From dave.burt at bbsrc.ac.uk Fri Mar 24 09:10:11 2006 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Fri, 24 Mar 2006 17:10:11 -0000 Subject: chicken GO proposal Message-ID: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Avian and Genome Biologists, Attached is a summary of a joint proposal between the Roslin Institute (Edinburgh) and GOA-EBI seeking funding from the BBSRC (UK) to support a chicken gene Ontology project - if you can send me a short email indicating your support and any comments/ideas on the proposal - this would enhance our application Regards, Dave Professor David Burt Roslin Institute (Edinburgh) Midlothian EH25 9PS, UK tel: +44-131-527-4218 fax: +44-131-440-0434 http://www.ark-genomics.org <> PS: pass this email on to others with an interest in the chicken and other avian genomes -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060324/fbd505f2/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: chicken_go_summary.doc Type: application/msword Size: 38400 bytes Desc: chicken_go_summary.doc Url : http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060324/fbd505f2/attachment.doc From richard-anderson at viraquest.com Fri Mar 24 10:24:32 2006 From: richard-anderson at viraquest.com (Richard Anderson) Date: Fri, 24 Mar 2006 12:24:32 -0600 Subject: [Chicken-genome] Re: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <003701c64f70$33adafb0$6501a8c0@vqrichard> This proposal will be very valuable for future research efforts and I am happy to support it. Richard D. Anderson President ViraQuest Inc. 310 West Zeller Street PO Box 525 North Liberty, Iowa 52317-0525 USA 319 665-4190 phone 319 665-4191 fax www.viraquest.com _____ From: chicken-genome-admin at lists.bbsrc.ac.uk [mailto:chicken-genome-admin at lists.bbsrc.ac.uk] On Behalf Of dave burt (RI) Sent: Friday, March 24, 2006 11:10 AM To: chickenanalysis at watson.wustl.edu; chicken-genome (Mailman List); farmanimals at geneontology.org Subject: [Chicken-genome] Re: chicken GO proposal Avian and Genome Biologists, Attached is a summary of a joint proposal between the Roslin Institute (Edinburgh) and GOA-EBI seeking funding from the BBSRC (UK) to support a chicken gene Ontology project - if you can send me a short email indicating your support and any comments/ideas on the proposal - this would enhance our application Regards, Dave Professor David Burt Roslin Institute (Edinburgh) Midlothian EH25 9PS, UK tel: +44-131-527-4218 fax: +44-131-440-0434 http://www.ark-genomics.org <> PS: pass this email on to others with an interest in the chicken and other avian genomes -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060324/d77eb14e/attachment.html From belmonte at salk.edu Fri Mar 24 10:50:41 2006 From: belmonte at salk.edu (Juan Carlos Belmonte) Date: Fri, 24 Mar 2006 10:50:41 -0800 Subject: [Chicken-genome] Re: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: This is to give my strongest support to the Chicken Ontology Project which I consider a superb scientific undertaking. Juan Carlos Izpisua Belmonte Professor Gene Expression Laboratories The Salk Institute for Biological Studies From j61056 at hpc.cmc.osaka-u.ac.jp Fri Mar 24 20:43:18 2006 From: j61056 at hpc.cmc.osaka-u.ac.jp (Hisato Kondoh) Date: Sat, 25 Mar 2006 13:43:18 +0900 Subject: [Chicken-genome] Re: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Gene Ontology is an essential element of functional genomics. I strongly support the project. Hisato Kondoh, Ph.D. Professor of Developmental Biology Graduate School of Frontier Biosciences Osaka University 1-3 Yamadaoka, Suita Osaka 565-0871 Japan At 5:10 PM +0000 06.3.24, dave burt \(RI\) wrote: >Avian and Genome Biologists, > >Attached is a summary of a joint proposal between the Roslin >Institute (Edinburgh) and GOA-EBI seeking funding from the BBSRC >(UK) to support a chicken gene Ontology project - if you can send me >a short email indicating your support and any comments/ideas on the >proposal - this would enhance our application > >Regards, Dave > >Professor David Burt >Roslin Institute (Edinburgh) >Midlothian EH25 9PS, UK >tel: +44-131-527-4218 >fax: +44-131-440-0434 >http://www.ark-genomics.org > ><> >PS: pass this email on to others with an interest in the chicken and >other avian genomes > > >Content-Type: application/msword;name="chicken_go_summary.doc" >Content-Description: chicken_go_summary.doc >Content-Disposition: attachment;filename="chicken_go_summary.doc" > >Attachment converted: Macintosh:chicken_go_summary.doc (WDBN/MSWD) (000672CF) -- Hisato