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GenPept and SRS indices

Peter Rice pmr at sanger.ac.uk
Wed Jul 31 15:16:11 EST 1996

In article <1996Jul31.192322.7931 at alw.nih.gov> susanc at helix.nih.gov (Susan Chacko) writes:
>   Has anyone added GenPept to their databases and also built
>   the SRS indices (for Lookup) for GenPept? 
>   I assume one would need a genpept.sdl file, and am hoping
>   to avoid creating one myself, as the syntax is not exactly simple.
>   Also, any information about which other sdl files need to be
>   changed (srsdb.sdl, any others?) would be much appreciated.
>   Hints, clues and guesses also welcome.

One of the great things about SRS is you can ask it who has a database
and then pick up the files you need  :-)

http://www.sanger.ac.uk/srs/status.html (among other places) lists all
the databases on the known SRSWWW servers.

GENPEPT is available at two sites according to the current listing.

Note: You could also try TREMBL/SPTREMBL but its format will change
in the next few months so there is a little more work (not much) to
be done to keep it running.

Each site should have the .sdl file available. Click on the "?!" on
the SRS status listing for EGNPEPT at the site of your choice. You
will get their help on GENPEPT, including at the bottom their
genpept.sdl file (or maybe genbank.sdl - new databases do not always
go in new files).

You should also pick up their hyperlink.sdl file, used to markup the
genpept entries for display, and see what GENPEPT-specific lines are
there. It is possible to put all this stuff into the genpept.sdl file,
but most sites keep to the original method of using hyperlink.sdl for
the markup parts.

Check the genpept.sdl file for a few obvious things

 o the filenames match what you called your genpept files
 o the database links are only to databases you have. For example,
   most SRS sites use EMBL because they are in Europe. You may want
   to change all these to GENBANK.
 o Add any extra links of extra indexing to match what you
   normally have
 o Worry a little about whether you need to pick up the other site's
   swissprot.sdl file (for example) to find how they do some other links
   (though you can work most of these out for yourself anyway). The
   help output you used to pick up the genpept.sdl file also tells
   you what databases are linked to GENPEPT there.

Put any extra bits for markup into your hyperlink.sdl file, or if you
know the tricks put them at the bottom of genpept.sdl.

In srsdb.sdl you will need to add 3 lines - include the genpept.sdl file,
say where your database is, and give it any unused number.

If you are really thorough, you should also update the help text in
wgetz_text.script (cut it out of the remote site's help page :-)
but most of the help is generated automatically anyway.

Then srssection, srscheck, srsupdate and off you go. The rest is automatic.

Oh yes, one more thing - if your server is not on the status page and
you would like it to be, then all you need to do is announce it here
and it will be added by the most active sites :-)
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, Cambs, CB10 1SA,
URL: http://www.sanger.ac.uk/~pmr/   | England

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