS changes, the version number will change, while the stable part will remain unchanged. This qualifier is valid only on CDS features which translate into a valid protein. The list of 3-letter prefixes will be maintained by EBI.
Subject to synchronisation of this change with GenBank and DDBJ, we plan to implement this new form of protein identifiers during 1998.

/codon
/codon_start
/exception
/translation
/transl_table
/transl_except

Starting at release 54, translation related qualifiers will only be valid with the CDS feature key and will be removed from the following list of non-CDS features:

C_region
D_segment
exon
J_segment
mat_peptide
N_region
sig_peptide
S_region
transit_peptide
V_region
V_segment

Written by: Peter Stoehr

Resources and further information

• European Bioinformatics Institute
  http://www.ebi.ac.uk/
• EMBL Nucleotide Sequence Database Homepage
  http://www.ebi.ac.uk/ebi_docs/embl_db/ebi/topembl.html
• EMBL latest release ftp site
  ftp://ftp.ebi.ac.uk/pub/databases/embl/release/

External sites are not endorsed by EMBL-EBI

Direct questions or comments to Bioinformer Editor. This page last modified Friday, 16 July, 1999.
ISSN 1462-1363. More information about the BioInformer.

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