[DAS] Link Command

[Dave Wall]

Geoff and I are stumped.  What I am looking for is a working example of the
link command.  I have other commands working but I cannot get the link
command to return an annotation.  I have tried a couple different severs
(Geoff tried others) but no success yet.  An example is

http://genome.ucsc.edu/cgi-bin/das/hg12/link?field=feature;id=GC.chr18.60000

It may be that my syntax is wrong, or maybe my whole approach is wrong.  Am
I going to the wrong server?  Is my use of the link command incorrect?
Thanks for any help!

David Wall
553-5329
IBM Life Sciences

----- Forwarded by Dave Wall/Rochester/IBM on 09/27/2002 10:38 AM -----
                                                                                                                        
                      Geoff Purdy                                                                                       
                      <gpurdy@cogentneuros        To:       Dave Wall/Rochester/IBM@IBMUS                               
                      cience.com>                 cc:                                                                   
                                                  Subject:  RE: [DAS] Getting Started With DAS                          
                      09/27/2002 09:36 AM                                                                               
                                                                                                                        
                                                                                                                        



Well, I'm out of ideas.  There is evidence that "link" works on the Sanger
DAS server as the pop-up menus are populated with additional information.
However, I've been unable to access that information using a script.

I suggest posting your question on the biodas list.  The collective
expertise on the list is orders of magnitude greater than my own.

I don't know of any alternatives to "link" for accessing annotation
details.
The reason I quoted "link" is that command names appear in italics in the
DAS documentation and italics isn't available in a plain text message.



> -----Original Message-----
> From: Dave Wall [mailto:dawall@us.ibm.com]
> Sent: Thursday, September 26, 2002 5:29 PM
> To: Geoff Purdy
> Subject: RE: [DAS] Getting Started With DAS
>
>
>
> Thanks for looking into it.  If I read between the lines a little it
almost
> sounds as if there is another way to get the annotation.  You  tried
three
> servers and none of them delivered the data via the link command.  Is
there
> another way to do it?
>
> David Wall
> 553-5329
> IBM Life Sciences
>
>
>

Dave,
You raise a good point here.  I notice that if I use the link command on
three different das servers, I see three different behaviors.

Last I saw, the UCSC DAS server was Jim Kent's C implementation of the DAS
specification.  As you pointed out, the link command gives no output (in
the
handful of cases I've tried).

I also tried a similar query on the Sanger Center DAS server (a Java
implementation, I believe).  This server gives the following message if a
feature doesn't have associated annotations:
   <h1>No extra information about this object</h1>
   <p>field: feature<br />id: 18/p11.32</p>

Finally, I tried CSHL's wormbase DAS server (a perl implementation by
Lincoln Stein).  This doesn't seem to implement the link command at all.

I notice that the "link" command is an annotation server specific command
(not part of reference server specification).  I'm unsure which of these
servers purport to be reference, annotation, or both.  Another possibility
is that different implementations of DAS may omit implementing portions of
the specification.

I'll give this a closer look, but I'm beginning to think this might be a
good subject for on-list discussion.


> -----Original Message-----
> From: Dave Wall [mailto:dawall@us.ibm.com]
> Sent: Thursday, September 26, 2002 4:15 PM
> To: Geoff Purdy
> Subject: RE: [DAS] Getting Started With DAS
>
>
>
> Thanks for offering to help!
>
> I have been having pretty good luck getting a list of data
> sources, types,
> segments, etc., but crash when I trying to get an annotation.
>  Here is an
> example for the purpose of verifying URL syntax ...
>
>
> http://genome.cse.ucsc.edu:80/cgi-bin/das/hg12/features?segmen
> t=18:1,100000
>
> In the returned data is
>       - <FEATURE id="GC.chr18.60000" label="GC">
>               <TYPE id="gcPercent" category="other" reference="no">GC
>             Percent</TYPE>
>               <METHOD />
>               <START>60001</START>
>               <END>80000</END>
>               <SCORE>0</SCORE>
>               <ORIENTATION>0</ORIENTATION>
>               <PHASE>-</PHASE>
>             - <GROUP id="GC.chr18.60000">
>                 <LINK href="
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60000-8
> 0000&db=hg12
>               ">Link to UCSC Browser</LINK>
>             </GROUP>
>           </FEATURE>
>
> I then send the following which returns a blank page.
>
> http://genome.cse.ucsc.edu/cgi-bin/das/hg12/link?field=feature
> ;id=GC.chr18.60000
>
> I am probably missing something obvious, but I sure can't
> figure out what
> it is.  Thanks again!
>
> David Wall
> 553-5329
> IBM Life Sciences