Kondoh, Ph.D. Professor of Developmental Biology Graduate School of Frontier Biosciences Osaka University 1-3 Yamadaoka, Suita Osaka 565-0871 Japan Phone: +81-6-6879-7963 Fax: +81-6-6877-1738 E-mail: j61056 at hpc.cmc.osaka-u.ac.jp -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060325/018411c7/attachment.html From venu.gopal at bbsrc.ac.uk Fri Mar 24 23:36:50 2006 From: venu.gopal at bbsrc.ac.uk (venu gopal (IAH-C)) Date: Sat, 25 Mar 2006 07:36:50 -0000 Subject: [Chicken-genome] Re: chicken GO proposal References: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <8975119BCD0AC5419D61A9CF1A923E95014AE6DB@iahce2ksrv1.iah.bbsrc.ac.uk> We work on oncogenic pathways in chicken and we will benefit immensely from this project. I am very happy to support this project. Dr. Venugopal Nair Head, Viral Oncogenesis Group Institute for Animal Health Compton Berkshire United Kingdom RG20 7NN Tel: 44 +1635 577356 Fax: 44 +1635 577263 E-mail: venu.gopal at bbsrc.ac.uk ________________________________ From: chicken-genome-admin at lists.bbsrc.ac.uk on behalf of dave burt (RI) Sent: Fri 3/24/2006 17:10 To: chickenanalysis at watson.wustl.edu; chicken-genome (Mailman List); farmanimals at geneontology.org Subject: [Chicken-genome] Re: chicken GO proposal Avian and Genome Biologists, Attached is a summary of a joint proposal between the Roslin Institute (Edinburgh) and GOA-EBI seeking funding from the BBSRC (UK) to support a chicken gene Ontology project - if you can send me a short email indicating your support and any comments/ideas on the proposal - this would enhance our application Regards, Dave Professor David Burt Roslin Institute (Edinburgh) Midlothian EH25 9PS, UK tel: +44-131-527-4218 fax: +44-131-440-0434 http://www.ark-genomics.org <> PS: pass this email on to others with an interest in the chicken and other avian genomes From cogburn at udel.edu Sat Mar 25 16:23:42 2006 From: cogburn at udel.edu (Larry Cogburn) Date: Sat, 25 Mar 2006 19:23:42 -0500 Subject: [Chicken-genome] Re: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <000a01c6506b$898ab710$8f49af80@Bethel64> Dear Dave: Your proposal for building a Chicken Gene Ontology is indeed very timely and would greatly enhance our transcriptional profiling studies. Although we have assembled more than 500,000 EST and mRNA sequences into a chicken gene index composed of 40,850 high-fidelity contigs (in silico cDNAs), our chicken EST database and Del-Mar 14K Chicken Integrated Systems Microarray both suffer from the lack of GO annotation. Investigators using chicken microarray platforms (including the new Affymetrix Chicken Genome Chip) would benefit immensely from functional annotation of spotted probes with GO terms. The availability of a comprehensive Chicken Gene Ontology database would boost the fledgling field of functional genomics in this new model organism. I fully support your very worthy proposal to build a Chicken Gene Ontology and look forward to using this valuable resource in the near future! Best regards, Larry ____________________________________________ / Larry A. Cogburn, Ph.D. /=) Professor (=/ Molecular Endocrinology/ / Functional Genomics (=\ \=) Phone: 302-831-1335 / FAX: 302-831-2822 /=) Lab: 302-831-2138 (or -0113) (=/ Email: cogburn at udel.edu / Website:http://cogburn.dbi.udel.edu (=\ \=) ____________________________________________ -----Original Message----- From: chicken-genome-admin at lists.bbsrc.ac.uk [mailto:chicken-genome-admin at lists.bbsrc.ac.uk] On Behalf Of dave burt (RI) Sent: Friday, March 24, 2006 12:10 PM To: chickenanalysis at watson.wustl.edu; chicken-genome (Mailman List); farmanimals at geneontology.org Subject: [Chicken-genome] Re: chicken GO proposal Avian and Genome Biologists, Attached is a summary of a joint proposal between the Roslin Institute (Edinburgh) and GOA-EBI seeking funding from the BBSRC (UK) to support a chicken gene Ontology project - if you can send me a short email indicating your support and any comments/ideas on the proposal - this would enhance our application Regards, Dave Professor David Burt Roslin Institute (Edinburgh) Midlothian EH25 9PS, UK tel: +44-131-527-4218 fax: +44-131-440-0434 http://www.ark-genomics.org <> PS: pass this email on to others with an interest in the chicken and other avian genomes -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060325/48e42f30/attachment.html From Sean.Kennedy at ec.gc.ca Sun Mar 26 05:42:10 2006 From: Sean.Kennedy at ec.gc.ca (Kennedy,Sean [NCR]) Date: Sun, 26 Mar 2006 08:42:10 -0500 Subject: [Chicken-genome] Re: chicken GO proposal Message-ID: This is to give enthusiastic support for this project. We work on the effects of environmental contaminants on gene expression in developing avian species, and your proposed project will provide information of enormous importance. Sean W. Kennedy, Ph.D. Environment Canada National Wildlife Research Centre Carleton University 1125 Colonel By Drive, Raven Road Ottawa, Ontario, Canada K1A 0H3 or K1S 5B6 (courier) Tel: 613-998-7384 Fax: 613-998-0458 Email: sean.kennedy at ec.gc.ca and Adjunct Professor, Centre for Advanced Research in Environmental Genomics (CAREG) and Department of Biology, University of Ottawa -----Original Message----- From: chicken-genome-admin at lists.bbsrc.ac.uk [mailto:chicken-genome-admin at lists.bbsrc.ac.uk] On Behalf Of dave burt (RI) Sent: Friday, March 24, 2006 12:10 PM To: chickenanalysis at watson.wustl.edu; chicken-genome (Mailman List); farmanimals at geneontology.org Subject: [Chicken-genome] Re: chicken GO proposal Avian and Genome Biologists, Attached is a summary of a joint proposal between the Roslin Institute (Edinburgh) and GOA-EBI seeking funding from the BBSRC (UK) to support a chicken gene Ontology project - if you can send me a short email indicating your support and any comments/ideas on the proposal - this would enhance our application Regards, Dave Professor David Burt Roslin Institute (Edinburgh) Midlothian EH25 9PS, UK tel: +44-131-527-4218 fax: +44-131-440-0434 http://www.ark-genomics.org <> PS: pass this email on to others with an interest in the chicken and other avian genomes -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060326/4355d7b0/attachment.html From burgess at cvm.msstate.edu Sun Mar 26 11:41:24 2006 From: burgess at cvm.msstate.edu (Shane Burgess) Date: Sun, 26 Mar 2006 13:41:24 -0600 Subject: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Dear Dave, RE: BBSRC for GO biocurator proposal Thank you for your email about your plans to submit a grant application to the BBSRC to begin your work to annotate the chicken genome's products using Gene Ontology. We fully support your plans, which will of course complement and support our ongoing GO annotation efforts at AgBase for the chicken (http://www.agbase.msstate.edu/). We wish you every success with the application. Yours sincerely, Shane, Susan and Fiona at AgBase. Shane C Burgess BVSc(Dist.), MRCVS., PhD. Department of Basic Sciences College of Veterinary Medicine Mississippi State University Box 6100 MS 39762-6100 USA Tel: (+ 1) 662 325 1239 Fax: (+ 1) 662 325 1031 Email: burgess at cvm.msstate.edu Important: Emails that you send may not get to my inbox. Worse, you will NOT receive a failure notification. I endeavor to answer all emails within 72 hours. If you do not receive a reply, please assume that I never got your email and re-send it. From Hans.Ellegren at ebc.uu.se Sun Mar 26 09:19:44 2006 From: Hans.Ellegren at ebc.uu.se (Hans Ellegren) Date: Sun, 26 Mar 2006 19:19:44 +0200 Subject: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: I enthusiastically support this initiative which should be of great important for a wide range of studies of the domestic chicken, including using chicken as a model for human disease and general biology. From our perspective, well developed GO annotation should be most valuable to evolutionary studies of the chicken genome and chicken genes. Regards, Hans Ellegren >Avian and Genome Biologists, > >Attached is a summary of a joint proposal >between the Roslin Institute (Edinburgh) and >GOA-EBI seeking funding from the BBSRC (UK) to >support a chicken gene Ontology project - if you >can send me a short email indicating your >support and any comments/ideas on the proposal - >this would enhance our application > >Regards, Dave > >Professor David Burt >Roslin Institute (Edinburgh) >Midlothian EH25 9PS, UK >tel: +44-131-527-4218 >fax: +44-131-440-0434 >http://www.ark-genomics.org > ><> >PS: pass this email on to others with an >interest in the chicken and other avian genomes > > >Content-Type: application/msword; > name="chicken_go_summary.doc" >Content-Description: chicken_go_summary.doc >Content-Disposition: attachment; > filename="chicken_go_summary.doc" > >Attachment converted: Macintosh >HD:chicken_go_summary.doc (WDBN/MSWD) (0016C4C2) -- Professor Hans Ellegren Dept of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyv?gen 18D SE-752 36 Uppsala Sweden Email: Hans.Ellegren at ebc.uu.se Phone: +46-18-4716460 Fax: +46-18-4716310 Lab home page: http://www.egs.uu.se/evbiol/index.html My home page: http://www.egs.uu.se/evbiol/Persons/Hans.