[DAS] (no subject)
Sidd Nakade
siddmr@yahoo.com
Fri, 18 Oct 2002 01:36:56 -0700 (PDT)
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Hello,
Can any one help me to setup configure a DAS server in Ensembl . We have a mirror of ensembl in our lab and we want to setup a DAS server with this.
your help wil be highly appreciated.
Regards
Sidd
das-request@biodas.org wrote:Send DAS mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. Re: Link Command (Lincoln Stein)
2. Re: Link Command (Dave Wall)
--__--__--
Message: 1
From: Lincoln Stein
Reply-To: lstein@cshl.org
Organization: Home
To: "Dave Wall" , das@biodas.org
Subject: Re: [DAS] Link Command
Date: Tue, 1 Oct 2002 07:32:22 -0400
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
> > 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:
> No extra information about this object
>
field: feature
id: 18/p11.32
>
> 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
> > -
> > GC
> > Percent
> >
> > 60001
> > 80000
> > 0
> > 0
> >
-
> > -
> >
> >
> > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60000-8
> > 0000&db=hg12
> > ">Link to UCSC Browser
> >
> >
> >
> > 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
>
> _______________________________________________
> DAS mailing list
> DAS@biodas.org
> http://biodas.org/mailman/listinfo/das
--
Lincoln Stein
lstein@cshl.org
--__--__--
Message: 2
Subject: Re: [DAS] Link Command
To: lstein@cshl.org, das@biodas.org
From: "Dave Wall"
Date: 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
Sequence" id=X subparts="yes" orientation="+" stop="17683571" start="1" size="17683571">X
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:
curated exon
curated
24479
24819
-
-
0
http://www.wormbase.org/db/get?name=Y73B3A.1;class=Sequence">
Y73B3A.1
I see the "link" which is part of the . Is that the
annotation or does this entry not have one since there is no
under the feature tag? Actually none of the entries have a
parameter under the feature tag. If one exists it is in the
section. Am I getting closer?
Thanks again!
David Wall
553-5329
IBM Life Sciences
Lincoln Stein
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
> > 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:
> No extra information about this object
>
field: feature
id: 18/p11.32
>
> 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
> > -
> > GC
> > Percent
> >
> > 60001
> > 80000
> > 0
> > 0
> >
-
> > -
> >
> >
> > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60000-8
> > 0000&db=hg12
> > ">Link to UCSC Browser
> >
> >
> >
> > 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
>
> _______________________________________________
> DAS mailing list
> DAS@biodas.org
> http://biodas.org/mailman/listinfo/das
--
Lincoln Stein
lstein@cshl.org
--__--__--
_______________________________________________
DAS mailing list
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http://biodas.org/mailman/listinfo/das
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<P>Hello,<BR> Can any one help me to setup configure a DAS server in Ensembl . We have a mirror of ensembl in our lab and we want to setup a DAS server with this.<BR>your help wil be highly appreciated. <BR>Regards<BR>Sidd
<P>
<P> <B><I>das-request@biodas.org</I></B> wrote:
