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errors in the Icarus files for prosite and pfam

Guy Bottu gbottu at bigben.vub.ac.be
Fri Aug 28 06:02:27 EST 1998


from : the Belgian EMBnet Node

	Dear fellow SRS server managers,

While installing the Pfam databank in our SRS server, I did stumble on
two errors.

1. Try to retrieve [prositedoc-id:PDOC00017]. You will see that the
entry is truncated. The reason is that the second line of the
description begins with a '[' and that the parser erroneously "believes"
that the references starts there.

The fix : in prositedoc.is replace
  f_des:      ~ {$Wrt:des}      ('[' {$Not} ln)* ~
by
  f_des:      ~ {$Wrt:des}      ('[ 1]' {$Not} ln)* ~

I just noticed that the EBI server has already fixed the problem, but
many other sites have not.

2. srsbuild reports that there are no valid references from Pfam to
PROSITE, while there should be. The reason is that Pfam actually
contains references to the PROSITEDOC table and not to the PROSITE table
with the SWISS-PROT entries.

The fix : in pfam.i replace
 $link:[@PFAM_DB to:@?PROSITE_DB token: 'link|PROSITE' toField:@DF_Accession]
by
 $link:[@PFAM_DB to:@?PROSITEDOC_DB token: 'link|PROSITE' toField:@DF_ID]

	Regards,
	Dr. Guy Bottu




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