SRS 4.08 indexing

Guy Bottu gbottu at ben.vub.ac.be
Wed Nov 20 14:11:58 EST 1996

Andrew T. Lloyd (atlloyd at acer.gen.tcd.ie) wrote:
: I have a minimal SRS setup here: SW PIR PRosite EMBL-without-ESTs
: but have problems getting the links sorted:
: the links from SW - EMBL are looking for the NI field and report

: no entries found

The SwissProt contains lines of the type :

DR   EMBL; M15203; G167391; -

So, they should be correctly parsed with the swissprot.sdl from
the distribution, since this contains :

    #field /gblid=%SWISSPROT_DR_FIELD
           /itype=link /ftype=@DF_LINK /idtype=@SRSxLINKID
           /begstr="DR   " /nextstr="DR EXIT " /maxlines=1

#readlink /id=%GENEMBL_REF /link=@SWISSPROT_EMBL_LINK,

link       = [emlink | pirlink | pdblink | proslink | rebaselink | mimlink];
emlink     = 'EMBL' ';' accno <wrt c=@GENEMBL_REF> ';';


      /lib1=@SWISSPROT_DB /lib2=@EMBL_DB
      /field1=@SWISSPROT_ID_FIELD /field2=@EMBL_ACC_FIELD
      /idtype1=@SRSxSEQID /idtype2=@SRSxSEQID

I really do not see what might go wrong...

: I also note that I have acquired (through no effort of mine!)
: a link from SW to MIM at wwwgdb.gdb.org but that this is asking
: for http://wwwgdb.gdb.org/omim/omimx which is "not found on
: this server"

I think OMIM is not available from the GDB site or they have changed
the path. Anyway, I get OMIM from the NCBI's Entrez site with :

/call="<a href=http://www3.ncbi.nlm.nih.gov/htbin-post/Omim/

That does work.

I hope this will help you.

	Guy Bottu

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