<BLOCKQUOTE style="BORDER-LEFT: #1010ff 2px solid; MARGIN-LEFT: 5px; PADDING-LEFT: 5px">Send DAS mailing list submissions to<BR>das@biodas.org<BR><BR>To subscribe or unsubscribe via the World Wide Web, visit<BR>http://biodas.org/mailman/listinfo/das<BR>or, via email, send a message with subject or body 'help' to<BR>das-request@biodas.org<BR><BR>You can reach the person managing the list at<BR>das-admin@biodas.org<BR><BR>When replying, please edit your Subject line so it is more specific<BR>than "Re: Contents of DAS digest..."<BR><BR><BR>Today's Topics:<BR><BR>1. Re: Link Command (Lincoln Stein)<BR>2. Re: Link Command (Dave Wall)<BR><BR>--__--__--<BR><BR>Message: 1<BR>From: Lincoln Stein <LSTEIN@CSHL.ORG><BR>Reply-To: lstein@cshl.org<BR>Organization: Home<BR>To: "Dave Wall" <DAWALL@US.IBM.COM>, das@biodas.org<BR>Subject: Re: [DAS] Link Command<BR>Date: Tue, 1 Oct 2002 07:32:22 -0400<BR><BR>You're not going crazy. It's just that all the servers to date have chosen to <BR>implement the client-side form of link (where the link information is <BR>returned gratis with every feature record) rather than implement server-side <BR>link. The servers should be returning an empty record, are they?<BR><BR>Lincoln<BR><BR>On Friday 27 September 2002 11:46 am, Dave Wall wrote:<BR>> Geoff and I are stumped. What I am looking for is a working example of the<BR>> link command. I have other commands working but I cannot get the link<BR>> command to return an annotation. I have tried a couple different severs<BR>> (Geoff tried others) but no success yet. An example is<BR>><BR>> http://genome.ucsc.edu/cgi-bin/das/hg12/link?field=feature;id=GC.chr18.6000<BR>>0<BR>><BR>> It may be that my syntax is wrong, or maybe my whole approach is wrong. Am<BR>> I going to the wrong server? Is my use of the link command incorrect?<BR>> Thanks for any help!<BR>><BR>> David Wall<BR>> 553-5329<BR>> IBM Life Sciences<BR>><BR>> ----- Forwarded by Dave Wall/Rochester/IBM on 09/27/2002 10:38 AM -----<BR>><BR>> Geoff Purdy<BR>> <GPURDY@COGENTNEUROS Dave<br To:>> Wall/Rochester/IBM@IBMUS cience.com> cc:<BR>> Subject: RE: [DAS]<BR>> Getting Started With DAS 09/27/2002 09:36 AM<BR>><BR>><BR>><BR>><BR>><BR>> Well, I'm out of ideas. There is evidence that "link" works on the Sanger<BR>> DAS server as the pop-up menus are populated with additional information.<BR>> However, I've been unable to access that information using a script.<BR>><BR>> I suggest posting your question on the biodas list. The collective<BR>> expertise on the list is orders of magnitude greater than my own.<BR>><BR>> I don't know of any alternatives to "link" for accessing annotation<BR>> details.<BR>> The reason I quoted "link" is that command names appear in italics in the<BR>> DAS documentation and italics isn't available in a plain text message.<BR>><BR>> > -----Original Message-----<BR>> > From: Dave Wall [mailto:dawall@us.ibm.com]<BR>> > Sent: Thursday, September 26, 2002 5:29 PM<BR>> > To: Geoff Purdy<BR>> > Subject: RE: [DAS] Getting Started With DAS<BR>> ><BR>> ><BR>> ><BR>> > Thanks for looking into it. If I read between the lines a little it<BR>><BR>> almost<BR>><BR>> > sounds as if there is another way to get the annotation. You tried<BR>><BR>> three<BR>><BR>> > servers and none of them delivered the data via the link command. Is<BR>><BR>> there<BR>><BR>> > another way to do it?<BR>> ><BR>> > David Wall<BR>> > 553-5329<BR>> > IBM Life Sciences<BR>><BR>> Dave,<BR>> You raise a good point here. I notice that if I use the link command on<BR>> three different das servers, I see three different behaviors.<BR>><BR>> Last I saw, the UCSC DAS server was Jim Kent's C implementation of the DAS<BR>> specification. As you pointed out, the link command gives no output (in<BR>> the<BR>> handful of cases I've tried).<BR>><BR>> I also tried a similar query on the Sanger Center DAS server (a Java<BR>> implementation, I believe). This server gives the following message if a<BR>> feature doesn't have associated annotations:<BR>>