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060326/0aaa360a/attachment.html From gandrillon at cgmc.univ-lyon1.fr Sun Mar 26 23:14:52 2006 From: gandrillon at cgmc.univ-lyon1.fr (Olivier Gandrillon) Date: Mon, 27 Mar 2006 09:14:52 +0200 Subject: [Chicken-genome] Re: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Dear Dave and all members of the chicken (avian) community :-) Our group is actively engaged in transcriptomic analysis of chicken progenitor cells by the use of SAGE. We are thus fully aware of the current limitations of chicken GO annotations, and we are therefore delighted to support this initiative that will enhance the biological relevance of current chicken GO annotations. May I suggest that a comparative, updated and critical analysis of the wealth of existing GO analysis softwares/sites would be very beneficial? Best regards Olivier Le 24/03/06 19:10, ??dave burt (RI)?? a ?crit?: > Avian and Genome Biologists, > > Attached is a summary of a joint proposal between the Roslin Institute > (Edinburgh) and GOA-EBI seeking funding from the BBSRC (UK) to support a > chicken gene Ontology project - if you can send me a short email indicating > your support and any comments/ideas on the proposal - this would enhance our > application > > Regards, Dave > > Professor David Burt > Roslin Institute (Edinburgh) > Midlothian EH25 9PS, UK > tel: +44-131-527-4218 > fax: +44-131-440-0434 > http://www.ark-genomics.org > > <> > PS: pass this email on to others with an interest in the chicken and other > avian genomes > -- NEW FAX NUMBER: : 04 72 43 26 85 !!!!!! SAUVONS LA RECHERCHE : http://prisma.insa-lyon.fr/SLR/ Dr Olivier Gandrillon Centre de g?n?tique mol?culaire et cellulaire UMR CNRS 5534 Universit? Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Rapha?l Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 E-mail: Gandrillon at cgmc.univ-lyon1.fr Web adress : Lab: http://www.cgmc.univ-lyon1.fr/Gandrillon/ Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html ?Partout la violence collective ?tait un crime d?ordre priv?. Quand elle ?clatait, on n??tait pas assassin? par des inconnus. C??tait vos voisins, les gens avec lesquels vous aviez partag? les hauts et les bas de l?existence, les gens dont les enfants avaient jou? avec vos propres enfants pas plus tard qu?hier. C??taient ces gens dont les yeux brillaient soudain de haine qui frapperaient ? votre porte au milieu de la nuit avec des torches enflamm?es dans leurs mains.? Salman Rushdie in ? Shalimar le clown ?. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060327/8ffb2565/attachment.html From weigend at tzv.fal.de Sun Mar 26 23:18:32 2006 From: weigend at tzv.fal.de (Dr. Steffen Weigend) Date: Mon, 27 Mar 2006 09:18:32 +0200 Subject: [Chicken-genome] Re: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <200603270918.32888.weigend@tzv.fal.de> Dear Dave, With great interest I have seen your application of chicken Gene Ontology project. The outcome of this project will be extremly useful to a large community of avian and developmental biologists and will have an important impact on future research in various directions including the improvement of our understanding of genetic diversity in poultry, one essential prerequisite to conserve, manage and utilize genetic resources. I strongly support your project application to the BBSRC. Best regards Steffen -- -------------------------------------------------- Dr. Steffen Weigend Institute for Animal Breeding Federal Agricultural Research Centre Mariensee; 31535 Neustadt; Germany Tel: +49 (0) 5034 871 180 Fax: +49 (0) 5034 871 143 e-mail: weigend at tzv.fal.de -------------------------------------------------- From burgess at cvm.msstate.edu Mon Mar 27 07:57:40 2006 From: burgess at cvm.msstate.edu (Shane Burgess) Date: Mon, 27 Mar 2006 09:57:40 -0600 Subject: NIH proposal for chicken genome annotation: request for support e-mail Message-ID: Dear All, It is great to see that, as we have all discussed previously, the proposal to seek funding from BBSRC to continue our community's chicken gene ontology (GO) annotation efforts is moving ahead. Of course we have sent a letter of support. Our own application was submitted to the NIH on Feb 1 2006. This proposal is to continue our GO functional-annotation of the chicken genome and to extend our experimental structural-annotation (preprint available). Below is the very brief synopsis of the proposal that was submitted as part of