From lstein at cshl.edu Tue Jul 5 14:59:52 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Tue, 5 Jul 2005 14:59:52 -0400 Subject: [DAS2] Thursday conf call In-Reply-To: References: Message-ID: <200507051459.53396.lstein@cshl.edu> Hi Gregg et al, Once a month, on the first Thursday of every month, I have a 3:00 eastern time Gramene conf call. I think this will conflict with this week's DS/2 conference call. The week after that I'm at PDB talking about structure-DAS, but I will be there for the July 21 meeting. In the meantime, I am working through all the bugs in Bugzilla and will hopefully have cleared all pending issues by July 21. lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From allenday at ucla.edu Fri Jul 8 04:07:59 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 8 Jul 2005 01:07:59 -0700 (PDT) Subject: [DAS2] assay das / mage-om mapping Message-ID: Hi all, I'm preparing my abstract for MGED 8, and as part of this I thought it would be a good idea to see if/how the commands I've laid for serving reagent, experiment, and assay results map to MAGE-OM concepts. I've attached here a few diagrams and zuml files showing: 1 the structure of (the relevant sections of) MAGE 2 the structure of the DAS/2 service. 3 the mapping between the MAGE and DAS/2 models I'd like to discuss this during our conference call next week. I also touched on the ontology DAS/2 service in diagram 2, I may have time to put together a full diagram by next week. -Allen -------------- next part -------------- A non-text attachment was scrubbed... Name: das-mage.tar.gz Type: application/x-gzip Size: 486813 bytes Desc: URL: From allenday at ucla.edu Fri Jul 8 14:34:49 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: References: Message-ID: So i figured a way around to get browser-viewable content from the server with the ?format= GET parameter. Not sure how much value there is in this, but here is a very simple graphical display of regions on the server, and their relative sizes. http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html All that's happening here is that ifyou request format=html, the server gives a Content-Type header of "text/xml" instead of "text/x-das-whatever+xml". The altered Content-Type, in combination with a stylesheet directive pointing to an XSL, allows the browser to show you a nice markup of the response. -Allen On Fri, 8 Jul 2005, Allen Day wrote: > Hi Andrew, > > I tried out your idea of having the XML returned by the DAS server include > an XSL reference at the top. It works, but I had to make some changes > that I'm not happy with: > > * the root XML element had to have the xmlns attribute removed, or the > transform wouldn't work. the xmlns:xlink and xml:base attributes were > okay to leave in. > > * my browser (firefox) refused to render the document unless i changed the > mimetype to text/xml. it didn't want to display text/x-das-sources+xml > > Any idea how to fix either of these? I took the liberty to modify the > content-type and remove the xmlns attribute from the root element, so you > can see the result on the production server: > > http://das.biopackages.net/das/genome > > -Allen > From Steve_Chervitz at affymetrix.com Wed Jul 13 17:09:43 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Wed, 13 Jul 2005 14:09:43 -0700 Subject: [DAS2] BioCyc pathway database sharing Message-ID: The current BioInform has an article about SRI's database adoption program for the computationally generated pathway databases. He says they are making available "peer-to-peer database sharing techniques": http://biocyc.org/intro.shtml#adopt From Steve_Chervitz at affymetrix.com Wed Jul 13 17:22:32 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Wed, 13 Jul 2005 14:22:32 -0700 Subject: [DAS2] Re: BioCyc pathway database sharing In-Reply-To: Message-ID: My earlier message got sent prematurely. Here's the link to the BioInform article: http://www.bioinform.com/articles/view-sl.asp?Article=200578124042 The reason I mention it is that it would be instructive to look into BioCyc's pathway tools in light of the pathway DAS extension being proposed in the DAS/2 continuation grant. This community may also be ideal candidate beta testers of pathway DAS prototypes. Steve > From: , Steve > Date: Wed, 13 Jul 2005 14:09:43 -0700 > To: DAS/2 > Subject: BioCyc pathway database sharing > > The current BioInform has an article about SRI's database adoption program for > the computationally generated pathway databases. He says they are making > available "peer-to-peer database sharing techniques": > > > > http://biocyc.org/intro.shtml#adopt From Steve_Chervitz at affymetrix.com Fri Jul 15 15:07:53 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 15 Jul 2005 12:07:53 -0700 Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: Message-ID: Neat trick, but I'm getting a server error now. Steve > From: Allen Day > Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) > To: Andrew Dalke > Cc: > Subject: [DAS2] xsl/content-type/browser fun > > So i figured a way around to get browser-viewable content from the server > with the ?format= GET parameter. Not sure how much value there is in > this, but here is a very simple graphical display of regions on the > server, and their relative sizes. > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html > > All that's happening here is that ifyou request format=html, the server > gives a