From FMcCarthy at cvm.msstate.edu Wed May 16 21:40:20 2007 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Wed, 16 May 2007 23:40:20 -0500 Subject: [farmanimals] pig GO annotation proposal Message-ID: Hi All, We are preparing a proposal seeking funding from USDA for GO annotation of pig gene products. We aim to provide literature annotation of existing pig gene products, prioritising this effort based on pig gene products represented on the pig oligo arrays. We will also provide a mechanism for researchers to submit GO annotation requests and provide opportunities to both learn more about the use of GO-based tools for modeling functional genomics data and how to do your own GO annotations. We would appreciate it if you can reply with a short email indicating your support and any comments and ideas regarding how you would like to use the gene ontology. We apologise to the few of you who may receive two copies of this email. Regards, Fiona McCarthy, Shane Burgess, Susan Bridges AgBase Departments of Basic Sciences & Computer Science and Engineering 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 schmidtc at udel.edu Fri May 25 09:17:41 2007 From: schmidtc at udel.edu (Carl Schmidt) Date: Fri, 25 May 2007 12:17:41 -0400 Subject: [farmanimals] proposal Message-ID: <5419EC6C-4FE4-440C-990E-A200564CE033@udel.edu> A group of us (Carl Schmidt, Gallus Gbrowse; Vijay Shankar, text processing; Keith Decker, grid based computer systems; Fiona McCarthy, GO annotation; Parker Antin, Geisha; and Peter D?Eustachio, Reactome) are preparing a proposal to the USDA seeking funding to develop bioinformatic and functional genomics resources for chicken. The bioinformatic systems we develop will be extendable for all agricultural species. We will provide (1) text mining capabilities to support GO and pathway annotation, (2) a pathways database based on experimental evidence (see http://128.175.126.139/gallusWiki/index.php/Reactome) and (3) ability for researchers to query different databases from the same web interface. We expect that providing these integrated tools and resources will be of enormous benefit for chicken researchers who routinely have to use data from several different sources, those who want to do biological modeling of their functional genomics datasets and researchers doing comparative biology studies. Moreover, the systems we develop can serve as a prototype for other agriculturally important species. If you feel these resources would be valuable for your research, we would appreciate it if you can reply with a short email indicating your support. In addition, we welcome any comments or ideas you have regarding the development of these resources and expected usage. To avoid cluttering this list, please send any responses to schmidtc at udel.edu Carl J. Schmidt Department of Animal and Food Sciences University of Delaware Newark, Delaware 19716 USA schmidtc at udel.edu From dave.burt at bbsrc.ac.uk Tue May 29 00:47:14 2007 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Tue, 29 May 2007 08:47:14 +0100 Subject: [farmanimals] proposal In-Reply-To: <5419EC6C-4FE4-440C-990E-A200564CE033@udel.edu> References: <5419EC6C-4FE4-440C-990E-A200564CE033@udel.edu> Message-ID: <1F16910BB8546C4DA5526FABB0C98D09075DA3@ebre2ksrv1.ebrc.bbsrc.ac.uk> Dear Carl and Colleagues, I fully support your proposal to seek USDA funds to develop bioinformatic and functional genomics resources for the chicken. This initiative will complement and support our work on the annotation and use of the chicken genome in medical, agricultural and biological research. I wish you every 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 Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute -----Original Message----- From: owner-farmanimals at genome.stanford.edu [mailto:owner-farmanimals at genome.stanford.edu] On Behalf Of Carl Schmidt Sent: 25 May 2007 17:18 To: farmanimals at genome.stanford.edu Cc: Carl Schmidt Subject: [farmanimals] proposal A group of us (Carl Schmidt, Gallus Gbrowse; Vijay Shankar, text processing; Keith Decker, grid based computer systems; Fiona McCarthy, GO annotation; Parker Antin, Geisha; and Peter D'Eustachio, Reactome) are preparing a proposal to the USDA seeking funding to develop bioinformatic and functional genomics resources for chicken. The bioinformatic systems we develop will be extendable for all agricultural species. We will provide (1) text mining capabilities to support GO and pathway annotation, (2) a pathways database based on experimental evidence (see http://128.175.126.139/gallusWiki/index.php/Reactome) and (3) ability for researchers to query different databases from the same web interface. We expect that providing these integrated tools and resources will be of enormous benefit for chicken researchers who routinely have to use data from several different sources, those who want to do biological modeling of their functional genomics datasets and researchers doing comparative biology studies. Moreover, the systems we develop can serve as a prototype for other agriculturally important species. If you feel these resources would be valuable for your research, we would appreciate it if you can reply with a short email indicating your support. In addition, we welcome any comments or ideas you have regarding the development of these resources and expected usage. To avoid cluttering this list, please send any responses to schmidtc at udel.edu Carl J. Schmidt Department of Animal and Food Sciences University of Delaware Newark, Delaware 19716 USA schmidtc at udel.edu From ian.dunn at bbsrc.ac.uk Wed May 30 01:14:06 2007 From: ian.dunn at bbsrc.ac.uk (ian dunn (RI)) Date: Wed, 30 May 2007 09:14:06 +0100 Subject: [farmanimals] Annotation Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45105F4063C@rie2ksrv1.ri.bbsrc.ac.uk> Dear Carl We would strongly support your initiative to annotate further the genome. Accurate and extensive annotation is essential to understanding the results from all genomic experiments. We use this data in support of our work to understand important production traits including bone strength/osteoporosis, egg shell quality and reproductive function in chickens. Yours Dr Ian Dunn Roslin Institute Roslin Midlothian EH25 9PS Scotland UK