[Open-bio-l] roll call for toolkit obda support

[Jeffrey Chang]

On Mon, Jul 22, 2002 at 03:35:55PM +0900, KATAYAMA Toshiaki wrote:
> At Sat, 20 Jul 2002 18:33:29 -0400 (EDT),
> Jason Eric Stajich wrote:
> > I'm unsure how much progress was made post-hackathon and we seemed to have
> > lost the whole matrix of checkboxes (the perf numbers are on the website
> > though) .  Can someone fill in the blanks/?
> 
> At Sat, 20 Jul 2002 16:29:07 -0700, Jeffrey Chang wrote:
> > > BioFetch
> > >   BioPython ?
> > 
> > What was this again?  Is this the seqdatabase.ini file?  If so, then
> > check one off for BioPython!
> 
> Jeff, my understanding on this is :
>   * seqdatabse.ini is for BioRegistry
>   * BioFetch is a method for the entry retrieval over HTTP
>     from the BioFetch server,
>       http://www.ebi.ac.uk/cgi-bin/dbfetch
>       http://bioruby.org/cgi-bin/biofetch.rb
>     etc.

Oh, in that case, we can retrieve records from the EBI server.  We
have not yet implemented support from bioruby.org.

What happened with the BioRegistry stuff?  Do we have a hard spec on
that yet?  I have a sample file that I've been using...


[embl-xembl-cgi]
protocol=xembl
location=http://www.ebi.ac.uk/cgi-bin/xembl/XEMBL.pl
params=format=Bsml
key=id
fallback_group=embl


[embl-dbfetch-cgi]
protocol=biofetch
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
params=db=embl&style=raw&format=embl
key=id
fallback_group=embl



Jeff