Protein IDs

Peter Rice pmr at sanger.ac.uk
Thu Jul 15 06:17:59 EST 1999


I spent a while this morning trying to track down entry
'[TREMBLNEW-ID:AAD17483]' which disappeared when I updated
SPTREMBL and TREMBLNEW.

It is now in SPTREMBL, and I found it eventually as
'[SPTREMBL-ACC:Q9Z6I5]'

What I would really like to do is find it by using the TREMBLNEW id
which should appear as a Protein-ID (prd) in the protein databases and EMBL.

Sadly, there is by default no Protein-ID index for swissprot,
swissnew, sptrembl or tremblnew. Is anyone out there indexing
Protein-IDs for the protein databases? It is there hiding in the DR
lines. If there is no 'standard' way I can invent something.

SRS5 (as EMBL is indexed on the EBI's FTP server) does index
/protein_id in the feature table, but SRS6 only does /db_xref which is
the obsolete pid not used in TREMBLNEW - so I can find it by
'[embl-prd:AAD17483*]' (that "*" is a nuisance and very confusing to
users - just because of the ".n" after - I would prefer to index just
the prefix because you only ever get the 'latest' version of the
protien in the database).

Curiously, DATABANKS at EBI does not seem to include the EMBL feature
fields in its index.


-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/




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