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
: INFO:
: 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
/find=link
...
#readlink /id=%GENEMBL_REF /link=@SWISSPROT_EMBL_LINK,
@SWISSPROT_GENBANK_LINK
...
link = [emlink | pirlink | pdblink | proslink | rebaselink | mimlink];
emlink = 'EMBL' ';' accno <wrt c=@GENEMBL_REF> ';';
...
#link /id=%SWISSPROT_EMBL_LINK
/weight=10
/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/
getmim?search=%s&field=number>%s</a>"
That does work.
I hope this will help you.
Guy Bottu