Content-Type header of "text/xml" instead of > "text/x-das-whatever+xml". The altered Content-Type, in combination with > a stylesheet directive pointing to an XSL, allows the browser to show you > a nice markup of the response. > > -Allen > > > On Fri, 8 Jul 2005, Allen Day wrote: > >> Hi Andrew, >> >> I tried out your idea of having the XML returned by the DAS server include >> an XSL reference at the top. It works, but I had to make some changes >> that I'm not happy with: >> >> * the root XML element had to have the xmlns attribute removed, or the >> transform wouldn't work. the xmlns:xlink and xml:base attributes were >> okay to leave in. >> >> * my browser (firefox) refused to render the document unless i changed the >> mimetype to text/xml. it didn't want to display text/x-das-sources+xml >> >> Any idea how to fix either of these? I took the liberty to modify the >> content-type and remove the xmlns attribute from the root element, so you >> can see the result on the production server: >> >> http://das.biopackages.net/das/genome >> >> -Allen >> > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From allenday at ucla.edu Fri Jul 15 15:10:21 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 15 Jul 2005 12:10:21 -0700 (PDT) Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: References: Message-ID: Yes, I made a lot of changes to the server yesterday -- bringing it up to date with CVS head at Gregg's request. The xslt stuff wasn't in CVS. I can add it if you think this is really a useful feature. -Allen On Fri, 15 Jul 2005, Chervitz, Steve wrote: > Neat trick, but I'm getting a server error now. > > Steve > > > > From: Allen Day > > Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) > > To: Andrew Dalke > > Cc: > > Subject: [DAS2] xsl/content-type/browser fun > > > > So i figured a way around to get browser-viewable content from the server > > with the ?format= GET parameter. Not sure how much value there is in > > this, but here is a very simple graphical display of regions on the > > server, and their relative sizes. > > > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html > > > > All that's happening here is that ifyou request format=html, the server > > gives a Content-Type header of "text/xml" instead of > > "text/x-das-whatever+xml". The altered Content-Type, in combination with > > a stylesheet directive pointing to an XSL, allows the browser to show you > > a nice markup of the response. > > > > -Allen > > > > > > On Fri, 8 Jul 2005, Allen Day wrote: > > > >> Hi Andrew, > >> > >> I tried out your idea of having the XML returned by the DAS server include > >> an XSL reference at the top. It works, but I had to make some changes > >> that I'm not happy with: > >> > >> * the root XML element had to have the xmlns attribute removed, or the > >> transform wouldn't work. the xmlns:xlink and xml:base attributes were > >> okay to leave in. > >> > >> * my browser (firefox) refused to render the document unless i changed the > >> mimetype to text/xml. it didn't want to display text/x-das-sources+xml > >> > >> Any idea how to fix either of these? I took the liberty to modify the > >> content-type and remove the xmlns attribute from the root element, so you > >> can see the result on the production server: > >> > >> http://das.biopackages.net/das/genome > >> > >> -Allen > >> > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > From Steve_Chervitz at affymetrix.com Fri Jul 15 15:14:09 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 15 Jul 2005 12:14:09 -0700 Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: Message-ID: > Yes, I made a lot of changes to the server yesterday -- bringing it up to > date with CVS head at Gregg's request. The xslt stuff wasn't in CVS. I > can add it if you think this is really a useful feature. I do. Steve > -Allen > > > On Fri, 15 Jul 2005, Chervitz, Steve wrote: > >> Neat trick, but I'm getting a server error now. >> >> Steve >> >> >>> From: Allen Day >>> Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) >>> To: Andrew Dalke >>> Cc: >>> Subject: [DAS2] xsl/content-type/browser fun >>> >>> So i figured a way around to get browser-viewable content from the server >>> with the ?format= GET parameter. Not sure how much value there is in >>> this, but here is a very simple graphical display of regions on the >>> server, and their relative sizes. >>> >>> http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html >>> >>> All that's happening here is that ifyou request format=html, the server >>> gives a Content-Type header of "text/xml" instead of >>> "text/x-das-whatever+xml". The altered Content-Type, in combination with >>> a stylesheet directive pointing to an XSL, allows the browser to show you >>> a nice markup of the response. >>> >>> -Allen >>> >>> >>> On Fri, 8 Jul 2005, Allen Day wrote: >>> >>>> Hi Andrew, >>>> >>>> I tried out your idea of having the XML returned by the DAS server include >>>> an XSL reference at the top. It works, but I had to make some changes >>>> that I'm not happy with: >>>> >>>> * the root XML element had to have the xmlns attribute removed, or the >>>> transform wouldn't work. the xmlns:xlink and xml:base attributes were >>>> okay to leave in. >>>> >>>> * my browser (firefox) refused to render the document unless i changed the >>>> mimetype to text/xml. it didn't want to display text/x-das-sources+xml >>>> >>>> Any idea how to fix either of