EMBL ID lines - molecule type change

Peter Stoehr stoehr at ebi.ac.uk
Mon Aug 18 11:39:36 EST 2003


This is to re-emphasise what has been described in EMBL database
release notes concerning a change to the molecule type data on
the ID lines of EMBL flat-file entries.

At release 76, it becomes mandatory for each database entry to have
a mol_type qualifier attached to its source feature(s). The list of
allowed molecule type values for this qualifier is given below.
This qualifier exists already, but has not been mandatory, eg:

FT   source          1..328
FT                   /mol_type="genomic RNA"

At release 76, and starting with daily update file r76u001.dat.gz
due around 21.8.2003, these molecule type vaules will replace those on 
the ID lines, which up to now have had the values "DNA", "RNA" or "XXX".

Here are several examples of ID lines and how they will become:

ID   MMIGH8B3   standard; RNA; MUS; 307 BP.
ID   MMIGH8B3   standard; mRNA; MUS; 307 BP.

ID   AB000191   standard; RNA; VRL; 497 BP.
ID   AB000191   standard; genomic RNA; VRL; 497 BP.

ID   AAAJ4153   standard; DNA; ORG; 1041 BP.
ID   AAAJ4153   standard; genomic DNA; ORG; 1041 BP.

ID   AB006734   standard; circular RNA; VRL; 328 BP.
ID   AB006734   standard; circular genomic RNA; VRL; 328 BP.

The allowed molecule type values for the /mol_type feature qualifier,
and for the ID line, are:
"genomic DNA", "genomic RNA", "mRNA", "tRNA", "rRNA", "snoRNA", "snRNA", 
"scRNA", "pre-mRNA", "other RNA", "other DNA", "unassigned DNA", 
"unassigned RNA"

If you have any questions about this, please do not hesitate to ask
at datalib at ebi.ac.uk

Regards,
Peter Stoehr
EMBL-EBI







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