<H1>No extra information about this object</H1><BR>>
<P>field: feature<BR>id: 18/p11.32</P><BR>><BR>> Finally, I tried CSHL's wormbase DAS server (a perl implementation by<BR>> Lincoln Stein). This doesn't seem to implement the link command at all.<BR>><BR>> I notice that the "link" command is an annotation server specific command<BR>> (not part of reference server specification). I'm unsure which of these<BR>> servers purport to be reference, annotation, or both. Another possibility<BR>> is that different implementations of DAS may omit implementing portions of<BR>> the specification.<BR>><BR>> I'll give this a closer look, but I'm beginning to think this might be a<BR>> good subject for on-list discussion.<BR>><BR>> > -----Original Message-----<BR>> > From: Dave Wall [mailto:dawall@us.ibm.com]<BR>> > Sent: Thursday, September 26, 2002 4:15 PM<BR>> > To: Geoff Purdy<BR>> > Subject: RE: [DAS] Getting Started With DAS<BR>> ><BR>> ><BR>> ><BR>> > Thanks for offering to help!<BR>> ><BR>> > I have been having pretty good luck getting a list of data<BR>> > sources, types,<BR>> > segments, etc., but crash when I trying to get an annotation.<BR>> > Here is an<BR>> > example for the purpose of verifying URL syntax ...<BR>> ><BR>> ><BR>> > http://genome.cse.ucsc.edu:80/cgi-bin/das/hg12/features?segmen<BR>> > t=18:1,100000<BR>> ><BR>> > In the returned data is<BR>> > - <FEATURE id=GC.chr18.60000 label="GC"><BR>> > <TYPE id=gcPercent reference="no" category="other">GC<BR>> > Percent</TYPE><BR>> > <METHOD></METHOD><BR>> > <START>60001</START><BR>> > <END>80000</END><BR>> > <SCORE>0</SCORE><BR>> > <ORIENTATION>0</ORIENTATION><BR>> > <PHASE>-</PHASE><BR>> > - <GROUP id=GC.chr18.60000><BR>> > <LINK href="<br>> ><br>> > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60000-8<br>> > 0000&db=hg12<br>> > ">Link to UCSC Browser</LINK><BR>> > </GROUP><BR>> > </FEATURE><BR>> ><BR>> > I then send the following which returns a blank page.<BR>> ><BR>> > http://genome.cse.ucsc.edu/cgi-bin/das/hg12/link?field=feature<BR>> > ;id=GC.chr18.60000<BR>> ><BR>> > I am probably missing something obvious, but I sure can't<BR>> > figure out what<BR>> > it is. Thanks again!<BR>> ><BR>> > David Wall<BR>> > 553-5329<BR>> > IBM Life Sciences<BR>><BR>> _______________________________________________<BR>> DAS mailing list<BR>> DAS@biodas.org<BR>> http://biodas.org/mailman/listinfo/das<BR><BR>-- <BR>Lincoln Stein<BR>lstein@cshl.org<BR><BR>--__--__--<BR><BR>Message: 2<BR>Subject: Re: [DAS] Link Command<BR>To: lstein@cshl.org, das@biodas.org<BR>From: "Dave Wall" <DAWALL@US.IBM.COM><BR>Date: Tue, 1 Oct 2002 10:30:23 -0500<BR><BR><BR>That makes some sense. The servers are returning an empty record so it<BR>sounds like that is what they are supposed to do. That means the<BR>information I am looking for is in the results of the 'feature' command(?).<BR><BR>Does an example scenario (using the wormbase server) become?<BR>http://www.wormbase.org/db/das/dsn. Returns the list of data sources on<BR>this server. The only server that is returned is 'elegans'<BR>http://www.wormbase.org/db/das/elegans/entry_points. Returns a list of<BR>entry points. For the purpose of this discussion I will select<BR><SEGMENT class="<br> Sequence" id=X subparts="yes" orientation="+" stop="17683571" start="1" size="17683571">X<BR></SEGMENT><BR>http://www.wormbase.org/db/das/elegans/features?segment=X:1,100000.