From dan.bolser at gmail.com Tue Apr 21 15:46:39 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 21 Apr 2009 20:46:39 +0100 Subject: [DAS] Das reference in science or nature? Message-ID: <2c8757af0904211246v1b11512bt821db17e6a1f3a5b@mail.gmail.com> Can anyone remind me the reference for the 'letter to nature' (or was it science) where DAS was discussed as being a solution to the problems of 'community annotation'? From th at sanger.ac.uk Tue Apr 21 17:38:08 2009 From: th at sanger.ac.uk (Tim Hubbard) Date: Tue, 21 Apr 2009 22:38:08 +0100 Subject: [DAS] Das reference in science or nature? In-Reply-To: <2c8757af0904211246v1b11512bt821db17e6a1f3a5b@mail.gmail.com> References: <2c8757af0904211246v1b11512bt821db17e6a1f3a5b@mail.gmail.com> Message-ID: >Can anyone remind me the reference for the 'letter to nature' (or was >it science) where DAS was discussed as being a solution to the >problems of 'community annotation'? Yep, it was me and Ewan. Hubbard T, Birney E (2000) Open annotation offers a democratic solution to genome sequencing. Nature 403(6772): 825. Best wishes, Tim -- ------------------------------------------------------------------------- Dr Tim Hubbard email: th at sanger.ac.uk Wellcome Trust Sanger Institute Tel (direct): +44 1223 496886 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton, Cambridgeshire. CB10 1SA. Fax: +44 1223 496802 URL: http://www.sanger.ac.uk/Teams/faculty/hubbard/ ------------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From toyop at gsc.riken.go.jp Wed Apr 22 01:06:18 2009 From: toyop at gsc.riken.go.jp (Tetsuro TOYODA) Date: Wed, 22 Apr 2009 14:06:18 +0900 Subject: [DAS] DAS for Semantic Web Message-ID: <019501c9c308$121858f0$36490ad0$@riken.go.jp> Dear all, We have started distributing RIKEN's various databases in the form of the Semantic Web. Please see, http://www.riken.jp/engn/r-world/info/release/press/2009/090331_2/index.html If the DAS project has any specification about sharing the RDF/OWL data, please let me know. Best, Tetsuro Toyoda, ph.D. RIKEN BASE (Bioinformatics And Systems Engineering) division http://omicspace.riken.jp/base/index.html From jeedward at yahoo.com Sun Apr 19 11:58:20 2009 From: jeedward at yahoo.com (John Edward) Date: Sun, 19 Apr 2009 08:58:20 -0700 (PDT) Subject: [DAS] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <200116.31028.qm@web45913.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers for the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? BCBGC-09 will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee From gsalazar at cs.uct.ac.za Thu Apr 30 06:22:36 2009 From: gsalazar at cs.uct.ac.za (Gustavo Salazar) Date: Thu, 30 Apr 2009 12:22:36 +0200 Subject: [DAS] DAS writeback Message-ID: <49F97BEC.6090208@cs.uct.ac.za> Hello all, After our discussion during the DAS workshop, I've been working implementing and redefining some things for the writeback, and that's why I haven't wrote the Writeback protocol proposal as I promised, so I'm sorry about it but I hope that when I put it, it will be of your interest. The main change I'm working is that now the input format is the same output (i.e. DASGFF), and the action to do is the HTTP method that is been used (POST:Create, PUT: Update, DELETE:delete, GET:query). The other feature that I'm working on, is that the response of the writeback server will be a DASGFF file that contains the information that was succesfully processed. I will try to put a document that describe this in more details in the next weeks. I want to first finish the implementation to publish both things together. Now, I have a question that I need to clarify to finish both document and implementation. I hope you can help me guys... * Is there any way to know really identify the segment from the GFF file? For instance the response of this server http://das.ensembl.org/das/ens_35_segdup_washu/features?segment=17:13650001,14649999 is something like: .... And the id of the segment is 17 because is from the chromosome 17, but it could be from any organism. I though in defining the ID as an URL formed with the http value of the GFF element plus the segment id, however it looks to me that it will be attached to the feature source and no to the reference; and therefore 2 features coming from different annotation servers but for the same segment will be hard to group in the same segment. This is very important, because the writeback server should be able to behave as an annotation server and if a client request features of a segment the wb server should return all the features there without discriminate by original source. This is really simple for proteins (My really interest) because the segment has the uniprot id, so i am sure what is the resource that the client want, but for chromosome info doesn't look that easy I hope you understand my problem, and somebody can help me. Regards, Gustavo Salazar