the application. Just like the Roslin group, we would be very grateful if you could send a short email indicating your support and any comments/ideas to improve community input for the enormous task of experimental-structural and GO annotation in the chicken. Please send the email to burgess at cvm.msstate.edu. For those who are not familiar with what is now available in terms of Gene Ontology annotation in the chicken please follow this link: http://www.agbase.msstate.edu/. Click on "Animals" and then "ChickGO". Please also send us comments as to how we can make this interface and our tools for modeling functional genomics datasets work better for you. You can do this directly on the site. Also, of course, we would be extremely happy to discuss our work and the proposal at the Workshop on CHICKEN GENOMICS & DEVELOPMENT at CSHL, May 8 - 11, 2005. Best wishes and thank you in advance Shane, Susan and Fiona at AgBase. NIH Abstract: The value of a genome sequence for biomedical comparative and functional genomics research entirely depends on the quality and accessibility of its annotation and on having approved symbols for each gene. This proposal significantly addresses the fundamental problems preventing the optimal utilization of the chicken genome sequence for comparative biology and functional genomics studies. The chicken genome was sequenced by NIH in 2004 because the chicken is the foremost non-mammalian vertebrate biomedical model organism and it is a principal biomedical model for understanding basic biology, behavior and disease. It is the de-facto model bird genome and it occupies a unique and important evolutionary niche. The chicken is an important model for comparative and evolutionary genomics. Chicken research has made seminal contributions to biomedicine. However, the chicken genome lacks comprehensive annotation and standardized gene symbols are not consistently used. This lack of genome annotation significantly prevents researchers from exploiting the full potential of the chicken genome model system for comparative and functional genomic studies. We will improve the chicken genome annotation by integrating high-throughput experimental data with standardized gene symbols and Gene Ontology functional-annotation. Our experimental-annotation will be a significant step towards fulfilling the research community need for a more comprehensively-annotated avian genome sequence. We will also provide computational tools for using this information in and easy and accessible way. Our data will will also link directly to the main genomics and proteomics databases and we will make all of this information easily accessible for the biomedical research community at our AgBase website. Shane C Burgess BVSc(Dist.), MRCVS., PhD. Department of Basic Sciences College of Veterinary Medicine Mississippi State University Box 6100 MS 39762-6100 USA Tel: (+ 1) 662 325 1239 Fax: (+ 1) 662 325 1031 Email: burgess at cvm.msstate.edu Important: Emails that you send may not get to my inbox. Worse, you will NOT receive a failure notification. I endeavor to answer all emails within 72 hours. If you do not receive a reply, please assume that I never got your email and re-send it. From burgess at cvm.msstate.edu Mon Mar 27 10:22:11 2006 From: burgess at cvm.msstate.edu (Shane Burgess) Date: Mon, 27 Mar 2006 12:22:11 -0600 Subject: Clarrification NIH proposal for chicken genome annotation In-Reply-To: <002601c651c2$d9d4e030$7f495f80@genomecenter.genome.washington.edu> References: <,> <002601c651c2$d9d4e030$7f495f80@genomecenter.genome.washington.edu> Message-ID: Question from: "Gane Ka-Shu Wong" on Monday, March 27, 2006 at 11:21 AM +0000 wrote: >competition is always good, and i support the agbase efforts to annotate >the chicken genome. however, will there be any efforts to coordinate with >the BBSRC project? it would be very confusing to the community if they >disagreed. Answer. Thank you for raising the issue. I had certainly hoped that my email did not suggest direct competition. To clarify,however, these two proposals are NOT competitive in any way. They are complimentary. We are following the example of the entire GO community, which is extremely collaborative and inclusive. The two proposals are working together to eventually achieve the same end for the good of the community. The chicken GO annotation task in front of us all is enormous and Roslyn, GOA and ourselves at AgBase have been communicating for many months now about how together we can best get this (perhaps endless) task