<BR>Returns a list of features against this segment. Many feature records<BR>are returned (around 300). An example record is:<BR><FEATURE id=Y73B3A.1 label="Y73B3A.1"><BR> <TYPE id=exon reference="no" category="transcription"><BR>curated exon</TYPE><BR> <METHOD id=curated>curated</METHOD><BR> <START>24479</START><BR> <END>24819</END><BR> <SCORE>-</SCORE><BR> <ORIENTATION>-</ORIENTATION><BR> <PHASE>0</PHASE><BR><GROUP id=Y73B3A.1><BR> <LINK href="<br> http://www.wormbase.org/db/get?name=Y73B3A.1;class=Sequence"><BR>Y73B3A.1</LINK><BR> </GROUP><BR> </FEATURE><BR><BR><BR>I see the "link" which is part of the <GROUP>. Is that the<BR>annotation or does this entry not have one since there is no <LINK><BR>under the feature tag? Actually none of the entries have a <LINK><BR>parameter under the feature tag. If one exists it is in the<BR><GROUP>section. Am I getting closer?<BR><BR>Thanks again!<BR><BR><BR><BR>David Wall<BR>553-5329<BR>IBM Life Sciences<BR><BR><BR><BR><BR>Lincoln Stein <BR><LSTEIN@CSHL.ORG>To: Dave Wall/Rochester/IBM@IBMUS, das@biodas.org <BR>cc: <BR>10/01/2002 06:32 Subject: Re: [DAS] Link Command <BR>AM <BR>Please respond to <BR>lstein <BR><BR><BR><BR><BR><BR>You're not going crazy. It's just that all the servers to date have chosen<BR>to<BR>implement the client-side form of link (where the link information is<BR>returned gratis with every feature record) rather than implement<BR>server-side<BR>link. The servers should be returning an empty record, are they?<BR><BR>Lincoln<BR><BR>On Friday 27 September 2002 11:46 am, Dave Wall wrote:<BR>> Geoff and I are stumped. What I am looking for is a working example of<BR>the<BR>> link command. I have other commands working but I cannot get the link<BR>> command to return an annotation. I have tried a couple different severs<BR>> (Geoff tried others) but no success yet. An example is<BR>><BR>><BR>http://genome.ucsc.edu/cgi-bin/das/hg12/link?field=feature;id=GC.chr18.6000<BR>>0<BR>><BR>> It may be that my syntax is wrong, or maybe my whole approach is wrong.<BR>Am<BR>> I going to the wrong server? Is my use of the link command incorrect?<BR>> Thanks for any help!<BR>><BR>> David Wall<BR>> 553-5329<BR>> IBM Life Sciences<BR>><BR>> ----- Forwarded by Dave Wall/Rochester/IBM on 09/27/2002 10:38 AM -----<BR>><BR>> Geoff Purdy<BR>> <GPURDY@COGENTNEUROS Dave<br To:>> Wall/Rochester/IBM@IBMUS cience.com> cc:<BR>> Subject: RE: [DAS]<BR>> Getting Started With DAS 09/27/2002 09:36 AM<BR>><BR>><BR>><BR>><BR>><BR>> Well, I'm out of ideas. There is evidence that "link" works on the<BR>Sanger<BR>> DAS server as the pop-up menus are populated with additional information.<BR>> However, I've been unable to access that information using a script.<BR>><BR>> I suggest posting your question on the biodas list. The collective<BR>> expertise on the list is orders of magnitude greater than my own.<BR>><BR>> I don't know of any alternatives to "link" for accessing annotation<BR>> details.<BR>> The reason I quoted "link" is that command names appear in italics in the<BR>> DAS documentation and italics isn't available in a plain text message.<BR>><BR>> > -----Original Message-----<BR>> > From: Dave Wall [mailto:dawall@us.ibm.com]<BR>> > Sent: Thursday, September 26, 2002 5:29 PM<BR>> > To: Geoff Purdy<BR>> > Subject: RE: [DAS] Getting Started With DAS<BR>> ><BR>> ><BR>> ><BR>> > Thanks for looking into it. If I read between the lines a little it<BR>><BR>> almost<BR>><BR>> > sounds as if there is another way to get the annotation. You tried<BR>><BR>> three<BR>><BR>> > servers and none of them delivered the data via the link command. Is<BR>><BR>> there<BR>><BR>> > another way to do it?