> -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Carola Kanz > Sent: 26 April 2006 16:29 > To: [EMAIL PROTECTED] > Subject: Forthcoming change in the EMBL flatfile format > > > Dear all, > > if you are working with the EMBL flatfile format and you are > not yet aware of the format change we are going to introduce > with the next release, please have a look at the following > announcement. > Carola > > > -------------------------------------------------------------- > ----------- > > Dear colleagues, > > We would like to announce the following important change in > the EMBL database in June this year. > > At the time of release 87 (available from JUN-2006) the > format of the EMBL flat file will undergo a change: the ID > line will have a different structure (see below) and the SV > line will be removed. > > The changes affecting the ID line structure are: > > * All tokens will be separated by a semicolon. > * The entry name will not be displayed, in its place > there will be > the primary accession number. > * The sequence version will be indicated. > * The topology will be a separate token and will be > indicated for > both circular and linear molecules. > * Both the data class and the taxonomic divisions will > be displayed. > > This is an example of the new ID line: > > ID CD789012; SV 4; linear; genomic DNA; HTG; MAM; 500 BP. > (1) (2) (3) (4) (5) (6) (7) > > > The tokens represent: > > 1. Primary accession number. > 2. 'SV' + sequence version number. > 3. Topology: 'circular' or 'linear'. > 4. Molecule type. > 5. Data class (ANN, CON, PAT, EST, GSS, HTC, HTG, MGA, WGS, TPA, > STS, STD, "normal" entries will have STD for standard). > 6. Taxonomic division (HUM, MUS, ROD, PRO, MAM, VRT, FUN, > PLN, ENV, > INV, SYN, UNC, VRL, PHG)." > 7. Sequence length + 'BP.'. > > The entry name will not be displayed any more in the ID line. > Since EMBL release 3 (Dec 1983) the stable identifier of an > entry has been the primary accession number. > > A mapping file (entryname to accession number) will be > provided with the next release for those entries where the > entryname doesn't coincide with the accession number. > > To give users a test dataset, one file with new-style ID > lines called new_id_line.test.gz was provided together with > the March release of the EMBL database: > ftp://ftp.ebi.ac.uk/pub/databases/embl/release/new_id_line.test.gz > > Feedback from users is sought; please use the "Contact us" > link at the bottom of the EBI home page and specify "EMBL" in > the feedback form. > > Note: this information was first made available on our > "Forthcoming changes" page ( > http://www.ebi.ac.uk/embl/Documentation/forthcomingchanges.htm > l#0606 ) and in the EMBL database release notes. > > > > > >
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