done in the most efficient way possible. These projects will be co-ordinated and we have documented how we plan to do this. Roslyn and GOA have provided us with letters of support for out NIH proposal just as we, of course, have provided a letter of support for the BBSRC proposal. AgBase was also involved in helping to put Roslyn and GOA get together on this in the first place. Regards Shane Shane C Burgess BVSc(Dist.), MRCVS., PhD. Department of Basic Sciences College of Veterinary Medicine Mississippi State University Box 6100 MS 39762-6100 USA Tel: (+ 1) 662 325 1239 Fax: (+ 1) 662 325 1031 Email: burgess at cvm.msstate.edu Important: Emails that you send may not get to my inbox. Worse, you will NOT receive a failure notification. I endeavor to answer all emails within 72 hours. If you do not receive a reply, please assume that I never got your email and re-send it. From dave.burt at bbsrc.ac.uk Tue Mar 28 00:54:35 2006 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Tue, 28 Mar 2006 09:54:35 +0100 Subject: chicken go proposal Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45102193352@rie2ksrv1.ri.bbsrc.ac.uk> Dear All, I wanted to thank all the support sent in so far (100's) Also thanks for ideas and volenteers to take an active role in the annotation process Keep sending in the thoughts, ideas, comments etc Regards, Dave Professor David Burt Roslin Institute (Edinburgh) Midlothian EH25 9PS, UK tel: +44-131-527-4218 fax: +44-131-440-0434 http://www.ark-genomics.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060328/0023abea/attachment.html From fmccarthy at cvm.msstate.edu Tue Mar 28 08:37:09 2006 From: fmccarthy at cvm.msstate.edu (Fiona McCarthy) Date: Tue, 28 Mar 2006 10:37:09 -0600 Subject: AgBase and TIGR Message-ID: Hi David, My understanding is that TIGR primarily assigns GO Annotations based on "inferred from electronic annotation" (IEA). This data is very useful for getting a broad coverage of gene products but it is assigned computationally and is not reviewed by curators. I believe that they have several microbial genomes where they are assigning GO using literature curation of experimental evidence. However TIGR have a lot of genomes and they do not try to do manual curation of all genomes. At AgBase we have been annotating proteins. We do not currently do IEA annotations; the IEA annotations you see at AgBase are downloaded from GOA. Instead we work first to get GO annotations inferred from structural or sequence homology (ISS) , then if there is no sequence homology we will manually curate the experimental data from published literature. Using ISS allows us to get a 'breadth' of coverage and then by curating literature we can get a much finer level of detail and find functions for proteins that may not have homology to other annotated proteins. AgBase understands the critical need for better microarray and EST annotations. We have very recently been working with a researcher at the University of Delaware to add GO annotations to ESTs and microarray data. We are certainly happy to take advice and suggestions from researchers about how best to direct our annotations so that you can get the GO annotations you require. All of what we do at AgBase is driven by our own experimental needs and we certainly understand the frustrations involved with trying to get a well annotated dataset. Please don't hesitate to contact us if you have any further questions or if we can be of assistance. Regards, Fiona McCarthy AgBase Biocurator Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031 http://www.agbase.msstate.edu/ ----- Original Message ----- Monday, March 27, 2006 1:24:22 PM Message From: Shane Burgess Subject: Re: Agbase vs. TIGR To: david clayton Fiona McCarthy David, Thank you so much for your email. I could reply personally but I would rather refer you to our resident expert Dr Fiona McCarthy. By doing so I will ensure that you get the best possible information. I know that Fi is out for the next couple of hours but she should reply to you and the group very soon. Regards Shane >Shane - I received your email request for endorsements of your NIH >chicken GO proposal, and I am happy to respond formally (will do so >shortly). Meantime, however, I wonder if you could clarify for me the >relationships between the annotations at AgBase and the ones on TIGR, >for example? We've been using TIGR (http://www.tigr.org/tigr-scripts/ >tgi/T_index.cgi?species=g_gallus) as our primary reference for >annotating zebra finch ESTs. Is your resource