<BR>> ><BR>> > David Wall<BR>> > 553-5329<BR>> > IBM Life Sciences<BR>><BR>> Dave,<BR>> You raise a good point here. I notice that if I use the link command on<BR>> three different das servers, I see three different behaviors.<BR>><BR>> Last I saw, the UCSC DAS server was Jim Kent's C implementation of the<BR>DAS<BR>> specification. As you pointed out, the link command gives no output (in<BR>> the<BR>> handful of cases I've tried).<BR>><BR>> I also tried a similar query on the Sanger Center DAS server (a Java<BR>> implementation, I believe). This server gives the following message if a<BR>> feature doesn't have associated annotations:<BR>>
<H1>No extra information about this object</H1><BR>>
<P>field: feature<BR>id: 18/p11.32</P><BR>><BR>> Finally, I tried CSHL's wormbase DAS server (a perl implementation by<BR>> Lincoln Stein). This doesn't seem to implement the link command at all.<BR>><BR>> I notice that the "link" command is an annotation server specific command<BR>> (not part of reference server specification). I'm unsure which of these<BR>> servers purport to be reference, annotation, or both. Another<BR>possibility<BR>> is that different implementations of DAS may omit implementing portions<BR>of<BR>> the specification.<BR>><BR>> I'll give this a closer look, but I'm beginning to think this might be a<BR>> good subject for on-list discussion.<BR>><BR>> > -----Original Message-----<BR>> > From: Dave Wall [mailto:dawall@us.ibm.com]<BR>> > Sent: Thursday, September 26, 2002 4:15 PM<BR>> > To: Geoff Purdy<BR>> > Subject: RE: [DAS] Getting Started With DAS<BR>> ><BR>> ><BR>> ><BR>> > Thanks for offering to help!<BR>> ><BR>> > I have been having pretty good luck getting a list of data<BR>> > sources, types,<BR>> > segments, etc., but crash when I trying to get an annotation.<BR>> > Here is an<BR>> > example for the purpose of verifying URL syntax ...<BR>> ><BR>> ><BR>> > http://genome.cse.ucsc.edu:80/cgi-bin/das/hg12/features?segmen<BR>> > t=18:1,100000<BR>> ><BR>> > In the returned data is<BR>> > - <FEATURE id=GC.chr18.60000 label="GC"><BR>> > <TYPE id=gcPercent reference="no" category="other">GC<BR>> > Percent</TYPE><BR>> > <METHOD></METHOD><BR>> > <START>60001</START><BR>> > <END>80000</END><BR>> > <SCORE>0</SCORE><BR>> > <ORIENTATION>0</ORIENTATION><BR>> > <PHASE>-</PHASE><BR>> > - <GROUP id=GC.chr18.60000><BR>> > <LINK href="<br>> ><br>> > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60000-8<br>> > 0000&db=hg12<br>> > ">Link to UCSC Browser</LINK><BR>> > </GROUP><BR>> > </FEATURE><BR>> ><BR>> > I then send the following which returns a blank page.<BR>> ><BR>> > http://genome.cse.ucsc.edu/cgi-bin/das/hg12/link?field=feature<BR>> > ;id=GC.chr18.60000<BR>> ><BR>> > I am probably missing something obvious, but I sure can't<BR>> > figure out what<BR>> > it is. Thanks again!<BR>> ><BR>> > David Wall<BR>> > 553-5329<BR>> > IBM Life Sciences<BR>><BR>> _______________________________________________<BR>> DAS mailing list<BR>> DAS@biodas.org<BR>> http://biodas.org/mailman/listinfo/das<BR><BR>--<BR>Lincoln Stein<BR>lstein@cshl.org<BR><BR><BR><BR><BR><BR><BR><BR>--__--__--<BR><BR>_______________________________________________<BR>DAS mailing list<BR>DAS@biodas.org<BR>http://biodas.org/mailman/listinfo/das<BR><BR><BR>End of DAS Digest</BLOCKQUOTE><p><br><hr size=1>Do you Yahoo!?<br>
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