these? I took the liberty to modify the >>>> content-type and remove the xmlns attribute from the root element, so you >>>> can see the result on the production server: >>>> >>>> http://das.biopackages.net/das/genome >>>> >>>> -Allen >>>> >>> _______________________________________________ >>> DAS2 mailing list >>> DAS2 at portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/das2 >> From allenday at ucla.edu Fri Jul 15 15:32:57 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 15 Jul 2005 12:32:57 -0700 (PDT) Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: References: Message-ID: We should discuss making the content type for all das2xml responses as text/xml then, and putting the das format information in an x-das-* header. That way you won't have to append the ?format=html for web browsers... it will just work. -Allen On Fri, 15 Jul 2005, Chervitz, Steve wrote: > > > Yes, I made a lot of changes to the server yesterday -- bringing it up to > > date with CVS head at Gregg's request. The xslt stuff wasn't in CVS. I > > can add it if you think this is really a useful feature. > > I do. > > Steve > > > -Allen > > > > > > On Fri, 15 Jul 2005, Chervitz, Steve wrote: > > > >> Neat trick, but I'm getting a server error now. > >> > >> Steve > >> > >> > >>> From: Allen Day > >>> Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) > >>> To: Andrew Dalke > >>> Cc: > >>> Subject: [DAS2] xsl/content-type/browser fun > >>> > >>> So i figured a way around to get browser-viewable content from the server > >>> with the ?format= GET parameter. Not sure how much value there is in > >>> this, but here is a very simple graphical display of regions on the > >>> server, and their relative sizes. > >>> > >>> http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html > >>> > >>> All that's happening here is that ifyou request format=html, the server > >>> gives a Content-Type header of "text/xml" instead of > >>> "text/x-das-whatever+xml". The altered Content-Type, in combination with > >>> a stylesheet directive pointing to an XSL, allows the browser to show you > >>> a nice markup of the response. > >>> > >>> -Allen > >>> > >>> > >>> On Fri, 8 Jul 2005, Allen Day wrote: > >>> > >>>> Hi Andrew, > >>>> > >>>> I tried out your idea of having the XML returned by the DAS server include > >>>> an XSL reference at the top. It works, but I had to make some changes > >>>> that I'm not happy with: > >>>> > >>>> * the root XML element had to have the xmlns attribute removed, or the > >>>> transform wouldn't work. the xmlns:xlink and xml:base attributes were > >>>> okay to leave in. > >>>> > >>>> * my browser (firefox) refused to render the document unless i changed the > >>>> mimetype to text/xml. it didn't want to display text/x-das-sources+xml > >>>> > >>>> Any idea how to fix either of these? I took the liberty to modify the > >>>> content-type and remove the xmlns attribute from the root element, so you > >>>> can see the result on the production server: > >>>> > >>>> http://das.biopackages.net/das/genome > >>>> > >>>> -Allen > >>>> > >>> _______________________________________________ > >>> DAS2 mailing list > >>> DAS2 at portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/das2 > >> > From suzi at fruitfly.org Sun Jul 17 16:53:20 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Sun, 17 Jul 2005 13:53:20 -0700 Subject: [DAS2] Re: BioCyc pathway database sharing In-Reply-To: References: Message-ID: <0216195a76eadf46add14a3cfd0d8092@fruitfly.org> Here is a little bit of additional information. Lincoln has just submitted a renewal application for the Reactome grant and it includes a collaboration with Peter K and Paul Thomas (ABI) to regularly exchange pathways. The plan is to use bioPax and I would guess that this can be DAS-ified without too much difficulty. It is interesting to see the migration of interaction sets (as this data gets refined) transmogrified into full-out pathway data, and all the intermediate forms in between. -S On Jul 13, 2005, at 2:22 PM, Chervitz, Steve wrote: > My earlier message got sent prematurely. Here's the link to the > BioInform > article: > http://www.bioinform.com/articles/view-sl.asp?Article=200578124042 > > The reason I mention it is that it would be instructive to look into > BioCyc's pathway tools in light of the pathway DAS extension being > proposed > in the DAS/2 continuation grant. This community may also be ideal > candidate > beta testers of pathway DAS prototypes. > > Steve > >> From: , Steve >> Date: Wed, 13 Jul 2005 14:09:43 -0700 >> To: DAS/2 >> Subject: BioCyc pathway database sharing >> >> The current BioInform has an article about SRI's database adoption >> program for >> the computationally generated pathway databases. He says they are >> making >> available "peer-to-peer database sharing techniques": >> >> >> >> http://biocyc.org/intro.shtml#adopt > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Mon Jul 18 12:47:36 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 18 Jul 2005 12:47:36 -0400 Subject: [DAS2] URGENT: biodas.org renewal Message-ID: <200507181247.37057.lstein@cshl.edu> Hi Robin, The Biodas.org DNS registration just expired. You are still technically the owner of this domain. Could you transfer it to me or simply renew it and I'll reimburse you? The web site is now inaccessible, so this is fairly urgent. Thanks, Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From