equivalent, >complementary, different somehow? > >david > >************************************************************** >David F. Clayton, Ph.D. >University of Illinois >Professor of Cell & Developmental Biology, Neuroscience, and >Bioengineering >Member, Beckman Institute and Institute for Genomic Biology >Associate Director, School of Molecular & Cellular Biology >phone: 217-244-3668 >fax: 503-213-6611 >mail: 601 S. Goodwin, B107 CLSL, Urbana IL 61801 >email: dclayton at uiuc.edu >URL: http://www.life.uiuc.edu/clayton/ > >Co-founder, Songbird Genome Organization: http://songbirdgenome.org/ >Director, Songbird Neurogenomics Initiative: http:// >titan.biotec.uiuc.edu/songbird/ > From dclayton at life.uiuc.edu Mon Mar 27 10:50:57 2006 From: dclayton at life.uiuc.edu (david clayton) Date: Mon, 27 Mar 2006 12:50:57 -0600 Subject: [Chicken-genome] Re: chicken GO proposal In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Dear Dave, I'm very happy to offer my enthusiastic endorsement of the proposal to move forward with a Chicken Gene Ontology project. As you know, we in the songbird research community are making very active use of chicken gene annotation to inform songbird genomics. (Indeed, the existence of an annotated chicken genome as a reference point was a key factor in the recent decision by NIH to obtain a whole genome sequence for a songbird, the zebra finch, as the second sequenced avian). In the long run, I anticipate the tide will flow both directions: songbird genomics is especially focused on neurobiology, and improving the depth and quality of annotation for brain-related genes is important for all of GO (and not just chicken GO). I look forward to your progress with keen interest! david ************************************************************** David F. Clayton, Ph.D. University of Illinois Professor of Cell & Developmental Biology, Neuroscience, and Bioengineering Member, Beckman Institute and Institute for Genomic Biology Associate Director, School of Molecular & Cellular Biology phone: 217-244-3668 fax: 503-213-6611 mail: 601 S. Goodwin, B107 CLSL, Urbana IL 61801 email: dclayton at uiuc.edu URL: http://www.life.uiuc.edu/clayton/ Co-founder, Songbird Genome Organization: http://songbirdgenome.org/ Director, Songbird Neurogenomics Initiative: http:// titan.biotec.uiuc.edu/songbird/ On Mar 24, 2006, at 11:10 AM, dave burt (RI) wrote: > Avian and Genome Biologists, > > Attached is a summary of a joint proposal between the Roslin > Institute (Edinburgh) and GOA-EBI seeking funding from the BBSRC > (UK) to support a chicken gene Ontology project - if you can send > me a short email indicating your support and any comments/ideas on > the proposal - this would enhance our application > > Regards, Dave > > Professor David Burt > Roslin Institute (Edinburgh) > Midlothian EH25 9PS, UK > tel: +44-131-527-4218 > fax: +44-131-440-0434 > http://www.ark-genomics.org > > <> > PS: pass this email on to others with an interest in the chicken > and other avian genomes > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060327/b6b63203/attachment.html From carba.vignal at free.fr Tue Mar 28 00:03:00 2006 From: carba.vignal at free.fr (Cathy et Alain Vignal) Date: Tue, 28 Mar 2006 10:03:00 +0200 Subject: [Chicken-genome] Re: chicken GO proposal References: <84DA9D8AC9B05F4B889E7C70238CB4510219333F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <006201c65242$3bfa0cc0$0200a8c0@carba> Re: chicken GO proposalDear Dave, he project described in the proposal is essential for the understanding of the only bird genome available to date for analysis. It will therefore benefit to many fields including evolutionary biology, developmental biology and agricultural research. Best wishes, Alain Vignal ----- Original Message ----- From: dave burt (RI) To: chickenanalysis at watson.wustl.edu ; chicken-genome (Mailman List) ; farmanimals at geneontology.org Sent: Friday, March 24, 2006 7:10 PM Subject: [Chicken-genome] Re: chicken GO proposal Avian and Genome Biologists, Attached is a summary of a joint proposal between the Roslin Institute (Edinburgh) and GOA-EBI seeking funding from the BBSRC (UK) to support a chicken gene Ontology project - if you can send me a short email indicating your support and any comments/ideas on the proposal - this would enhance our application Regards, Dave Professor David Burt Roslin Institute (Edinburgh) Midlothian EH25 9PS, UK tel: +44-131-527-4218 fax: +44-131-440-0434 http://www.ark-genomics.org <> PS: pass this email on to others with an interest in the