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EMBL Indexing

Thure Etzold etzold at embl-heidelberg.de
Tue Jan 30 08:22:31 EST 1996


Peter M. Woollard x4523 wrote:
> 
> Hello,
>       I am getting an error building the ID indeces for EMBL, has anyone ideas
> on how to convince SRS that there is space?
> 
> Unix %  srsbuild -i EMNEW EMBL -xdir 'SRSINX:' -odir 'SRSINX:' -env 'unix'
> e__settoosmall, set has not enough space for IDs
> attempt to copy 1890 IDs where only for 1000 is space
> 

the link between EMNEW and EMBL uses accession numbers - both primary and secondary -
which can result in an 'explosion' of links if there are many entries 
sharing the same secondary accession number which seems to be more often the
case - it is possible to set the limit to a higher value

in srsbuild.c


#define BLDxMAXTMPSETSIZE 3000 ...or higher

a better solution is to change the link so that it uses the entry names instead of
the accession number - this assumes that entries once renamed are sufficiently 
different to be treated as new entries  - any comments on that?

here is the modified link from EMNEW to EMBL (in embl.sdl)

#link /id=%EMNEW_EMBL_LINK
      /lib1=@EMBLNEW_DB /lib2=@EMBL_DB /type=index
      /field1=@EMNEW_ID_FIELD /field2=@EMBL_ID_FIELD
      /idtype1=@SRSxSEQID /idtype2=@SRSxSEQID

another and possibly the best solution would be to create at least for one of the two
the accession index with only the primary accession number ...i am not sure how important
it is to make the secondary accession number searchable anyway ....for the 'normal' user
that is

regards
thure




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