Steve_Chervitz at affymetrix.com Mon Jul 18 21:36:39 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Mon, 18 Jul 2005 18:36:39 -0700 Subject: [DAS2] Re: BioCyc pathway database sharing In-Reply-To: <0216195a76eadf46add14a3cfd0d8092@fruitfly.org> Message-ID: Cool. And speaking of interactions, I interacted with some of the biopathways folks at the ISMB in Detroit and mentioned our vision of the pathways extension to DAS for the continuation grant. They seemed very interested and eager to have some way to enable distributed pathway annotation. They also were interested in helping contribute ideas/verbiage for the pathways section of the continuation grant. They recommended that we post a blurb about what we are doing to the Biopax wiki, then send a message to their discussion list with a pointer to this wiki entry. Sound reasonable? Steve > From: Suzanna Lewis > Date: Sun, 17 Jul 2005 13:53:20 -0700 > To: "Chervitz, Steve" > Cc: DAS/2 > Subject: Re: [DAS2] Re: BioCyc pathway database sharing > > Here is a little bit of additional information. Lincoln has just > submitted a renewal application for the Reactome grant and it includes > a collaboration with Peter K and Paul Thomas (ABI) to regularly > exchange pathways. The plan is to use bioPax and I would guess that > this can be DAS-ified without too much difficulty. > > It is interesting to see the migration of interaction sets (as this > data gets refined) transmogrified into full-out pathway data, and all > the intermediate forms in between. > > -S > > On Jul 13, 2005, at 2:22 PM, Chervitz, Steve wrote: > >> My earlier message got sent prematurely. Here's the link to the >> BioInform >> article: >> http://www.bioinform.com/articles/view-sl.asp?Article=200578124042 >> >> The reason I mention it is that it would be instructive to look into >> BioCyc's pathway tools in light of the pathway DAS extension being >> proposed >> in the DAS/2 continuation grant. This community may also be ideal >> candidate >> beta testers of pathway DAS prototypes. >> >> Steve >> >>> From: , Steve >>> Date: Wed, 13 Jul 2005 14:09:43 -0700 >>> To: DAS/2 >>> Subject: BioCyc pathway database sharing >>> >>> The current BioInform has an article about SRI's database adoption >>> program for >>> the computationally generated pathway databases. He says they are >>> making >>> available "peer-to-peer database sharing techniques": >>> >>> >>> >>> http://biocyc.org/intro.shtml#adopt >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > From Steve_Chervitz at affymetrix.com Thu Jul 21 19:01:37 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Thu, 21 Jul 2005 16:01:37 -0700 Subject: [DAS2] Pseudomonas community annotation project Message-ID: Gregg, Here's the database I mentioned to you today after the teleconf: http://www.pseudomonas.com/index.html They aren't using DAS, but rather a centralized process. They allow users to update the underlying sequence, but there are issues: http://www.pseudomonas.com/seq_update_note.html These folks may be a good source of ideas for the writeback part of the DAS/2 spec. Also, it would be a interesting test for DAS to see how hard it would be to migrate them to a DAS-based system. Steve From suzi at fruitfly.org Thu Jul 21 20:52:23 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 21 Jul 2005 17:52:23 -0700 Subject: [DAS2] Pseudomonas community annotation project In-Reply-To: References: Message-ID: <245a864a841b15e89bff9e0a96bc3070@fruitfly.org> ACK!. I missed the call didn't I? Double drat, sorry to have gotten distracted for the crucial period. I agree this would be a good group to contact. -S On Jul 21, 2005, at 4:01 PM, Chervitz, Steve wrote: > Gregg, > > Here's the database I mentioned to you today after the teleconf: > > http://www.pseudomonas.com/index.html > > They aren't using DAS, but rather a centralized process. They allow > users to > update the underlying sequence, but there are issues: > http://www.pseudomonas.com/seq_update_note.html > > These folks may be a good source of ideas for the writeback part of the > DAS/2 spec. Also, it would be a interesting test for DAS to see how > hard it > would be to migrate them to a DAS-based system. > > Steve > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From sima at fruitfly.org Thu Jul 28 20:04:13 2005 From: sima at fruitfly.org (Sima Misra) Date: Thu, 28 Jul 2005 17:04:13 -0700 (PDT) Subject: [DAS2] New DAS2 specific aims Message-ID: This is a repost since my message didn't go through to the entire DAS2 list earlier today. Apologies to anyone receiving it twice. Best wishes, sima ---------- Forwarded message ---------- Date: Thu, 28 Jul 2005 14:52:59 -0700 From: Sima Misra To: Gregg Helt , DAS/2 , Lincoln Stein Cc: Suzanna Lewis , Mark Gibson , Nomi Harris , Sima Misra Subject: New DAS2 specific aims Please find attached a new draft of the specific aims for the DAS2 renewal, based on the discussion today. Suzi and I tried to figure out who would write particular sections of the grant, but of course folks should weigh in on rewording/reordering the aims and whether the assignments should be changed. This is just a starting point. Best wishes, sima -------------- next part -------------- A non-text attachment was scrubbed... Name: DAS2_renewal_aims.7.28.05.doc Type: application/msword Size: 57856 bytes Desc: URL: From lstein at cshl.edu Tue Jul 5 18:59:52 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Tue, 