[Bioperl-l] XEMBL deprecation

Chris Fields cjfields at uiuc.edu
Fri Feb 16 09:05:08 EST 2007


I added the warning yesterday.

We can add something to the project priority list on modifying XEMBL  
to use DBFetch instead; I like the SOAP-based interface.  I am  
thinking of a similar interface for NCBI eutils but I haven't had  
time to work on it.

chris

On Feb 16, 2007, at 7:55 AM, Lincoln Stein wrote:

> Oh, looks like someone has inserted the warnings already. Good.
>
> Lincoln
>
> On 2/16/07, Lincoln Stein <lstein at cshl.edu > wrote:I like the idea  
> of converting these over to use DBFetch's SOAP services. On the  
> other hand, it isn't llikely that I'm going to have time to do this  
> anytime soon.
>
> Probably the best thing to do is to issue a warning and return  
> undef if someone tries to use othe XEMBL module. I'll make that  
> change.
>
> Lincoln
>
>
> On 2/15/07, Chris Fields < cjfields at uiuc.edu> wrote: I have gone  
> ahead and marked Bio::DB::XEMBL and Bio::DB::XEMBLService
> both for deprecation in the wiki and in CVS (though I haven't set any
> timeline):
>
> http://www.bioperl.org/wiki/Deprecated_modules
>
> The XEMBL web services are no longer available, and it looks like
> everything is running through DBFetch now.  The XEMBL tests are
> skipped if no server is detected, so they shouldn't cause any
> problems with Bioperl installations.
>
> Lincoln, was there anything to salvage from these?  I noticed they
> used SOAP::Lite, so maybe we could convert these over to a SOAP-based
> interface to DBFetch web services?
>
> chris
>
>
>
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT michelse at cshl.edu
>
>
>
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT michelse at cshl.edu

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list