Missing /db_xref in 1104 GenBank Update products

Mark Cavanaugh cavanaug at ncbi.nlm.nih.gov
Tue Nov 4 13:59:31 EST 2003

Greetings GenBank Users,

Due to a problem with Taxonomy services that occurred on the
morning of November 4, 2003, the nc1104 GenBank Incremental
Update (GIU) products contain 4973 EST and 850 GSS sequences
which lack pointers to the NCBI Taxonomy database.

In the GenBank flatfile, this results in source features that
lack the usual /db_xref qualifier. For example:

     source          1..4880
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"   <<< missing

And in ASN.1 format, this results in BioSource descriptors 
that lack the usual Org-ref.db Dbtag identifiers. For example:

      org {
        taxname "Homo sapiens" ,
        common "human" ,
        db {
            db "taxon" ,    <<
            tag             << missing
              id 9606 } } , <<

See, for example, CF886832 and CG783296 .

The affected records will be incorporated in tomorrow's nc1105
products, with the missing Taxonomy identifiers restored.

Our apologies for any inconvenience that this may have caused.

Mark Cavanaugh


- gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc
- GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/       
- GENBANKB e-mail: messages sent to genbankb at net.bio.net
- subscribe: e-mail biosci-server at net.bio.net with: subscribe genbankb
- unsub: e-mail biosci-server at net.bio.net with: unsubscribe genbankb      
- GenBank on the WWW, see:  http://www.ncbi.nlm.nih.gov/Genbank/
- problems with GENBANKB? E-mail moderator: francis at cmmt.ubc.ca                  

More information about the Genbankb mailing list

Send comments to us at biosci-help [At] net.bio.net