5 Jul 2005 14:59:52 -0400 Subject: [DAS2] Thursday conf call In-Reply-To: References: Message-ID: <200507051459.53396.lstein@cshl.edu> Hi Gregg et al, Once a month, on the first Thursday of every month, I have a 3:00 eastern time Gramene conf call. I think this will conflict with this week's DS/2 conference call. The week after that I'm at PDB talking about structure-DAS, but I will be there for the July 21 meeting. In the meantime, I am working through all the bugs in Bugzilla and will hopefully have cleared all pending issues by July 21. lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From allenday at ucla.edu Fri Jul 8 08:07:59 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 8 Jul 2005 01:07:59 -0700 (PDT) Subject: [DAS2] assay das / mage-om mapping Message-ID: Hi all, I'm preparing my abstract for MGED 8, and as part of this I thought it would be a good idea to see if/how the commands I've laid for serving reagent, experiment, and assay results map to MAGE-OM concepts. I've attached here a few diagrams and zuml files showing: 1 the structure of (the relevant sections of) MAGE 2 the structure of the DAS/2 service. 3 the mapping between the MAGE and DAS/2 models I'd like to discuss this during our conference call next week. I also touched on the ontology DAS/2 service in diagram 2, I may have time to put together a full diagram by next week. -Allen -------------- next part -------------- A non-text attachment was scrubbed... Name: das-mage.tar.gz Type: application/x-gzip Size: 486813 bytes Desc: URL: From allenday at ucla.edu Fri Jul 8 18:34:49 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: References: Message-ID: So i figured a way around to get browser-viewable content from the server with the ?format= GET parameter. Not sure how much value there is in this, but here is a very simple graphical display of regions on the server, and their relative sizes. http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html All that's happening here is that ifyou request format=html, the server gives a Content-Type header of "text/xml" instead of "text/x-das-whatever+xml". The altered Content-Type, in combination with a stylesheet directive pointing to an XSL, allows the browser to show you a nice markup of the response. -Allen On Fri, 8 Jul 2005, Allen Day wrote: > Hi Andrew, > > I tried out your idea of having the XML returned by the DAS server include > an XSL reference at the top. It works, but I had to make some changes > that I'm not happy with: > > * the root XML element had to have the xmlns attribute removed, or the > transform wouldn't work. the xmlns:xlink and xml:base attributes were > okay to leave in. > > * my browser (firefox) refused to render the document unless i changed the > mimetype to text/xml. it didn't want to display text/x-das-sources+xml > > Any idea how to fix either of these? I took the liberty to modify the > content-type and remove the xmlns attribute from the root element, so you > can see the result on the production server: > > http://das.biopackages.net/das/genome > > -Allen > From Steve_Chervitz at affymetrix.com Wed Jul 13 21:09:43 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Wed, 13 Jul 2005 14:09:43 -0700 Subject: [DAS2] BioCyc pathway database sharing Message-ID: The current BioInform has an article about SRI's database adoption program for the computationally generated pathway databases. He says they are making available "peer-to-peer database sharing techniques": http://biocyc.org/intro.shtml#adopt From Steve_Chervitz at affymetrix.com Wed Jul 13 21:22:32 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Wed, 13 Jul 2005 14:22:32 -0700 Subject: [DAS2] Re: BioCyc pathway database sharing In-Reply-To: Message-ID: My earlier message got sent prematurely. Here's the link to the BioInform article: http://www.bioinform.com/articles/view-sl.asp?Article=200578124042 The reason I mention it is that it would be instructive to look into BioCyc's pathway tools in light of the pathway DAS extension being proposed in the DAS/2 continuation grant. This community may also be ideal candidate beta testers of pathway DAS prototypes. Steve > From: , Steve > Date: Wed, 13 Jul 2005 14:09:43 -0700 > To: DAS/2 > Subject: BioCyc pathway database sharing > > The current BioInform has an article about SRI's database adoption program for > the computationally generated pathway databases. He says they are making > available "peer-to-peer database sharing techniques": > > > > http://biocyc.org/intro.shtml#adopt From Steve_Chervitz at affymetrix.com Fri Jul 15 19:07:53 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 15 Jul 2005 12:07:53 -0700 Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: Message-ID: Neat trick, but I'm getting a server error now. Steve > From: Allen Day > Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) > To: Andrew Dalke > Cc: > Subject: [DAS2] xsl/content-type/browser fun > > So i figured a way around to get browser-viewable content from the server > with the ?format= GET parameter. Not sure how much value there is in > this, but here is a very simple graphical display of regions on the > server, and their relative sizes. > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html > > All that's happening here is that ifyou request format=html, the server > gives a Content-Type header of "text/xml" instead of > "text/x-das-whatever+xml". The altered Content-Type, in