[DAS] Link Command
Dave Wall
dawall@us.ibm.com
Tue, 1 Oct 2002 10:30:23 -0500
That makes some sense. The servers are returning an empty record so it
sounds like that is what they are supposed to do. That means the
information I am looking for is in the results of the 'feature' command(?).
Does an example scenario (using the wormbase server) become?
http://www.wormbase.org/db/das/dsn. Returns the list of data sources on
this server. The only server that is returned is 'elegans'
http://www.wormbase.org/db/das/elegans/entry_points. Returns a list of
entry points. For the purpose of this discussion I will select
<SEGMENT id="X" size="17683571" start="1" stop="17683571" class="
Sequence" orientation="+" subparts="yes">X
</SEGMENT>
http://www.wormbase.org/db/das/elegans/features?segment=X:1,100000.
Returns a list of features against this segment. Many feature records
are returned (around 300). An example record is:
<FEATURE id="Y73B3A.1" label="Y73B3A.1">
<TYPE id="exon" category="transcription" reference="no">
curated exon</TYPE>
<METHOD id="curated">curated</METHOD>
<START>24479</START>
<END>24819</END>
<SCORE>-</SCORE>
<ORIENTATION>-</ORIENTATION>
<PHASE>0</PHASE>
<GROUP id="Y73B3A.1">
<LINK href="
http://www.wormbase.org/db/get?name=Y73B3A.1;class=Sequence">
Y73B3A.1</LINK>
</GROUP>
</FEATURE>
I see the "link" which is part of the <group>. Is that the
annotation or does this entry not have one since there is no <link>
under the feature tag? Actually none of the entries have a <link>
parameter under the feature tag. If one exists it is in the
<group> section. Am I getting closer?
Thanks again!
David Wall
553-5329
IBM Life Sciences
Lincoln Stein
<lstein@cshl.org> To: Dave Wall/Rochester/IBM@IBMUS, das@biodas.org
cc:
10/01/2002 06:32 Subject: Re: [DAS] Link Command
AM
Please respond to
lstein
You're not going crazy. It's just that all the servers to date have chosen
to
implement the client-side form of link (where the link information is
returned gratis with every feature record) rather than implement
server-side
link. The servers should be returning an empty record, are they?
Lincoln
On Friday 27 September 2002 11:46 am, Dave Wall wrote:
> 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.chr18.6000
>0
>
> 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
>
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--
Lincoln Stein
lstein@cshl.org