chicken and other avian genomes ------------------------------------------------------------------------------ No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.3.0/290 - Release Date: 23/03/06 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060328/ff67a996/attachment.html -------------- next part -------------- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.3.2/294 - Release Date: 27/03/06 From fmccarthy at cvm.msstate.edu Wed Mar 29 06:59:09 2006 From: fmccarthy at cvm.msstate.edu (Fiona McCarthy) Date: Wed, 29 Mar 2006 08:59:09 -0600 Subject: review of GOanalysis for gene expression data Message-ID: Hi All, Olivier mentioned that a review of GO analysis software/sites would be very beneficial. There was a review of GO functional profiling tools published last year: "Ontological analysis of gene expression data: current tools, limitations, and open problems." Purvesh Khatri, Sorin Draghici http://bioinformatics.oxfordjournals.org/cgi/reprint/bti565v1 My understanding is that this review is not meant to be all encompassing but the authors do discuss 14 gene expression analysis tools in detail. regards, Fiona AgBase Biocurator Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031 http://www.agbase.msstate.edu/ From: Olivier Gandrillon <[ nospamhere:gandrillon at cgmc.univ-lyon1.fr?Subject=Re:%20[Chicken-genome]%20Re:%20chicken%20GO%20proposal ]gandrillon at cgmc.univ-lyon1.fr> Date: Sun Mar 26 2006 - 23:14:52 PST May I suggest that a comparative, updated and critical analysis of the wealth of existing GO analysis softwares/sites would be very beneficial? Best regards Olivier From dave.burt at bbsrc.ac.uk Thu Mar 30 00:29:01 2006 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Thu, 30 Mar 2006 09:29:01 +0100 Subject: chicken GO annotators? Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45102193356@rie2ksrv1.ri.bbsrc.ac.uk> Dear All, Many thanks for the huge amount of support for the chicken GO proposal Next I would like to hear from those labs willing to take a more active role in the "Gene Ontology Annotation" process itself? As part of the proposal we will provide software, access to GO resources and databases, training etc so you can enter your own GO terms for genes you are interested in [for example see Leif's email below]. So together with EBI, Roslin, Agbase, and other labs the chicken community can catch up very quickly with other model species. SO, PLEASE SEND ME YOU DETAILS - DO NOT RESPOND TO THIS LIST - apparently many email boxes were overloaded in the last calls (so a great success?!). Dave Professor David Burt Roslin Institute (Edinburgh) Midlothian EH25 9PS, UK tel: +44-131-527-4218 fax: +44-131-440-0434 http://www.ark-genomics.org >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Dave, I strongly support this initiative which I consider a very important step in making available genomic resources even more powerful for research. One suggestion for the proposal is that one develops convenient tools for the community to contribute to this program. Individual researchers should be able to submit important information that are published or even unpublished. Sincerely Leif Andersson Uppsala University Swedish University of Agricultural Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20060330/e6e90743/attachment.html From burgess at cvm.msstate.edu Fri Mar 31 07:22:04 2006 From: burgess at cvm.msstate.edu (Shane Burgess) Date: Fri, 31 Mar 2006 09:22:04 -0600 Subject: This is one way you can now use GO and submit your GO annotations Message-ID: Dear all , Dave is doing a wonderful job of raising the awareness of GO. However, it is clear that many of you are new to Gene Ontology and this email is just to let you all know that you already can submit your own GO annotations for agricultural species (for which you will be acknowledged in the database). You can also use GO to model your microarray and other functional genomics data right now. The information is available at AgBase http://www.agbase.msstate.edu/ Its not quite as easy as it sounds to do GO annotation. But we have been working with the GO consortium (especially GOA and the Mouse Genome Institute) for sometime now to make it easier for our research communities. Just email us with any questions you have. We can advise you on the evidence codes. We can also format your accession files. We will be talking about GO in much more detail at the Cold Spring Harbor Laboratories Workshop on CHICKEN GENOMICS & DEVELOPMENT May 7 - 10, 2006. Regards Shane, Susan and Fiona (at AgBase).