combination with > a stylesheet directive pointing to an XSL, allows the browser to show you > a nice markup of the response. > > -Allen > > > On Fri, 8 Jul 2005, Allen Day wrote: > >> Hi Andrew, >> >> I tried out your idea of having the XML returned by the DAS server include >> an XSL reference at the top. It works, but I had to make some changes >> that I'm not happy with: >> >> * the root XML element had to have the xmlns attribute removed, or the >> transform wouldn't work. the xmlns:xlink and xml:base attributes were >> okay to leave in. >> >> * my browser (firefox) refused to render the document unless i changed the >> mimetype to text/xml. it didn't want to display text/x-das-sources+xml >> >> Any idea how to fix either of these? I took the liberty to modify the >> content-type and remove the xmlns attribute from the root element, so you >> can see the result on the production server: >> >> http://das.biopackages.net/das/genome >> >> -Allen >> > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From allenday at ucla.edu Fri Jul 15 19:10:21 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 15 Jul 2005 12:10:21 -0700 (PDT) Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: References: Message-ID: Yes, I made a lot of changes to the server yesterday -- bringing it up to date with CVS head at Gregg's request. The xslt stuff wasn't in CVS. I can add it if you think this is really a useful feature. -Allen On Fri, 15 Jul 2005, Chervitz, Steve wrote: > Neat trick, but I'm getting a server error now. > > Steve > > > > From: Allen Day > > Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) > > To: Andrew Dalke > > Cc: > > Subject: [DAS2] xsl/content-type/browser fun > > > > So i figured a way around to get browser-viewable content from the server > > with the ?format= GET parameter. Not sure how much value there is in > > this, but here is a very simple graphical display of regions on the > > server, and their relative sizes. > > > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html > > > > All that's happening here is that ifyou request format=html, the server > > gives a Content-Type header of "text/xml" instead of > > "text/x-das-whatever+xml". The altered Content-Type, in combination with > > a stylesheet directive pointing to an XSL, allows the browser to show you > > a nice markup of the response. > > > > -Allen > > > > > > On Fri, 8 Jul 2005, Allen Day wrote: > > > >> Hi Andrew, > >> > >> I tried out your idea of having the XML returned by the DAS server include > >> an XSL reference at the top. It works, but I had to make some changes > >> that I'm not happy with: > >> > >> * the root XML element had to have the xmlns attribute removed, or the > >> transform wouldn't work. the xmlns:xlink and xml:base attributes were > >> okay to leave in. > >> > >> * my browser (firefox) refused to render the document unless i changed the > >> mimetype to text/xml. it didn't want to display text/x-das-sources+xml > >> > >> Any idea how to fix either of these? I took the liberty to modify the > >> content-type and remove the xmlns attribute from the root element, so you > >> can see the result on the production server: > >> > >> http://das.biopackages.net/das/genome > >> > >> -Allen > >> > > _______________________________________________ > > DAS2 mailing list > > DAS2 at portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/das2 > From Steve_Chervitz at affymetrix.com Fri Jul 15 19:14:09 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Fri, 15 Jul 2005 12:14:09 -0700 Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: Message-ID: > Yes, I made a lot of changes to the server yesterday -- bringing it up to > date with CVS head at Gregg's request. The xslt stuff wasn't in CVS. I > can add it if you think this is really a useful feature. I do. Steve > -Allen > > > On Fri, 15 Jul 2005, Chervitz, Steve wrote: > >> Neat trick, but I'm getting a server error now. >> >> Steve >> >> >>> From: Allen Day >>> Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) >>> To: Andrew Dalke >>> Cc: >>> Subject: [DAS2] xsl/content-type/browser fun >>> >>> So i figured a way around to get browser-viewable content from the server >>> with the ?format= GET parameter. Not sure how much value there is in >>> this, but here is a very simple graphical display of regions on the >>> server, and their relative sizes. >>> >>> http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html >>> >>> All that's happening here is that ifyou request format=html, the server >>> gives a Content-Type header of "text/xml" instead of >>> "text/x-das-whatever+xml". The altered Content-Type, in combination with >>> a stylesheet directive pointing to an XSL, allows the browser to show you >>> a nice markup of the response. >>> >>> -Allen >>> >>> >>> On Fri, 8 Jul 2005, Allen Day wrote: >>> >>>> Hi Andrew, >>>> >>>> I tried out your idea of having the XML returned by the DAS server include >>>> an XSL reference at the top. It works, but I had to make some changes >>>> that I'm not happy with: >>>> >>>> * the root XML element had to have the xmlns attribute removed, or the >>>> transform wouldn't work. the xmlns:xlink and xml:base attributes were >>>> okay to leave in. >>>> >>>> * my browser (firefox) refused to render the document unless i changed the >>>> mimetype to text/xml. it didn't want to display text/x-das-sources+xml >>>> >>>> Any idea how to fix either of