Swissprot to EMBL link ?

Peter Rice pmr at sanger.ac.uk
Thu Feb 6 06:09:28 EST 1997

In article <atlloyd-0502971448430001 at gen035.gen.tcd.ie> atlloyd at acer.gen.tcd.ie (Andrew T. Lloyd) writes:
>   SRS 4.08 question,
>   Can someone tell me what .sdl to change so that the link from
>   SwissProt to EMBL points at the Accession Number rather than
>   the gi number ?  I am wildly guessing it might be:
>   c=@FETCH_NUCACCNO somewhere in hyperlink.sdl.  Thanks for your
>   help mummy/daddy.

You can pick up (almost) any site's SDL files through their database
help pages (the exceptions are new databases where the
/oddfile="dbname.sdl" bit was left out accidentally).

For example, http://www.embl-heidelberg.de/srs/srsc?-info+swissprot

Pick up Thure's swissprot.sdl and hyperlink.sdl files (at the bottom
of the page) and use diff to find the changes.

Most differences in hyperlink.sdl will be for other databases (this is
so much cleaner in SRS 5 :-) but you should easily find the line(s) you need.

Comparing mine to yours (swissprot.sdl that is, best saved as text
from netscape) :

swissprot.sdl looks fine.

hyperlink.sdl needs one small change (I lost a few spaces to make it
fit better in this posting).


emblref = 'EMBL;' ~A-Z0-9~ ';' ~A-Z0-9~ <wrt c=@FETCH_EMBL f=@F_INSERTHLINK>;


emblref = 'EMBL;' ~A-Z0-9~ <wrt c=@FETCH_NUCACCNO f=@F_INSERTHLINK>;

So you are looking at the second "Xnnnnnn" text, and using it as an
EMBL ID (which it isn't). Sanger looks at the first "Xnnnnn" text, and
uses it as an EMBL accession number.

That should be all you need. Change it, srssection to update the
definitions, and browse away.

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

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