From lstein at cshl.edu Mon Jan 8 10:22:29 2007 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 8 Jan 2007 10:22:29 -0500 Subject: [DAS2] No DAS/2 teleconference this Monday, rescheduled for Jan 8th In-Reply-To: References: Message-ID: <6dce9a0b0701080722j31202961gceacdfdadae152ae@mail.gmail.com> Are we on for today? Lincoln On 12/30/06, Helt,Gregg wrote: > > Just wanted to let everyone know that the next DAS/2 teleconference has > been rescheduled for Monday January 8th, 9:30 AM PST. It was originally > scheduled for Monday Jan 1, but it's a day off for many. > > thanks, > Gregg > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- 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 From Gregg_Helt at affymetrix.com Mon Jan 8 11:47:54 2007 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Mon, 8 Jan 2007 08:47:54 -0800 Subject: [DAS2] No DAS/2 teleconference this Monday, rescheduled for Jan 8th Message-ID: Yep, 9:30 AM PST. talk to you soon, Gregg -----Original Message----- From: lincoln.stein at gmail.com [mailto:lincoln.stein at gmail.com] On Behalf Of Lincoln Stein Sent: Monday, January 08, 2007 7:22 AM To: Helt,Gregg Cc: das2 at lists.open-bio.org Subject: Re: [DAS2] No DAS/2 teleconference this Monday, rescheduled for Jan 8th Are we on for today? Lincoln On 12/30/06, Helt,Gregg wrote: Just wanted to let everyone know that the next DAS/2 teleconference has been rescheduled for Monday January 8th, 9:30 AM PST. It was originally scheduled for Monday Jan 1, but it's a day off for many. thanks, Gregg _______________________________________________ DAS2 mailing list DAS2 at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/das2 -- 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 From Steve_Chervitz at affymetrix.com Mon Jan 8 16:32:00 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 08 Jan 2007 13:32:00 -0800 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 8 Jan 2007 Message-ID: Notes from the biweekly DAS/2 teleconference, 8 Jan 2007 $Id: das2-teleconf-2007-01-08.txt,v 1.1 2007/01/08 20:05:30 sac Exp $ Teleconference Info: * Schedule: Biweekly on Monday * Time of Day: 9:30 AM PST, 17:30 GMT * Dialin (US): 800-531-3250 * Dialin (Intl): 303-928-2693 * Toll-free UK: 08 00 40 49 467 * Toll-free France: 08 00 907 839 * Conference ID: 2879055 * Passcode: 1365 Attendees: Affy: Steve Chervitz, Gregg Helt CSHL: Lincoln Stein Dalke Scientific: Andrew Dalke Note taker: Steve Chervitz Action items are flagged with '[A]'. These notes are checked into the biodas.org CVS repository at das/das2/notes/. Instructions on how to access this repository are at http://biodas.org DISCLAIMER: The note taker aims for completeness and accuracy, but these goals are not always achievable, given the desire to get the notes out with a rapid turnaround. So don't consider these notes as complete minutes from the meeting, but rather abbreviated, summarized versions of what was discussed. There may be errors of commission and omission. Participants are welcome to post comments and/or corrections to these as they see fit. Agenda ------- * Status reports * URIs for global seq IDs gh: On the das2 get html spec, I took out all xxx comments. Just committed today. not all fixed, but adjusted language as needed. Remaining xxx comments are still present as html comments. we can keep editing, looking for hidden comments, adding info as we can. I also refined some text, discussing coordinate elements, where to find uri for those. put in pointer to global seq ids page on biowiki, said it will soon be incorporated in sanger registry. Todo: alignments, and address global seq id fuzziness. should be able to clean up the seq id stuff based on today's teleconf. so really just aligmnent examples. [A] Gregg will add alignment examples to das2 get spec html version [A] Announce das2 get spec (html and xml) when alignment examples are complete [A] discuss with andreas how to incorporate global seq ids into registry gh: now weh have gobal seq ids in biowiki, added by lincoln, but editable by anyone (handy). I want to integerate into sanger das2 registry, and generate from that or vice versa a das2 server that serves those things up. makes sense to have those uris served up as versioned source in a das2 document. now, coord uris are only available in the biowiki page. ad: only need to be abstract strings if there's no need to resolve them. gh: want these to be uris for a das2 versioned source. ad: get ncbi to do it? gh: not necessary. just make them accessible through the das2 registry. doesn't matter where it is. ad: how use? gh: someone can then go to das2 registry and see all the ones that have a global coordinate system. ad: can be done now. gh: want to avoid screen scraping the html page. ls: need to have a set of url's for parsable documents with coord systems? gh: we have xml for versioned sources in segments xml document. there's direct mapping from v-source id to coord uri, and a direct mapping from segment reference uri to segment id. we need a v-source document where each has a uri for global coord system. there would be just one capability -- segments, retrievable in the segments xml. ls: right. who's maintianing? there are 1000s of genomes. ad: coordinate element has other slots, attributes, what else is needed? gh: there is no central way to look at all coords that are available? ad: why needed? can't you get it from the sources document without looking something else up? ls: registry could compile a unique list of that and produce a report which has a list of all coordinates followed by all data sources that use that coord system. would be useful. would show who is using various systems. Spot bugs like two servers using diff coord systems for the same taxon. Server could show coord systems on a per-taxon basis, no additional query needed. gh: another example: part of the problem for me is relationship between coord uris and segment reference uris. ls: why? no consistency enforced in spec. gh: no guarantee that if you use the same coord uri that you'll use the same