these? I took the liberty to modify the >>>> content-type and remove the xmlns attribute from the root element, so you >>>> can see the result on the production server: >>>> >>>> http://das.biopackages.net/das/genome >>>> >>>> -Allen >>>> >>> _______________________________________________ >>> DAS2 mailing list >>> DAS2 at portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/das2 >> From allenday at ucla.edu Fri Jul 15 19:32:57 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 15 Jul 2005 12:32:57 -0700 (PDT) Subject: [DAS2] xsl/content-type/browser fun In-Reply-To: References: Message-ID: We should discuss making the content type for all das2xml responses as text/xml then, and putting the das format information in an x-das-* header. That way you won't have to append the ?format=html for web browsers... it will just work. -Allen On Fri, 15 Jul 2005, Chervitz, Steve wrote: > > > Yes, I made a lot of changes to the server yesterday -- bringing it up to > > date with CVS head at Gregg's request. The xslt stuff wasn't in CVS. I > > can add it if you think this is really a useful feature. > > I do. > > Steve > > > -Allen > > > > > > On Fri, 15 Jul 2005, Chervitz, Steve wrote: > > > >> Neat trick, but I'm getting a server error now. > >> > >> Steve > >> > >> > >>> From: Allen Day > >>> Date: Fri, 8 Jul 2005 11:34:49 -0700 (PDT) > >>> To: Andrew Dalke > >>> Cc: > >>> Subject: [DAS2] xsl/content-type/browser fun > >>> > >>> So i figured a way around to get browser-viewable content from the server > >>> with the ?format= GET parameter. Not sure how much value there is in > >>> this, but here is a very simple graphical display of regions on the > >>> server, and their relative sizes. > >>> > >>> http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region?format=html > >>> > >>> All that's happening here is that ifyou request format=html, the server > >>> gives a Content-Type header of "text/xml" instead of > >>> "text/x-das-whatever+xml". The altered Content-Type, in combination with > >>> a stylesheet directive pointing to an XSL, allows the browser to show you > >>> a nice markup of the response. > >>> > >>> -Allen > >>> > >>> > >>> On Fri, 8 Jul 2005, Allen Day wrote: > >>> > >>>> Hi Andrew, > >>>> > >>>> I tried out your idea of having the XML returned by the DAS server include > >>>> an XSL reference at the top. It works, but I had to make some changes > >>>> that I'm not happy with: > >>>> > >>>> * the root XML element had to have the xmlns attribute removed, or the > >>>> transform wouldn't work. the xmlns:xlink and xml:base attributes were > >>>> okay to leave in. > >>>> > >>>> * my browser (firefox) refused to render the document unless i changed the > >>>> mimetype to text/xml. it didn't want to display text/x-das-sources+xml > >>>> > >>>> Any idea how to fix either of these? I took the liberty to modify the > >>>> content-type and remove the xmlns attribute from the root element, so you > >>>> can see the result on the production server: > >>>> > >>>> http://das.biopackages.net/das/genome > >>>> > >>>> -Allen > >>>> > >>> _______________________________________________ > >>> DAS2 mailing list > >>> DAS2 at portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/das2 > >> > From suzi at fruitfly.org Sun Jul 17 20:53:20 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Sun, 17 Jul 2005 13:53:20 -0700 Subject: [DAS2] Re: BioCyc pathway database sharing In-Reply-To: References: Message-ID: <0216195a76eadf46add14a3cfd0d8092@fruitfly.org> Here is a little bit of additional information. Lincoln has just submitted a renewal application for the Reactome grant and it includes a collaboration with Peter K and Paul Thomas (ABI) to regularly exchange pathways. The plan is to use bioPax and I would guess that this can be DAS-ified without too much difficulty. It is interesting to see the migration of interaction sets (as this data gets refined) transmogrified into full-out pathway data, and all the intermediate forms in between. -S On Jul 13, 2005, at 2:22 PM, Chervitz, Steve wrote: > My earlier message got sent prematurely. Here's the link to the > BioInform > article: > http://www.bioinform.com/articles/view-sl.asp?Article=200578124042 > > The reason I mention it is that it would be instructive to look into > BioCyc's pathway tools in light of the pathway DAS extension being > proposed > in the DAS/2 continuation grant. This community may also be ideal > candidate > beta testers of pathway DAS prototypes. > > Steve > >> From: , Steve >> Date: Wed, 13 Jul 2005 14:09:43 -0700 >> To: DAS/2 >> Subject: BioCyc pathway database sharing >> >> The current BioInform has an article about SRI's database adoption >> program for >> the computationally generated pathway databases. He says they are >> making >> available "peer-to-peer database sharing techniques": >> >> >> >> http://biocyc.org/intro.shtml#adopt > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Mon Jul 18 16:47:36 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 18 Jul 2005 12:47:36 -0400 Subject: [DAS2] URGENT: biodas.org renewal Message-ID: <200507181247.37057.lstein@cshl.edu> Hi Robin, The Biodas.org DNS registration just expired. You are still technically the owner of this domain. Could you transfer it to me or simply renew it and I'll reimburse you? The web site is now inaccessible, so this is fairly urgent. Thanks, Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From