From dan.bolser at gmail.com Tue Apr 21 19:46:39 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 21 Apr 2009 20:46:39 +0100 Subject: [DAS] Das reference in science or nature? Message-ID: <2c8757af0904211246v1b11512bt821db17e6a1f3a5b@mail.gmail.com> Can anyone remind me the reference for the 'letter to nature' (or was it science) where DAS was discussed as being a solution to the problems of 'community annotation'? From th at sanger.ac.uk Tue Apr 21 21:38:08 2009 From: th at sanger.ac.uk (Tim Hubbard) Date: Tue, 21 Apr 2009 22:38:08 +0100 Subject: [DAS] Das reference in science or nature? In-Reply-To: <2c8757af0904211246v1b11512bt821db17e6a1f3a5b@mail.gmail.com> References: <2c8757af0904211246v1b11512bt821db17e6a1f3a5b@mail.gmail.com> Message-ID: >Can anyone remind me the reference for the 'letter to nature' (or was >it science) where DAS was discussed as being a solution to the >problems of 'community annotation'? Yep, it was me and Ewan. Hubbard T, Birney E (2000) Open annotation offers a democratic solution to genome sequencing. Nature 403(6772): 825. Best wishes, Tim -- ------------------------------------------------------------------------- Dr Tim Hubbard email: th at sanger.ac.uk Wellcome Trust Sanger Institute Tel (direct): +44 1223 496886 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton, Cambridgeshire. CB10 1SA. Fax: +44 1223 496802 URL: http://www.sanger.ac.uk/Teams/faculty/hubbard/ ------------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From toyop at gsc.riken.go.jp Wed Apr 22 05:06:18 2009 From: toyop at gsc.riken.go.jp (Tetsuro TOYODA) Date: Wed, 22 Apr 2009 14:06:18 +0900 Subject: [DAS] DAS for Semantic Web Message-ID: <019501c9c308$121858f0$36490ad0$@riken.go.jp> Dear all, We have started distributing RIKEN's various databases in the form of the Semantic Web. Please see, http://www.riken.jp/engn/r-world/info/release/press/2009/090331_2/index.html If the DAS project has any specification about sharing the RDF/OWL data, please let me know. Best, Tetsuro Toyoda, ph.D. RIKEN BASE (Bioinformatics And Systems Engineering) division http://omicspace.riken.jp/base/index.html From jeedward at yahoo.com Sun Apr 19 15:58:20 2009 From: jeedward at yahoo.com (John Edward) Date: Sun, 19 Apr 2009 08:58:20 -0700 (PDT) Subject: [DAS] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <200116.31028.qm@web45913.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers for the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? BCBGC-09 will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee From gsalazar at cs.uct.ac.za Thu Apr 30 10:22:36 2009 From: gsalazar at cs.uct.ac.za (Gustavo Salazar) Date: Thu, 30 Apr 2009 12:22:36 +0200 Subject: [DAS] DAS writeback Message-ID: <49F97BEC.6090208@cs.uct.ac.za> Hello all, After our discussion during the DAS workshop, I've been working implementing and redefining some things for the writeback, and that's why I haven't wrote the Writeback protocol proposal as I promised, so I'm sorry about it but I hope that when I put it, it will be of your interest. The main change I'm working is that now the input format is the same output (i.e. DASGFF), and the action to do is the HTTP method that is been used (POST:Create, PUT: Update, DELETE:delete, GET:query). The other feature that I'm working on, is that the response of the writeback server will be a DASGFF file that contains the information that was succesfully processed. I will try to put a document that describe this in more details in the next weeks. I want to first finish the implementation to publish both things together. Now, I have a question that I need to clarify to finish both document and implementation. I hope you can help me guys... * Is there any way to know really identify the segment from the GFF file? For instance the response of this server http://das.ensembl.org/das/ens_35_segdup_washu/features?segment=17:13650001,14649999 is something like: .... And the id of the segment is 17 because is from the chromosome 17, but it could be from any organism. I though in defining the ID as an URL formed with the http value of the GFF element plus the segment id, however it looks to me that it will be attached to the feature source and no to the reference; and therefore 2 features coming from different annotation servers but for the same segment will be hard to group in the same segment. This is very important, because the writeback server should be able to behave as an annotation server and if a client request features of a segment the wb server should return all the features there without discriminate by original source. This is really simple for proteins (My really interest) because the segment has the uniprot id, so i am sure what is the resource that the client want, but for chromosome info doesn't look that easy I hope you understand my problem, and somebody can help me. Regards, Gustavo Salazar