reference uri. another problem: looking at biowiki doesn't tell you how to construct a coord element. coord elem has attribs for taxonomy, authority, etc. ls: the coordinates url should point to the biowiki page with correct anchor, need a line for each coord system. I didn't give url to coord system. gh: attribs aren't on the wiki page. gh: people need to know that's what they should use in the das2 documents. we should show on page: "name for das2 full coordinates element is 'such and such'". people can then cut and paste. ls: ok. [A] lincoln will post additional attributes on global seq id biowiki page gh: then screen scaping by registry to grab all coordinates to make them available. ad: why do screen scraping? gh: ... ls: when people add info in the registry, then that goes in. gh: if using wrong authority? ls: it goes in wrong. gh: would like the server to catch it. ad: when registring a server, it presents a drop down field gh: where does it get that list? ad: best to ask andreas. gh: should be within biodas.org sc: wikification progress of biodas.org - can migrate global seq ids page there when it's ready. gh: might be best to let Andreas decide, to manage it on his server. sc: he's been active in the initial wikification work, so maybe he'll be ok maintaining/migrating it there. ls: some confusion over where to add this info (biodas.org, wiki of that, or open-bio.org wiki). only want to do this once. [A] steve/andreas will complete biodas.org wiki migration and notify all gh: status continued - alignment examples to spec are still to do. igb release in december: pays attention to coord uri's should be able to match up biopackages and affymetrix das2 servers v-sources on the same genome and overlay rather than making a new genome. in the next month: working on getting transcriptome data in a das2 server. lincoln had mentioned NCI interest in this. most of code is in place to serve up affy transcriptome data as graphs, a datum every 20 bp, e.g., efficient slicing from whole chromosomes, to get what you need for das range query, and bring them into igb as slices. working on serving up in alternative formats (e.g., UCSC's wiggle) rather than just affy binary format. Return options - graph the size of whole chromosome (now), or more per region, put score in a das score element, which would be a very large document. ls: be prepared to return in a das2 xml document, each score in an element, not sensible over whole chromosome, but ok for a limited region. A good form of compatibility. gh: size issues - could give a 'request too large' error. ls: could use http compression. NCI will likely never support the specialized format, so if you don't give das2 xml format, it will not be available to that client. ls: brian gilman - can't pay him to do more work on that contract. gh: might be able to pay him via affy. need to get this going within next month, couple of publications need it. ls: status: - took xml parser for perl das2 client, cleaned it up, put it on perl cpan website, underlies parsing and processing of das2 streams. pure perl, no requirements for c libraries, not validating sax client (so it's faster than the c libries). it does namespace handling, multi-threaded. offered as a standard reference. missing handling of features (types, sources, segments) -- big hole. NCI java client library went thru it's approval process, still doing various tests and qualifications before folding into main NCI source code repository. Hapmap data source still in progress. Just xml parser on cpan, full server not complete. gh: using biopackages server? ls: yes, an instance at CSHL (or will). ad: holidays and was sick for last month. working on proxy code, rewriting, fixing. sc: regarding your das2 committment? ad: making up for sick time last month. plan is to get proxy stuff done, then that's it for das. gh: (more status) also working on getting the das2 feature query support fleshed out. handle any combination of filters. coming soon, moving to new affy server hardware. on steve's plate. sc: worked on biodas.org wikification. some server configuration issues. have made a good start with Andreas' help, but more to do. should be in place later this month. some html get spec edits, fixes. planning to help gregg set up new hardware for affy das server. can then support more arrays, genome versions, organisms. gh: hardware - hoping it would be here. approved by purchasing on 1/5/07. PO likely went out to vendor, so should be in within a week. we have requests in to support more versions, probe set location for exons on older genome versions. sc: transcript annotations? gh: background - affy chp data has no genome location, just probe set id and score. IGB takes that data and merges with genome info to build heat maps to look at data. Been tricky to determine most efficient way to do that. Need to have both probe set level and transcript level data. in progress. [A] steve talk with UCSC about meeting focussed on das in feb/march [A] Next das2 teleconf: 22 Jan 2007 From aloraine at gmail.com Thu Jan 11 14:05:36 2007 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 11 Jan 2007 13:05:36 -0600 Subject: [DAS2] ids to coordinates? Message-ID: <83722dde0701111105m7a884b04id0e4608f38f7d252@mail.gmail.com> Greetings all, Sorry if I already asked this and spaced on the answer... Can I give a DAS2 server (and if yes, which one?) a list of HUGO gene names and then get back the start and end coordinate of the gene on hg17? (Note: the current version is hg18.) I'm doing a candidate gene-based population genetics project, and I need to be able to quickly get back the boundaries of a bunch of genes (as determined in the usual way, e..g, cDNA-to-genome alignments) where I have the HUGO name but that's it. I think maybe Lincoln mentioned something like this was available via a site at CSHL, or maybe Hapmap? I think it would be pretty nifty if the nicely-funded Hapmap project could provide such a service, if it does not already :-) Yours, Ann -- Ann Loraine Assistant Professor Departments of Genetics, Biostatistics, and Computer Information Sciences University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From Steve_Chervitz at affymetrix.com Thu Jan 11 14:13:10 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Thu, 11 Jan 2007 11:13:10 -0800 Subject: [DAS2] Ontology URIs In-Reply-To: Message-ID: Forwarding this message to the das/2 discussion at Suzi's request. Suzi: Could you give an example of hash vs slash-type URIs? Steve > ---------- Forwarded message ---------- > From: "Suzanna Lewis" > To: Gregg_Helt at affymetrix.com > Date: Thu, 11 Jan 2007 11:42:16 +0000 > Subject: Re: Ontology URIs (was RE: types.rnc) > Hi Gregg, > > A couple of months ago you asked me what NCBO might be doing in terms of > URIs. The discussion has finally begun, and so I'm forwarding this to you > because I thought you might want to comment as well. Good to have feedback > from everyone who will be affected. > > I think we need to address the URI issue ASAP. The questions raised at > HCLSIG highlight the importance of the issue (putting them here coz > not everyone on cBio technical would have seen them). The main ones > till now are: > > 1 - If the authors have their own namespace URI, that means they have > to maintain a copy of the ontology at their own site. I wonder how > will the synchronization between the bioportal to the external site be > established? > > ** This assumes that a URI = URL, which is not required by the URI > spec. URI resolution services, such as LSID are bound to enter the > discussion here. > > 2 - If an ontology is to adopt the URI that the bioportal provides, I > wonder what kind of URI, in terms of the hash vs. slash, that the > bioportal will support. For a samll sized ontology, the hash URI > would be sufficient and ideal. But if the ontology's size is huge, I > do believe the slash URI should be used to avoid the unnecessary > import. From the implementation point of view, however, supporting > slash URI would take a lot more hassle than supporting the hash URI. I > wonder if bioportal will be able to support that? > > ** Slash = hassle to implement the server. Hash = easy to implement > the server, > > For OBO to OWL, we chose the hash. > > 3- One comment on versioning issues (question2) . The matter is more > complex than the answer suggests. If a clinical system ever refers to > a URI in BioPortal this URI should stay forever. Even if a new version > of the ontology is deployed the original URI should still point to the > old term or concept, even if it is deprecated. So versioning is more > than a development or collaboration issue. I don't know wether the > answer given to question 3 solves this. > > -Nigam. > > cbio-technical-bounces at lists.stanford.edu wrote on : > > Do we have a policy for URIs? > > Should we form a URI working group? > --++**==--++**==--++**==--++**==--++**==--++**==--++**== > cbio-technical mailing list cbio-technical at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/cbio-technical > > --++**==--++**==--++**==--++**==--++**==--++**==--++**== > cbio-technical mailing list > cbio-technical at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/cbio-technical ------ End of Forwarded Message From Steve_Chervitz at affymetrix.com Thu Jan 11 15:21:25 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Thu, 11 Jan 2007 12:21:25 -0800 Subject: [DAS2] ids to coordinates? In-Reply-To: <83722dde0701111105m7a884b04id0e4608f38f7d252@mail.gmail.com> Message-ID: Ann, Here's my response from a similar question you asked last May: http://lists.open-bio.org/pipermail/das2/2006-June/000735.html The example URLs I gave for the Affymetrix DAS/2 server no longer work (not implemented -- but Gregg is planning to fix this in the near future). For now I'd recommend using the biopackages server. Example: http://das.biopackages.net/das/genome/human/17/feature?name=ACTA1 You can include multiple name=XXX parameters in the query to retrieve data for all gene names in the same response document (multiple feature filters with the same name are OR'd together, as described here: http://biodas.org/documents/das2/das2_get.html#feature_filters ). Cheers, Steve > From: Ann Loraine > Date: Thu, 11 Jan 2007 13:05:36 -0600 > To: DAS/2 > Subject: [DAS2] ids to coordinates? > > Greetings all, > > Sorry if I already asked this and spaced on the answer... > > Can I give a DAS2 server (and if yes, which one?) a list of HUGO gene > names and then get back the start and end coordinate of the gene on > hg17? (Note: the current version is hg18.) > > I'm doing a candidate gene-based population genetics project, and I > need to be able to quickly get back the boundaries of a bunch of genes > (as determined in the usual way, e..g, cDNA-to-genome alignments) > where I have the HUGO name but that's it. > > I think maybe Lincoln mentioned something like this was available via > a site at CSHL, or maybe Hapmap? > > I think it would be pretty nifty if the nicely-funded Hapmap project > could provide such a service, if it does not already :-) > > Yours, > > Ann > > -- > Ann Loraine > Assistant Professor > Departments of Genetics, Biostatistics, > and Computer Information Sciences > University of Alabama at Birmingham > http://www.transvar.org > 205-996-4155 > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 From WONG_MARIE_VIVIAN_NONLILLY at LILLY.COM Mon Jan 15 20:51:40 2007 From: WONG_MARIE_VIVIAN_NONLILLY at LILLY.COM (Marie Vivian Wong NONLILLY) Date: Tue, 16 Jan 2007 09:51:40 +0800 Subject: [DAS2] Proserver & Ensembl Message-ID: Hi, Is there a way to add more fields in the pop-up menu in Proserver? Besides the required features like id, start, end etc...for example if I want to add gene_start and gene_end to the feature list, is there a way to do this currently? thanks, Marie From aquinn at ebi.ac.uk Thu Jan 18 07:11:59 2007 From: aquinn at ebi.ac.uk (Antony Quinn) Date: Thu, 18 Jan 2007 12:11:59 -0000 Subject: [DAS2] AstroDAS: Astronomy Distributed Annotation System Message-ID: <458928D5.2010909@ebi.ac.uk> It's amazing what you can find on Google... AstroDAS considers the identification of entities across sky nodes to be a database integration problem. Its solution, inspired in part by the BioDAS effort in bioinformatics, features an annotation database with a web service interface to store and query annotations. The use of web services provides interoperability with the rest of the Virtual Observatory. Our prototype system resolves queries on astronomy catalogues using mapping tables that are dynamically constructed from annotations of celestial object matches. http://homepages.inf.ed.ac.uk/rbose/research_t2p2.htm From dalke at dalkescientific.com Thu Jan 18 08:52:58 2007 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 18 Jan 2007 14:52:58 +0100 Subject: [DAS2] AstroDAS: Astronomy Distributed Annotation System In-Reply-To: <458928D5.2010909@ebi.ac.uk> References: <458928D5.2010909@ebi.ac.uk> Message-ID: <6fee816dd03400055d1299b3cdaf4cc7@dalkescientific.com> On Dec 20, 2006, at 1:13 PM, Antony Quinn wrote: > AstroDAS considers the identification of entities across sky nodes to > be > a database integration problem. Its solution, inspired in part by the > BioDAS effort in bioinformatics, features an annotation database with a > web service interface to store and query annotations. LOL! Cool! Andrew dalke at dalkescientific.com From ap3 at sanger.ac.uk Mon Jan 22 06:33:29 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Mon, 22 Jan 2007 11:33:29 +0000 Subject: [DAS2] DAS related workshops in u.k. Message-ID: Hi all, The Biosapiens Network ( http://www.biosapiens.info/ ) is a project that has a strong commitment to DAS and has been very pro-active in setting up DAS/1 servers (lots of protein data) and developing DAS clients. Around this EU-wide collaboration we are organizing two DAS-related workshops to which we would like to invite you as well. They will both be held in the last week of February, location is the Genome Campus in Hinxton / Cambridge, U.K. workshop 1: DAS client developers workshop Monday 26/2/2007 main organizer: Andreas Prlic for more info please see: http://www.sanger.ac.uk/Users/ap3/dasworkshop.html workshop 2: BioSapiens Feature Classification (Ontology) Workshop Tuesday, 27/2/2007, Wednesday, 28/2/2007 main organizer: Henning Hermjakob fore more details please see attachment. Regards, Andreas -------------- next part -------------- A non-text attachment was scrubbed... Name: meetingAnnouncement.doc Type: application/msword Size: 23040 bytes Desc: not available URL: -------------- next part -------------- ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 From allenday at ucla.edu Thu Jan 25 03:28:15 2007 From: allenday at ucla.edu (Allen Day) Date: Thu, 25 Jan 2007 00:28:15 -0800 Subject: [DAS2] missing lock documentation Message-ID: <5c24dcc30701250028n8e2e8eete643bc98d63dafe7@mail.gmail.com> http://biodas.org/documents/das2/das2_locks.html any idea where this went? it is referenced at the end of http://biodas.org/documents/das2/das2_writeback.html -Allen From Steve_Chervitz at affymetrix.com Thu Jan 25 13:20:54 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Thu, 25 Jan 2007 10:20:54 -0800 Subject: [DAS2] missing lock documentation In-Reply-To: <5c24dcc30701250028n8e2e8eete643bc98d63dafe7@mail.gmail.com> Message-ID: The separate locking document has not yet been created. It's been on Andrew's plate for a while, perhaps he just hasn't committed it: http://lists.open-bio.org/pipermail/das2/2006-May/000711.html The locking stuff that was in the das2_get.html document was moved long ago (by me) into the das2_put.html document (revision 1.22 of the get doc). The put document later became obsolete, superceded by das2_writeback.html, so there aren't any links to that put doc anywhere on the site. You can still view the put doc, though I don't know how much of the thinking about how locking should work has changed since this text was writted (~Fall 2005): http://biodas.org/documents/das2/das2_put.html Steve > From: Allen Day > Reply-To: > Date: Thu, 25 Jan 2007 00:28:15 -0800 > To: DAS/2 > Subject: [DAS2] missing lock documentation > > http://biodas.org/documents/das2/das2_locks.html > > any idea where this went? it is referenced at the end of > > http://biodas.org/documents/das2/das2_writeback.html > > -Allen > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 From WONG_MARIE_VIVIAN_NONLILLY at LILLY.COM Thu Jan 25 21:27:17 2007 From: WONG_MARIE_VIVIAN_NONLILLY at LILLY.COM (Marie Vivian Wong NONLILLY) Date: Fri, 26 Jan 2007 10:27:17 +0800 Subject: [DAS2] Proserver Q on notes array Message-ID: Hi all, I have a proserver question.. showing of the notes array in IE via ensembl does not work. It only shows the first element in the array. But it works in firefox!!! However, our official browser is IE...is there a workaround? thanks! Marie From Steve_Chervitz at affymetrix.com Fri Jan 26 17:43:54 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 26 Jan 2007 14:43:54 -0800 Subject: [DAS2] Proserver Q on notes array In-Reply-To: Message-ID: Marie, You might have better luck sending your ProServer questions to the Ensembl helpdesk, or to the Sanger folks that developed it. Don't know how many ProServer experts there are on this list. Ensembl provides some documentation on ProServer here: http://www.ensembl.org/info/data/external_data/das/das_server.html Sounds like you have a web browser compatibility issue, which can be tricky from the coder's point of view. Consider convincing your group to use a more standards-compliant browser like Firefox (which can even be trickier ;). Cheers, Steve > From: Marie Vivian Wong NONLILLY > Date: Fri, 26 Jan 2007 10:27:17 +0800 > To: > Subject: [DAS2] Proserver Q on notes array > > > > > > Hi all, > > I have a proserver question.. > > showing of the notes array in IE via ensembl does not work. > It only shows the first element in the array. > > But it works in firefox!!! > > However, our official browser is IE...is there a workaround? > > > thanks! > Marie > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 From lstein at cshl.edu Mon Jan 8 15:22:29 2007 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 8 Jan 2007 10:22:29 -0500 Subject: [DAS2] No DAS/2 teleconference this Monday, rescheduled for Jan 8th In-Reply-To: References: Message-ID: <6dce9a0b0701080722j31202961gceacdfdadae152ae@mail.gmail.com> Are we on for today? Lincoln On 12/30/06, Helt,Gregg wrote: > > Just wanted to let everyone know that the next DAS/2 teleconference has > been rescheduled for Monday January 8th, 9:30 AM PST. It was originally > scheduled for Monday Jan 1, but it's a day off for many. > > thanks, > Gregg > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- 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 From Gregg_Helt at affymetrix.com Mon Jan 8 16:47:54 2007 From: Gregg_Helt at affymetrix.com (Helt,Gregg) Date: Mon, 8 Jan 2007 08:47:54 -0800 Subject: [DAS2] No DAS/2 teleconference this Monday, rescheduled for Jan 8th Message-ID: Yep, 9:30 AM PST. talk to you soon, Gregg -----Original Message----- From: lincoln.stein at gmail.com [mailto:lincoln.stein at gmail.com] On Behalf Of Lincoln Stein Sent: Monday, January 08, 2007 7:22 AM To: Helt,Gregg Cc: das2 at lists.open-bio.org Subject: Re: [DAS2] No DAS/2 teleconference this Monday, rescheduled for Jan 8th Are we on for today? Lincoln On 12/30/06, Helt,Gregg wrote: Just wanted to let everyone know that the next DAS/2 teleconference has been rescheduled for Monday January 8th, 9:30 AM PST. It was originally scheduled for Monday Jan 1, but it's a day off for many. thanks, Gregg _______________________________________________ DAS2 mailing list DAS2 at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/das2 -- 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 From Steve_Chervitz at affymetrix.com Mon Jan 8 21:32:00 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 08 Jan 2007 13:32:00 -0800 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 8 Jan 2007 Message-ID: Notes from the biweekly DAS/2 teleconference, 8 Jan 2007 $Id: das2-teleconf-2007-01-08.txt,v 1.1 2007/01/08 20:05:30 sac Exp $ Teleconference Info: * Schedule: Biweekly on Monday * Time of Day: 9:30 AM PST, 17:30 GMT * Dialin (US): 800-531-3250 * Dialin (Intl): 303-928-2693 * Toll-free UK: 08 00 40 49 467 * Toll-free France: 08 00 907 839 * Conference ID: 2879055 * Passcode: 1365 Attendees: Affy: Steve Chervitz, Gregg Helt CSHL: Lincoln Stein Dalke Scientific: Andrew Dalke Note taker: Steve Chervitz Action items are flagged with '[A]'. These notes are checked into the biodas.org CVS repository at das/das2/notes/. Instructions on how to access this repository are at http://biodas.org DISCLAIMER: The note taker aims for completeness and accuracy, but these goals are not always achievable, given the desire to get the notes out with a rapid turnaround. So don't consider these notes as complete minutes from the meeting, but rather abbreviated, summarized versions of what was discussed. There may be errors of commission and omission. Participants are welcome to post comments and/or corrections to these as they see fit. Agenda ------- * Status reports * URIs for global seq IDs gh: On the das2 get html spec, I took out all xxx comments. Just committed today. not all fixed, but adjusted language as needed. Remaining xxx comments are still present as html comments. we can keep editing, looking for hidden comments, adding info as we can. I also refined some text, discussing coordinate elements, where to find uri for those. put in pointer to global seq ids page on biowiki, said it will soon be incorporated in sanger registry. Todo: alignments, and address global seq id fuzziness. should be able to clean up the seq id stuff based on today's teleconf. so really just aligmnent examples. [A] Gregg will add alignment examples to das2 get spec html version [A] Announce das2 get spec (html and xml) when alignment examples are complete [A] discuss with andreas how to incorporate global seq ids into registry gh: now weh have gobal seq ids in biowiki, added by lincoln, but editable by anyone (handy). I want to integerate into sanger das2 registry, and generate from that or vice versa a das2 server that serves those things up. makes sense to have those uris served up as versioned source in a das2 document. now, coord uris are only available in the biowiki page. ad: only need to be abstract strings if there's no need to resolve them. gh: want these to be uris for a das2 versioned source. ad: get ncbi to do it? gh: not necessary. just make them accessible through the das2 registry. doesn't matter where it is. ad: how use? gh: someone can then go to das2 registry and see all the ones that have a global coordinate system. ad: can be done now. gh: want to avoid screen scraping the html page. ls: need to have a set of url's for parsable documents with coord systems? gh: we have xml for versioned sources in segments xml document. there's direct mapping from v-source id to coord uri, and a direct mapping from segment reference uri to segment id. we need a v-source document where each has a uri for global coord system. there would be just one capability -- segments, retrievable in the segments xml. ls: right. who's maintianing? there are 1000s of genomes. ad: coordinate element has other slots, attributes, what else is needed? gh: there is no central way to look at all coords that are available? ad: why needed? can't you get it from the sources document without looking something else up? ls: registry could compile a unique list of that and produce a report which has a list of all coordinates followed by all data sources that use that coord system. would be useful. would show who is using various systems. Spot bugs like two servers using diff coord systems for the same taxon. Server could show coord systems on a per-taxon basis, no additional query needed. gh: another example: part of the problem for me is relationship between coord uris and segment reference uris. ls: why? no consistency enforced in spec. gh: no guarantee that if you use the same coord uri that you'll use the same reference uri. another problem: looking at biowiki doesn't tell you how to construct a coord element. coord elem has attribs for taxonomy, authority, etc. ls: the coordinates url should point to the biowiki page with correct anchor, need a line for each coord system. I didn't give url to coord system. gh: attribs aren't on the wiki page. gh: people need to know that's what they should use in the das2 documents. we should show on page: "name for das2 full coordinates element is 'such and such'". people can then cut and paste. ls: ok. [A] lincoln will post additional attributes on global seq id biowiki page gh: then screen scaping by registry to grab all coordinates to make them available. ad: why do screen scraping? gh: ... ls: when people add info in the registry, then that goes in. gh: if using wrong authority? ls: it goes in wrong. gh: would like the server to catch it. ad: when registring a server, it presents a drop down field gh: where does it get that list? ad: best to ask andreas. gh: should be within biodas.org sc: wikification progress of biodas.org - can migrate global seq ids page there when it's ready. gh: might be best to let Andreas decide, to manage it on his server. sc: he's been active in the initial wikification work, so maybe he'll be ok maintaining/migrating it there. ls: some confusion over where to add this info (biodas.org, wiki of that, or open-bio.org wiki). only want to do this once. [A] steve/andreas will complete biodas.org wiki migration and notify all gh: status continued - alignment examples to spec are still to do. igb release in december: pays attention to coord uri's should be able to match up biopackages and affymetrix das2 servers v-sources on the same genome and overlay rather than making a new genome. in the next month: working on getting transcriptome data in a das2 server. lincoln had mentioned NCI interest in this. most of code is in place to serve up affy transcriptome data as graphs, a datum every 20 bp, e.g., efficient slicing from whole chromosomes, to get what you need for das range query, and bring them into igb as slices. working on serving up in alternative formats (e.g., UCSC's wiggle) rather than just affy binary format. Return options - graph the size of whole chromosome (now), or more per region, put score in a das score element, which would be a very large document. ls: be prepared to return in a das2 xml document, each score in an element, not sensible over whole chromosome, but ok for a limited region. A good form of compatibility. gh: size issues - could give a 'request too large' error. ls: could use http compression. NCI will likely never support the specialized format, so if you don't give das2 xml format, it will not be available to that client. ls: brian gilman - can't pay him to do more work on that contract. gh: might be able to pay him via affy. need to get this going within next month, couple of publications need it. ls: status: - took xml parser for perl das2 client, cleaned it up, put it on perl cpan website, underlies parsing and processing of das2 streams. pure perl, no requirements for c libraries, not validating sax client (so it's faster than the c libries). it does namespace handling, multi-threaded. offered as a standard reference. missing handling of features (types, sources, segments) -- big hole. NCI java client library went thru it's approval process, still doing various tests and qualifications before folding into main NCI source code repository. Hapmap data source still in progress. Just xml parser on cpan, full server not complete. gh: using biopackages server? ls: yes, an instance at CSHL (or will). ad: holidays and was sick for last month. working on proxy code, rewriting, fixing. sc: regarding your das2 committment? ad: making up for sick time last month. plan is to get proxy stuff done, then that's it for das. gh: (more status) also working on getting the das2 feature query support fleshed out. handle any combination of filters. coming soon, moving to new affy server hardware. on steve's plate. sc: worked on biodas.org wikification. some server configuration issues. have made a good start with Andreas' help, but more to do. should be in place later this month. some html get spec edits, fixes. planning to help gregg set up new hardware for affy das server. can then support more arrays, genome versions, organisms. gh: hardware - hoping it would be here. approved by purchasing on 1/5/07. PO likely went out to vendor, so should be in within a week. we have requests in to support more versions, probe set location for exons on older genome versions. sc: transcript annotations? gh: background - affy chp data has no genome location, just probe set id and score. IGB takes that data and merges with genome info to build heat maps to look at data. Been tricky to determine most efficient way to do that. Need to have both probe set level and transcript level data. in progress. [A] steve talk with UCSC about meeting focussed on das in feb/march [A] Next das2 teleconf: 22 Jan 2007 From aloraine at gmail.com Thu Jan 11 19:05:36 2007 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 11 Jan 2007 13:05:36 -0600 Subject: [DAS2] ids to coordinates? Message-ID: <83722dde0701111105m7a884b04id0e4608f38f7d252@mail.gmail.com> Greetings all, Sorry if I already asked this and spaced on the answer... Can I give a DAS2 server (and if yes, which one?) a list of HUGO gene names and then get back the start and end coordinate of the gene on hg17? (Note: the current version is hg18.) I'm doing a candidate gene-based population genetics project, and I need to be able to quickly get back the boundaries of a bunch of genes (as determined in the usual way, e..g, cDNA-to-genome alignments) where I have the HUGO name but that's it. I think maybe Lincoln mentioned something like this was available via a site at CSHL, or maybe Hapmap? I think it would be pretty nifty if the nicely-funded Hapmap project could provide such a service, if it does not already :-) Yours, Ann -- Ann Loraine Assistant Professor Departments of Genetics, Biostatistics, and Computer Information Sciences University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From Steve_Chervitz at affymetrix.com Thu Jan 11 19:13:10 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Thu, 11 Jan 2007 11:13:10 -0800 Subject: [DAS2] Ontology URIs In-Reply-To: Message-ID: Forwarding this message to the das/2 discussion at Suzi's request. Suzi: Could you give an example of hash vs slash-type URIs? Steve > ---------- Forwarded message ---------- > From: "Suzanna Lewis" > To: Gregg_Helt at affymetrix.com > Date: Thu, 11 Jan 2007 11:42:16 +0000 > Subject: Re: Ontology URIs (was RE: types.rnc) > Hi Gregg, > > A couple of months ago you asked me what NCBO might be doing in terms of > URIs. The discussion has finally begun, and so I'm forwarding this to you > because I thought you might want to comment as well. Good to have feedback > from everyone who will be affected. > > I think we need to address the URI issue ASAP. The questions raised at > HCLSIG highlight the importance of the issue (putting them here coz > not everyone on cBio technical would have seen them). The main ones > till now are: > > 1 - If the authors have their own namespace URI, that means they have > to maintain a copy of the ontology at their own site. I wonder how > will the synchronization between the bioportal to the external site be > established? > > ** This assumes that a URI = URL, which is not required by the URI > spec. URI resolution services, such as LSID are bound to enter the > discussion here. > > 2 - If an ontology is to adopt the URI that the bioportal provides, I > wonder what kind of URI, in terms of the hash vs. slash, that the > bioportal will support. For a samll sized ontology, the hash URI > would be sufficient and ideal. But if the ontology's size is huge, I > do believe the slash URI should be used to avoid the unnecessary > import. From the implementation point of view, however, supporting > slash URI would take a lot more hassle than supporting the hash URI. I > wonder if bioportal will be able to support that? > > ** Slash = hassle to implement the server. Hash = easy to implement > the server, > > For OBO to OWL, we chose the hash. > > 3- One comment on versioning issues (question2) . The matter is more > complex than the answer suggests. If a clinical system ever refers to > a URI in BioPortal this URI should stay forever. Even if a new version > of the ontology is deployed the original URI should still point to the > old term or concept, even if it is deprecated. So versioning is more > than a development or collaboration issue. I don't know wether the > answer given to question 3 solves this. > > -Nigam. > > cbio-technical-bounces at lists.stanford.edu wrote on : > > Do we have a policy for URIs? > > Should we form a URI working group? > --++**==--++**==--++**==--++**==--++**==--++**==--++**== > cbio-technical mailing list cbio-technical at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/cbio-technical > > --++**==--++**==--++**==--++**==--++**==--++**==--++**== > cbio-technical mailing list > cbio-technical at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/cbio-technical ------ End of Forwarded Message From Steve_Chervitz at affymetrix.com Thu Jan 11 20:21:25 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Thu, 11 Jan 2007 12:21:25 -0800 Subject: [DAS2] ids to coordinates? In-Reply-To: <83722dde0701111105m7a884b04id0e4608f38f7d252@mail.gmail.com> Message-ID: Ann, Here's my response from a similar question you asked last May: http://lists.open-bio.org/pipermail/das2/2006-June/000735.html The example URLs I gave for the Affymetrix DAS/2 server no longer work (not implemented -- but Gregg is planning to fix this in the near future). For now I'd recommend using the biopackages server. Example: http://das.biopackages.net/das/genome/human/17/feature?name=ACTA1 You can include multiple name=XXX parameters in the query to retrieve data for all gene names in the same response document (multiple feature filters with the same name are OR'd together, as described here: http://biodas.org/documents/das2/das2_get.html#feature_filters ). Cheers, Steve > From: Ann Loraine > Date: Thu, 11 Jan 2007 13:05:36 -0600 > To: DAS/2 > Subject: [DAS2] ids to coordinates? > > Greetings all, > > Sorry if I already asked this and spaced on the answer... > > Can I give a DAS2 server (and if yes, which one?) a list of HUGO gene > names and then get back the start and end coordinate of the gene on > hg17? (Note: the current version is hg18.) > > I'm doing a candidate gene-based population genetics project, and I > need to be able to quickly get back the boundaries of a bunch of genes > (as determined in the usual way, e..g, cDNA-to-genome alignments) > where I have the HUGO name but that's it. > > I think maybe Lincoln mentioned something like this was available via > a site at CSHL, or maybe Hapmap? > > I think it would be pretty nifty if the nicely-funded Hapmap project > could provide such a service, if it does not already :-) > > Yours, > > Ann > > -- > Ann Loraine > Assistant Professor > Departments of Genetics, Biostatistics, > and Computer Information Sciences > University of Alabama at Birmingham > http://www.transvar.org > 205-996-4155 > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 From WONG_MARIE_VIVIAN_NONLILLY at LILLY.COM Tue Jan 16 01:51:40 2007 From: WONG_MARIE_VIVIAN_NONLILLY at LILLY.COM (Marie Vivian Wong NONLILLY) Date: Tue, 16 Jan 2007 09:51:40 +0800 Subject: [DAS2] Proserver & Ensembl Message-ID: Hi, Is there a way to add more fields in the pop-up menu in Proserver? Besides the required features like id, start, end etc...for example if I want to add gene_start and gene_end to the feature list, is there a way to do this currently? thanks, Marie From aquinn at ebi.ac.uk Thu Jan 18 12:11:59 2007 From: aquinn at ebi.ac.uk (Antony Quinn) Date: Thu, 18 Jan 2007 12:11:59 -0000 Subject: [DAS2] AstroDAS: Astronomy Distributed Annotation System Message-ID: <458928D5.2010909@ebi.ac.uk> It's amazing what you can find on Google... AstroDAS considers the identification of entities across sky nodes to be a database integration problem. Its solution, inspired in part by the BioDAS effort in bioinformatics, features an annotation database with a web service interface to store and query annotations. The use of web services provides interoperability with the rest of the Virtual Observatory. Our prototype system resolves queries on astronomy catalogues using mapping tables that are dynamically constructed from annotations of celestial object matches. http://homepages.inf.ed.ac.uk/rbose/research_t2p2.htm From dalke at dalkescientific.com Thu Jan 18 13:52:58 2007 From: dalke at dalkescientific.com (Andrew Dalke) Date: Thu, 18 Jan 2007 14:52:58 +0100 Subject: [DAS2] AstroDAS: Astronomy Distributed Annotation System In-Reply-To: <458928D5.2010909@ebi.ac.uk> References: <458928D5.2010909@ebi.ac.uk> Message-ID: <6fee816dd03400055d1299b3cdaf4cc7@dalkescientific.com> On Dec 20, 2006, at 1:13 PM, Antony Quinn wrote: > AstroDAS considers the identification of entities across sky nodes to > be > a database integration problem. Its solution, inspired in part by the > BioDAS effort in bioinformatics, features an annotation database with a > web service interface to store and query annotations. LOL! Cool! Andrew dalke at dalkescientific.com From ap3 at sanger.ac.uk Mon Jan 22 11:33:29 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Mon, 22 Jan 2007 11:33:29 +0000 Subject: [DAS2] DAS related workshops in u.k. Message-ID: Hi all, The Biosapiens Network ( http://www.biosapiens.info/ ) is a project that has a strong commitment to DAS and has been very pro-active in setting up DAS/1 servers (lots of protein data) and developing DAS clients. Around this EU-wide collaboration we are organizing two DAS-related workshops to which we would like to invite you as well. They will both be held in the last week of February, location is the Genome Campus in Hinxton / Cambridge, U.K. workshop 1: DAS client developers workshop Monday 26/2/2007 main organizer: Andreas Prlic for more info please see: http://www.sanger.ac.uk/Users/ap3/dasworkshop.html workshop 2: BioSapiens Feature Classification (Ontology) Workshop Tuesday, 27/2/2007, Wednesday, 28/2/2007 main organizer: Henning Hermjakob fore more details please see attachment. Regards, Andreas -------------- next part -------------- A non-text attachment was scrubbed... Name: meetingAnnouncement.doc Type: application/msword Size: 23040 bytes Desc: not available URL: -------------- next part -------------- ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 From allenday at ucla.edu Thu Jan 25 08:28:15 2007 From: allenday at ucla.edu (Allen Day) Date: Thu, 25 Jan 2007 00:28:15 -0800 Subject: [DAS2] missing lock documentation Message-ID: <5c24dcc30701250028n8e2e8eete643bc98d63dafe7@mail.gmail.com> http://biodas.org/documents/das2/das2_locks.html any idea where this went? it is referenced at the end of http://biodas.org/documents/das2/das2_writeback.html -Allen From Steve_Chervitz at affymetrix.com Thu Jan 25 18:20:54 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Thu, 25 Jan 2007 10:20:54 -0800 Subject: [DAS2] missing lock documentation In-Reply-To: <5c24dcc30701250028n8e2e8eete643bc98d63dafe7@mail.gmail.com> Message-ID: The separate locking document has not yet been created. It's been on Andrew's plate for a while, perhaps he just hasn't committed it: http://lists.open-bio.org/pipermail/das2/2006-May/000711.html The locking stuff that was in the das2_get.html document was moved long ago (by me) into the das2_put.html document (revision 1.22 of the get doc). The put document later became obsolete, superceded by das2_writeback.html, so there aren't any links to that put doc anywhere on the site. You can still view the put doc, though I don't know how much of the thinking about how locking should work has changed since this text was writted (~Fall 2005): http://biodas.org/documents/das2/das2_put.html Steve > From: Allen Day > Reply-To: > Date: Thu, 25 Jan 2007 00:28:15 -0800 > To: DAS/2 > Subject: [DAS2] missing lock documentation > > http://biodas.org/documents/das2/das2_locks.html > > any idea where this went? it is referenced at the end of > > http://biodas.org/documents/das2/das2_writeback.html > > -Allen > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 From WONG_MARIE_VIVIAN_NONLILLY at LILLY.COM Fri Jan 26 02:27:17 2007 From: WONG_MARIE_VIVIAN_NONLILLY at LILLY.COM (Marie Vivian Wong NONLILLY) Date: Fri, 26 Jan 2007 10:27:17 +0800 Subject: [DAS2] Proserver Q on notes array Message-ID: Hi all, I have a proserver question.. showing of the notes array in IE via ensembl does not work. It only shows the first element in the array. But it works in firefox!!! However, our official browser is IE...is there a workaround? thanks! Marie From Steve_Chervitz at affymetrix.com Fri Jan 26 22:43:54 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 26 Jan 2007 14:43:54 -0800 Subject: [DAS2] Proserver Q on notes array In-Reply-To: Message-ID: Marie, You might have better luck sending your ProServer questions to the Ensembl helpdesk, or to the Sanger folks that developed it. Don't know how many ProServer experts there are on this list. Ensembl provides some documentation on ProServer here: http://www.ensembl.org/info/data/external_data/das/das_server.html Sounds like you have a web browser compatibility issue, which can be tricky from the coder's point of view. Consider convincing your group to use a more standards-compliant browser like Firefox (which can even be trickier ;). Cheers, Steve > From: Marie Vivian Wong NONLILLY > Date: Fri, 26 Jan 2007 10:27:17 +0800 > To: > Subject: [DAS2] Proserver Q on notes array > > > > > > Hi all, > > I have a proserver question.. > > showing of the notes array in IE via ensembl does not work. > It only shows the first element in the array. > > But it works in firefox!!! > > However, our official browser is IE...is there a workaround? > > > thanks! > Marie > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2