Steve_Chervitz at affymetrix.com Tue Jul 19 01:36:39 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Mon, 18 Jul 2005 18:36:39 -0700 Subject: [DAS2] Re: BioCyc pathway database sharing In-Reply-To: <0216195a76eadf46add14a3cfd0d8092@fruitfly.org> Message-ID: Cool. And speaking of interactions, I interacted with some of the biopathways folks at the ISMB in Detroit and mentioned our vision of the pathways extension to DAS for the continuation grant. They seemed very interested and eager to have some way to enable distributed pathway annotation. They also were interested in helping contribute ideas/verbiage for the pathways section of the continuation grant. They recommended that we post a blurb about what we are doing to the Biopax wiki, then send a message to their discussion list with a pointer to this wiki entry. Sound reasonable? Steve > From: Suzanna Lewis > Date: Sun, 17 Jul 2005 13:53:20 -0700 > To: "Chervitz, Steve" > Cc: DAS/2 > Subject: Re: [DAS2] Re: BioCyc pathway database sharing > > Here is a little bit of additional information. Lincoln has just > submitted a renewal application for the Reactome grant and it includes > a collaboration with Peter K and Paul Thomas (ABI) to regularly > exchange pathways. The plan is to use bioPax and I would guess that > this can be DAS-ified without too much difficulty. > > It is interesting to see the migration of interaction sets (as this > data gets refined) transmogrified into full-out pathway data, and all > the intermediate forms in between. > > -S > > On Jul 13, 2005, at 2:22 PM, Chervitz, Steve wrote: > >> My earlier message got sent prematurely. Here's the link to the >> BioInform >> article: >> http://www.bioinform.com/articles/view-sl.asp?Article=200578124042 >> >> The reason I mention it is that it would be instructive to look into >> BioCyc's pathway tools in light of the pathway DAS extension being >> proposed >> in the DAS/2 continuation grant. This community may also be ideal >> candidate >> beta testers of pathway DAS prototypes. >> >> Steve >> >>> From: , Steve >>> Date: Wed, 13 Jul 2005 14:09:43 -0700 >>> To: DAS/2 >>> Subject: BioCyc pathway database sharing >>> >>> The current BioInform has an article about SRI's database adoption >>> program for >>> the computationally generated pathway databases. He says they are >>> making >>> available "peer-to-peer database sharing techniques": >>> >>> >>> >>> http://biocyc.org/intro.shtml#adopt >> >> _______________________________________________ >> DAS2 mailing list >> DAS2 at portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > From Steve_Chervitz at affymetrix.com Thu Jul 21 23:01:37 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Thu, 21 Jul 2005 16:01:37 -0700 Subject: [DAS2] Pseudomonas community annotation project Message-ID: Gregg, Here's the database I mentioned to you today after the teleconf: http://www.pseudomonas.com/index.html They aren't using DAS, but rather a centralized process. They allow users to update the underlying sequence, but there are issues: http://www.pseudomonas.com/seq_update_note.html These folks may be a good source of ideas for the writeback part of the DAS/2 spec. Also, it would be a interesting test for DAS to see how hard it would be to migrate them to a DAS-based system. Steve From suzi at fruitfly.org Fri Jul 22 00:52:23 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 21 Jul 2005 17:52:23 -0700 Subject: [DAS2] Pseudomonas community annotation project In-Reply-To: References: Message-ID: <245a864a841b15e89bff9e0a96bc3070@fruitfly.org> ACK!. I missed the call didn't I? Double drat, sorry to have gotten distracted for the crucial period. I agree this would be a good group to contact. -S On Jul 21, 2005, at 4:01 PM, Chervitz, Steve wrote: > Gregg, > > Here's the database I mentioned to you today after the teleconf: > > http://www.pseudomonas.com/index.html > > They aren't using DAS, but rather a centralized process. They allow > users to > update the underlying sequence, but there are issues: > http://www.pseudomonas.com/seq_update_note.html > > These folks may be a good source of ideas for the writeback part of the > DAS/2 spec. Also, it would be a interesting test for DAS to see how > hard it > would be to migrate them to a DAS-based system. > > Steve > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 From sima at fruitfly.org Fri Jul 29 00:04:13 2005 From: sima at fruitfly.org (Sima Misra) Date: Thu, 28 Jul 2005 17:04:13 -0700 (PDT) Subject: [DAS2] New DAS2 specific aims Message-ID: This is a repost since my message didn't go through to the entire DAS2 list earlier today. Apologies to anyone receiving it twice. Best wishes, sima ---------- Forwarded message ---------- Date: Thu, 28 Jul 2005 14:52:59 -0700 From: Sima Misra To: Gregg Helt , DAS/2 , Lincoln Stein Cc: Suzanna Lewis , Mark Gibson , Nomi Harris , Sima Misra Subject: New DAS2 specific aims Please find attached a new draft of the specific aims for the DAS2 renewal, based on the discussion today. Suzi and I tried to figure out who would write particular sections of the grant, but of course folks should weigh in on rewording/reordering the aims and whether the assignments should be changed. This is just a starting point. Best wishes, sima -------------- next part -------------- A non-text attachment was scrubbed... Name: DAS2_renewal_aims.7.28.05.doc Type: application/msword Size: 57856 bytes Desc: URL: