From dave.burt at bbsrc.ac.uk Wed Dec 7 02:32:56 2005 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Wed, 7 Dec 2005 10:32:56 -0000 Subject: Farm animals - chickGO Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45102192FED@rie2ksrv1.ri.bbsrc.ac.uk> All, I would like to start off 6threads, I will just list them here and then take up each one in separate emails But 1st let me congratulate Jena, Evelyn and everyione for getting this started - well done! OK the topics I would like to cover are specific to "chickGO" but can be adapted for other farmed animals 1. Core aims of chickGO [recent doc from Dave B and Shane B] 2. How to increase profile [meetings, workshops, software, training, etc] 3. GO annotation [the search for annotators, grants, letters of support for grants, etc] 4. Gene names/descriptions/nomenclature [based on HGNC] 5. GO applications - databases {Ensembl, NCBI, etc], tools [GenMAPP, OntoExpress, etc], other ontology groups [phenotypes, chick Atlas, etc], and of course letters of supports for grants 6. Finally, grants to make this work [GOA-Roslin BBSRC application for 2006, etc] OK these should keep us busy! 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/20051207/86e4fb8d/attachment.html From dave.burt at bbsrc.ac.uk Wed Dec 7 02:48:05 2005 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Wed, 7 Dec 2005 10:48:05 -0000 Subject: How to increase profile [meetings, workshops, software, training, etc] Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45102192FEF@rie2ksrv1.ri.bbsrc.ac.uk> 2. How to increase profile [meetings, workshops, software, training, etc] This is important to increase number of GO annotators, support for further funding, etc Some idea? - May 7/10 2006 we will hold the next Chicken genome conference at cold spring harbor - and we will invite Shane to provide an overview of chickGO - other meetinsg would be the genome meeting itself at CSH, Plant & Animal Genome (San Diego) - we should make a concerted effort to spread the idea - so what would be useful would be to share powerpoint slides, make a common poster - other ideas? - as part of our grant proposals we will have - travel, training, sharing of software - In addition we should be proactive and enlist those we think will be interested in this project (either as annotators, users...). I have CC'd to parker, Olivier and Simon who I am sure will be interested 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/20051207/c060dd36/attachment.html From dave.burt at bbsrc.ac.uk Wed Dec 7 02:53:12 2005 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Wed, 7 Dec 2005 10:53:12 -0000 Subject: GO annotation [the search for annotators, grants, letters of support for grants, etc] Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45102192FF0@rie2ksrv1.ri.bbsrc.ac.uk> 3. GO annotation [the search for annotators, grants, letters of support for grants, etc] - AgBase and GOA will be the focus for entry of GO annotation, info etc which can then me stored in the master database at AgBase - I think increasing our profile will bring in new contacts for GO annotation - but we can also target meetings (e.g. immunologists at Avian Immunoglogy meeting, or Developmental Biologists at SDB, etc) - what about a few short overview tagetted at specific journals? Developmental Biology, Animals Genetics, etc - again we need letter of support for the project (grants) 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/20051207/cc24e75d/attachment.html From dave.burt at bbsrc.ac.uk Wed Dec 7 02:56:05 2005 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Wed, 7 Dec 2005 10:56:05 -0000 Subject: Gene names/descriptions/nomenclature [based on HGNC] Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45102192FF1@rie2ksrv1.ri.bbsrc.ac.uk> 4. Gene names/descriptions/nomenclature [based on HGNC] As far as chicken gene nomenclature we decided years ago to adopt the human system, if possible Crittenden LB, Bitgood JJ, Burt DW. (1995). In: Genetic Nomenclature Guide - Chick. (Ed. A. Stewart). Trends in Genetics 11 (Suppl.), 33-34. Crittenden LB, Bitgood JJ, Burt DW, Ponce de Leon FA, Tixier-Boichard M. (1996). Nomenclature for naming loci, alleles, linkage groups and chromosomes to be used in poultry genome publications and databases. Genetics, Selection Evol. 28, 289-297. Burt DW. (1999). In: Genetic Nomenclature Guide. Trends in Genetics, November Supplement. Also on a www link HGNC: http://www.gene.ucl.ac.uk/nomenclature/guidelines.html Chicken: http://poultry.mph.msu.edu/about/NOME1195.html I think we should link up with HGNC? This process is best linked to the GO process? 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/20051207/9935f9cc/attachment.html From dave.burt at bbsrc.ac.uk Wed Dec 7 03:01:00 2005 From: dave.burt at bbsrc.ac.uk (dave burt (RI)) Date: Wed, 7 Dec 2005 11:01:00 -0000 Subject: Farm Animal - GO applications Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45102192FF2@rie2ksrv1.ri.bbsrc.ac.uk> 5. GO applications - databases {Ensembl, NCBI, GO, etc] - tools [Affymetrix, GenMAPP, OntoExpress, etc] - other ontology groups [phenotypes, chick Atlas, etc] - The idea here - is to identify the databases/tool providers who will use the chickGO annotations - I assume they would also be interested in this mail list - and then get letters of support for grants to support the annotation process OK that's enough Looking forward to the discussion and ideas 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/20051207/e457f719/attachment.html From OLP at stowers-institute.org Wed Dec 7 06:43:02 2005 From: OLP at stowers-institute.org (=?iso-8859-1?Q?Pourqui=E9=2C_Olivier?=) Date: Wed, 7 Dec 2005 08:43:02 -0600 Subject: How to increase profile [meetings, workshops, software, training, etc] Message-ID: Sure I am interested. I have a computing scientist joining the lab soon. He will work on a database on embryonic segmentation and I am sure he will interested in participating to this efforts Olivier Olivier Pourquie, PhD Investigator, Howard Hughes Medical Institute Stowers Institute for Medical Research 1000 East 50th Street Kansas City, Missouri, 64110, USA Phone : 816 926 4442 Fax : 816-926-2095 E-mail : olp at stowers-institute.org http://www.stowers-institute.org/ -----Original Message----- From: dave burt (RI) [mailto:dave.burt at bbsrc.ac.uk] Sent: Wednesday, December 07, 2005 4:48 AM To: farmanimals at geneontology.org; Pourqui?, Olivier; pba at U.Arizona.EDU; sjh at bms.umist.ac.uk Subject: Re: How to increase profile [meetings, workshops, software, training, etc] 2. How to increase profile [meetings, workshops, software, training, etc] This is important to increase number of GO annotators, support for further funding, etc Some idea? - May 7/10 2006 we will hold the next Chicken genome conference at cold spring harbor - and we will invite Shane to provide an overview of chickGO - other meetinsg would be the genome meeting itself at CSH, Plant & Animal Genome (San Diego) - we should make a concerted effort to spread the idea - so what would be useful would be to share powerpoint slides, make a common poster - other ideas? - as part of our grant proposals we will have - travel, training, sharing of software - In addition we should be proactive and enlist those we think will be interested in this project (either as annotators, users...). I have CC'd to parker, Olivier and Simon who I am sure will be interested 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/20051207/7e4814a1/attachment.html From fmccarthy at cvm.msstate.edu Wed Dec 7 11:10:56 2005 From: fmccarthy at cvm.msstate.edu (Fiona McCarthy) Date: Wed, 07 Dec 2005 13:10:56 -0600 Subject: Core aims of chickGO Message-ID: 1. Core aims of chickGO [recent doc from Dave B and Shane B] Hi All, I am looking at the document that Shane and Dave have put together and it seems that everyone is in agreement on the key points. Copying from the text of the documents Dave and Shane sent out, these key points are: 1. Manual annotations of chicken gene products to GO will be accepted from both AgBase and RI-EBI. Primary GO data for chicken gene products will be stored at one site AgBase under the leadership of Shane Burgess. 2. Both teams will provide workshops and access to software to help chicken researchers to do GO annotations, during the course of their functional genomics work. 3. Gene nomenclature and gene descriptions will be coordinated as part of the GO annotation process. The nomenclature effort will be developed in collaboration with HGNC. 4. ChickGO will organise and coordinate international collaborations through meetings and workshops; to include AgBase, Roslin Institute, EBI, University of Manchester, INRA, University of Arizona and others. According to the action plan we have agreed on the aims and overall objectives. My feeling is that we should try to organise a time and agenda for a phone conference to specifically address the mechanisms for each of these core aims. How does the week of 23-25 Jan 2006 suit everybody? Also, Evelyn made the comment that it would be nice to have an explanation for "who's who" on the ChickGO list. I agree. Does anyone have any suggestions for how to do this? 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 From fmccarthy at cvm.msstate.edu Wed Dec 7 12:07:37 2005 From: fmccarthy at cvm.msstate.edu (Fiona McCarthy) Date: Wed, 07 Dec 2005 14:07:37 -0600 Subject: Gene names/descriptions/nomenclature [based on HGNC] In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45102192FF1@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45102192FF1@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Hi Dave, Thank you for raising the issue of chicken nomenclature amongst this group. I agree with you that the chicken nomenclature should be based on HGNC guidelines, as outlined in the references you included below. This is the model we are using for chicken nomenclature. We are currently working in collaboration with HGNC to build a core database of chicken nomenclature based on human orthologs. I have sent an email to Ruth Lovering and Matt Wright at HGNC to let them know about this discussion group. At this point, I will leave it to them to fill in details regarding chicken nomenclature. 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 "dave burt \(RI\)" writes: >4. Gene names/descriptions/nomenclature [based on HGNC] > >As far as chicken gene nomenclature we decided years ago to adopt the >human system, if possible > >Crittenden LB, Bitgood JJ, Burt DW. (1995). In: Genetic Nomenclature >Guide - Chick. (Ed. A. Stewart). Trends in Genetics 11 (Suppl.), 33-34. > >Crittenden LB, Bitgood JJ, Burt DW, Ponce de Leon FA, Tixier-Boichard M. >(1996). Nomenclature for naming loci, alleles, linkage groups and >chromosomes to be used in poultry genome publications and databases. >Genetics, Selection Evol. 28, 289-297. > >Burt DW. (1999). In: Genetic Nomenclature Guide. Trends in Genetics, >November Supplement. > > > > >Also on a www link > >HGNC: [ http://www.gene.ucl.ac.uk/nomenclature/guidelines.html >]http://www.gene.ucl.ac.uk/nomenclature/guidelines.html > >Chicken: [ http://poultry.mph.msu.edu/about/NOME1195.html >]http://poultry.mph.msu.edu/about/NOME1195.html > >I think we should link up with HGNC? > >This process is best linked to the GO process? > >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 ]http://www.ark-genomics.org > From fmccarthy at cvm.msstate.edu Wed Dec 7 13:05:32 2005 From: fmccarthy at cvm.msstate.edu (Fiona McCarthy) Date: Wed, 07 Dec 2005 15:05:32 -0600 Subject: How to increase profile In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45102192FEF@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45102192FEF@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Hi Dave, "dave burt \(RI\)" on Wednesday, December 07, 2005 at 4:48 AM +0000 wrote: > >- other meetinsg would be the genome meeting itself at CSH, Plant & >Animal Genome (San Diego) - we should make a concerted effort to spread >the idea Both Shane & I will be at the Plant and Animal Genome Conference in January and we will be stopping in for at least part of the GO Session. As of right now my presentation will include information about how to contact the GO Farm Animals Interest Group. Also, I am getting in early here, but another meeting we should also keep in mind that there will be a GO Users Meeting in 2006, and probably there will be a GO Annotation training camp in 2006 where we can find recruits. >- so what would be useful would be to share powerpoint slides, make a >common poster - other ideas? It might be a good idea to have a short list of contacts along with their areas of interest/expertise. This would make a good handout to go with our talks and it would certainly help us to communicate with each other. 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 > > From cherry at genome.Stanford.EDU Wed Dec 7 15:37:36 2005 From: cherry at genome.Stanford.EDU (Mike Cherry) Date: Wed, 7 Dec 2005 15:37:36 -0800 Subject: Fwd: FarmAnimals special interest group added References: <9AB50F06-C353-4759-81AA-AE584CBE9B28@genome.stanford.edu> Message-ID: <10DDBCD1-EB10-41A9-ACCE-95A1C32B77E8@genome.stanford.edu> This message was posted to the GOFRIENDS list but some on the FARMANIMALS list may not be subscribed there. -Mike Begin forwarded message: > From: Mike Cherry > Date: December 7, 2005 11:47:45 AM PST > To: gofriends at genome.stanford.edu > Subject: FarmAnimals special interest group added > > A new Special Interest mailing list has been created for > discussions of farm animal genome annotations. To subscribe send a > message to farmanimals-request at geneontology.org and in the body of > the message say: > > subscribe > > This and the other special interest mailing lists are listed at the > GO site at: > > http://www.geneontology.org/GO.mailing.lists.shtml > > -Mike > From jclark at ebi.ac.uk Thu Dec 8 01:50:26 2005 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 08 Dec 2005 09:50:26 +0000 Subject: Core aims of chickGO In-Reply-To: References: Message-ID: <439801E2.6020000@ebi.ac.uk> Hi Fiona, > Also, Evelyn made the comment that it would be nice to have an explanation > for "who's who" on the ChickGO list. I agree. Does anyone have any > suggestions for how to do this? I'll put this together. I know most of it already and I can ask around a bit to get extra information. Jen From camon at ebi.ac.uk Thu Dec 8 02:49:46 2005 From: camon at ebi.ac.uk (Evelyn Camon) Date: Thu, 08 Dec 2005 10:49:46 +0000 Subject: How to increase profile References: <84DA9D8AC9B05F4B889E7C70238CB45102192FEF@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <43980FCA.7040807@ebi.ac.uk> Hi Fiona RE: handouts for PAG All Good suggestions. The EBI produce a series of nice simple handouts about db services and GO and GOA are included in those. Jennifer could perhaps bring a few with her to PAG to distribute. Perhaps an extra page could be added to it concerning the farm animal interest group, perhaps you could talk to Jen about that. We are all doing a little bit GO and GOA outreach but Jennifer Clark is the GO curator in the GO Consortium assigned the role of outreach officer and she is the hub to which we feed back all our contacts to. She is creating a small database of groups interested in GO. cheers Evelyn Fiona McCarthy wrote: > Hi Dave, > > "dave burt \(RI\)" on Wednesday, December 07, 2005 > at 4:48 AM +0000 wrote: > >>- other meetinsg would be the genome meeting itself at CSH, Plant & >>Animal Genome (San Diego) - we should make a concerted effort to spread >>the idea > > > > Both Shane & I will be at the Plant and Animal Genome Conference in > January and we will be stopping in for at least part of the GO Session. As > of right now my presentation will include information about how to contact > the GO Farm Animals Interest Group. > > Also, I am getting in early here, but another meeting we should also keep > in mind that there will be a GO Users Meeting in 2006, and probably there > will be a GO Annotation training camp in 2006 where we can find recruits. > > >>- so what would be useful would be to share powerpoint slides, make a >>common poster - other ideas? > > > It might be a good idea to have a short list of contacts along with their > areas of interest/expertise. This would make a good handout to go with our > talks and it would certainly help us to communicate with each other. > > 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 > > >> > > > > > From jclark at ebi.ac.uk Thu Dec 8 05:10:29 2005 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 08 Dec 2005 13:10:29 +0000 Subject: who we are Message-ID: <439830C5.9040706@ebi.ac.uk> Hi, I've tried to write down what everybody's involvement is in the group so we all have a rough idea what's there and what's missing. Can people let me know if the list below is anything like correct? There are a few people I wasn't sure how to summarise, and some who I don't know so much about, and I'd really appreciate any information you can give me. Thanks, Jen Susan Bridges - AgBase (all species) Shane Burgess - AgBase (all species) Dave Burt - Chicken Evelyn Camon - Gene Ontology Annotation Group Jennifer Clark - Gene Ontology Editorial Office Christian Diot Christine Elsik - Bovine Genome Database Alex Evans - Reproduction in farm animals Richard Fitzpatrick Yann Guiguen Fran?ois Hatey - PigNet Andy Law - Bioinformatics (Roslin Institute) Patrice Martin Fiona McCarthy - AgBase (all species) Dermot Morris - Ivan Morrison - Ruminants Frank Panitz Sinead Waters From Christian.Diot at rennes.inra.fr Thu Dec 8 06:39:29 2005 From: Christian.Diot at rennes.inra.fr (Christian Diot) Date: Thu, 08 Dec 2005 15:39:29 +0100 Subject: who we are In-Reply-To: <439830C5.9040706@ebi.ac.uk> References: <439830C5.9040706@ebi.ac.uk> Message-ID: <439845A1.10802@rennes.inra.fr> Hi all, Some informations about me and my group. I am involved with my group (Join Research Unit of Animal Genetic, INRA and Agrocampus Rennes) in chicken genomics, (genome and gene expression analyses of variability) and in gene annotation. We are in contact with the group of Anita Burgun involved in bioinformatics and especially in Gene Ontology and what she calls "semantic-web". Together we plan to work in the topic of database knowledge extraction in the context of species specificities, taking the chicken as one of the models. Problably Anita will subscribe to the list in the following days and say more words about that. regards, Christian ---------------------------------------------- Christian Diot, PhD Head of the Joint Research Unit Animal Genetics INRA-Agrocampus Rennes CS 84215 65 rue de Saint-Brieuc 35042 Rennes cedex, France phone : +33 (0)223 485 461 fax : +33 (0)223 485 470 email : Christian.Diot at rennes.inra.fr ---------------------------------------------- J Clark a ?crit : > Hi, > > I've tried to write down what everybody's involvement is in the group > so we all have a rough idea what's there and what's missing. Can > people let me know if the list below is anything like correct? There > are a few people I wasn't sure how to summarise, and some who I don't > know so much about, and I'd really appreciate any information you can > give me. > > Thanks, > > Jen > > Susan Bridges - AgBase (all species) > Shane Burgess - AgBase (all species) > Dave Burt - Chicken > Evelyn Camon - Gene Ontology Annotation Group > Jennifer Clark - Gene Ontology Editorial Office > Christian Diot > Christine Elsik - Bovine Genome Database > Alex Evans - Reproduction in farm animals > Richard Fitzpatrick > Yann Guiguen > Fran?ois Hatey - PigNet > Andy Law - Bioinformatics (Roslin Institute) > Patrice Martin > Fiona McCarthy - AgBase (all species) > Dermot Morris - > Ivan Morrison - Ruminants > Frank Panitz > Sinead Waters > > > From jclark at ebi.ac.uk Thu Dec 8 06:42:30 2005 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 08 Dec 2005 14:42:30 +0000 Subject: Introductions Message-ID: <43984656.9050305@ebi.ac.uk> Hi, I'm getting information in from people about their involvement with farm animal biology and I think others might be interested to see as well, so we all know where everybody's coming from. I've pasted the few I have below. If other list members could briefly write directly to the list and state their interests then that would be great. All this is archived so we only have to do it once. The archive is on the GO ftp site (ftp://ftp.geneontology.org/pub/go). Chris Elsik: 1) bovine - annotating gene products (eventually) and using the GO to annotate ESTs and microarrays. 2) pig - using GO to annotate ESTs and microarrays 3) sheep - using GO to annotate ESTs and microarrays Alex Evans: There is a significant group here in UCD, Dublin, that is intersted in cattle. Particular interests are in reproductive tissues, growth, and the immune system. We have a lesser interest in similar tissues in sheep. We also have a programme on the genomics of exercise in horses. Dave Burt - Chicken and all avian genomes, ARK-genomics www.ARK-genomics.org, AvianNET www.chicken-genome.org, Arkdb http://www.thearkdb.org/browser?species=chicken QTLdb (BBSRC with Andy Law), Ensembl-chick (BBSRC project with Ewan B, Dave B, Andy Law, Simon Hubbard) Jennifer Clark GO Editorial Office I'm assigned to keep track of discussions with new groups who are considering starting annotating to GO. I visit meetings to give talks encouraging groups to annotate to GO. I also help write the Gene Ontologies, particularly the developmental processes and plant processes. Thanks, Jen From schmidtc at udel.edu Thu Dec 8 07:50:11 2005 From: schmidtc at udel.edu (Carl Schmidt) Date: Thu, 8 Dec 2005 10:50:11 -0500 Subject: Introductions Message-ID: Our group is interested in gene annotation and knowledgebase development. Of particular interest is developing methods for knowledge extraction from distributed resources. We have developed GoFigure, an online resource for GO annotation prediction and GallusKB a knowledgebase focused on chicken ESTs and predicted annotation. GoFigure: http://udgenome.ags.udel.edu/frm_go.html GallusKB Home page: http://udgenome.ags.udel.edu/gallus/index.php GallusKB advanced query: http://udgenome.ags.udel.edu/gallus/ display.php?form=Complex Carl J. Schmidt Associate Professor Department of Animal & Food Sciences 051 Townsend Hall University of Delaware Newark, DE 19717 schmidtc at udel.edu 302-831-1334 Fax: 302-831-2822 http://udel.edu/~schmidtc -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20051208/b57c0e2c/attachment.html From camon at ebi.ac.uk Thu Dec 8 08:00:48 2005 From: camon at ebi.ac.uk (Evelyn Camon) Date: Thu, 08 Dec 2005 16:00:48 +0000 Subject: Introductions References: <43984656.9050305@ebi.ac.uk> Message-ID: <439858B0.70503@ebi.ac.uk> Evelyn Camon: I coordinate the GO annotation (GOA) group (http://www.ebi.ac.uk/GOA) at the EBI. We produce GO annotations to over 98,000 species annotated in the UniProtKb/Swiss-Prot and TrEMBL databases. We have 20 curators , 3 full time GOA and 17 part-time GOA(also working on UniProtKb). The full time GOA curators also help to create the InterPro2go and spkw2go mappings. GOA is specifically funded for GO curation of the Human Proteome but we are also involved in curating other mammalian species. We are currently collaborating with Dave Burt(Roslin) and Fiona McCarty(AgBase)in Chicken GO annotation. For groups wishing to get started in GO annotation we can provide training and access to our online GO annotation tool. GOA produces: GOA-UniProt(redundant dataset, all species),and species specific files (non-redundant)GOA-Human, GOA-Mouse, GOA-Rat, GOA-Chicken,GOA-Arabidopsis, GOA-ZebraFish (and next year GOA-DOG and GOA-Cow:-) The GOA annotators share an office with GO editors. So Jen and I can see each other. The EBI is also the home of SWISS-PROT,InterPro, EMBL, IntAct, PRIDE, CHEBI, MSD, Ensembl, ASD, ClusTr and ArrayExpress. My biological background is in bovine immunology, at GOA however I curating all types of proteins, species and fields of biology. cheers Evelyn GOA Coordinator Senior Scientific Curator European Bioinformatic Institute Wellcome Trust Genome Campus E-mail: camon at ebi.ac.uk Tel:01223-494465 Fax:01223-494468 J Clark wrote: > Hi, > > I'm getting information in from people about their involvement with farm > animal biology and I think others might be interested to see as well, so > we all know where everybody's coming from. I've pasted the few I have > below. If other list members could briefly write directly to the list > and state their interests then that would be great. All this is archived > so we only have to do it once. The archive is on the GO ftp site > (ftp://ftp.geneontology.org/pub/go). > > Chris Elsik: > 1) bovine - annotating gene products (eventually) and using the GO to > annotate ESTs and microarrays. > 2) pig - using GO to annotate ESTs and microarrays > 3) sheep - using GO to annotate ESTs and microarrays > > Alex Evans: > There is a significant group here in UCD, Dublin, that is intersted in > cattle. Particular interests are in reproductive tissues, growth, and the > immune system. We have a lesser interest in similar tissues in sheep. > We also have a programme on the genomics of exercise in horses. > > Dave Burt - > Chicken and all avian genomes, > ARK-genomics www.ARK-genomics.org, > AvianNET www.chicken-genome.org, > Arkdb http://www.thearkdb.org/browser?species=chicken > QTLdb (BBSRC with Andy Law), > Ensembl-chick (BBSRC project with Ewan B, Dave B, Andy Law, Simon Hubbard) > > Jennifer Clark > GO Editorial Office > I'm assigned to keep track of discussions with new groups who are > considering starting annotating to GO. I visit meetings to give talks > encouraging groups to annotate to GO. I also help write the Gene > Ontologies, particularly the developmental processes and plant processes. > > Thanks, > > Jen > > > > > > > > From burgess at cvm.msstate.edu Thu Dec 8 08:38:24 2005 From: burgess at cvm.msstate.edu (Shane Burgess) Date: Thu, 08 Dec 2005 10:38:24 -0600 Subject: How to increase profile [meetings, workshops, software, training, etc] In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45102192FEF@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45102192FEF@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: "dave burt \(RI\)" on Wednesday, December 07, 2005 at 4:48 AM +0000 wrote: 2. How to increase profile [meetings, workshops, software, training, etc] This is important to increase number of GO annotators, support for further funding, etc Some idea? - May 7/10 2006 we will hold the next Chicken genome conference at cold spring harbor - and we will invite Shane to provide an overview of chickGO OK - other meetinsg would be the genome meeting itself at CSH, Yes, you are right about that I have just returned from the Conference for reasearch workers in animal diseases where I spoke with on "GO and immunology" using data from my lab to illustrate the point. Immediately after I spoke at the first USDA NRI grant holders compulsory meeting and GO was again featured in the work for that grant. I will be attending this meeting for at least the next 5 years so that venue is covered. This meeting is open and I had a lot of people who are doing functional genomics asking me about GO (not our disease work sigh ;-) ). - Plant & Animal Genome (San Diego) - we should make a concerted effort to spread the idea I am speaking in the Chicken genome section of this meeting specifically on ChickGO at AgBase and Fiona is speaking in the Ruminant Section on CowGO and SheepGO. I am also invited to the speak at the general proteomics section and GO will be mentioned there as the fundamental basis for our Modeling. Of course Jen has her very own GO session. Jen and I are discussing how we can best integrate this whole thing. Do you all think that we could/should push to have a specific GO/Ontology/Annotation session session at PAG every year? Certainly, given the fundamental nature of GO (and other ontologies) for modeling functional genomics data (and even structurally annotating genomes to some degrees), there is a strong argument here. Especially as proteomics, with a much smaller interest group, has its own session. Also I plan to speak with the USDA genome administrators at PAG. - so what would be useful would be to share powerpoint slides, make a common poster - other ideas? Yes. Susan Fi and I do this routinely send each other our ppts and, speaking for Fi and I at least, I am very happy to send these to be archived somewhere "on the www" if it helps all involved. A common poster would be great. If we hurry I can put it up at PAG. - as part of our grant proposals we will have - travel, training, sharing of software Yes we really need to generate a lot of support , and letters of support, from the animal and plant communities (in addition of letters of support from each other). I mention plants here because Dawn Luthe (corn) has been greatly involved in the money for AgBase and, in the USA at least, plants have MUCH more access to money. This one of the reasons why it's "agBase" and not "LivestockBase". Though having said at AgBase, money earmarked for a species is spent on that species. This is why chicken is the most advanced animal, followed by cow. - In addition we should be proactive and enlist those we think will be interested in this project (either as annotators, users?). Yes I agree. The paradigm that we have here at AgBase is that we provide a service and port of call for people who are interested in using GO in Ag species. Also, at AgBase, we think that the communities are too small and poorly funded to replicate what is happening at , for example, MGI in mouse. So we are encouraging those PIs who need GO annotations for their genes of interest, and in situations were we haven't already done the manual annotations, to manually annotate their genes of interest as experts in their area of interest. We also hold a database of all papers PMID numbers that we manually annotate (you just can?t see it on AgBase yet) so that 1. people don?t have to re-annotate the same papers over and over again (believe me, no wants to annotate more papers than they need to) and 2. we can identify papers that can be used in annotation QC. Christine at TAMU will hold a database for her bovine manual GO annotations and Christine and AgBase will swap these with each other.Of course we have come full circle here because people will need to know how to GO annotate. So here at AgBase we have a 12 hour long course (we developed this after Fiona spent two weeks at MGI with Judy Blake?s group). This course is kind of an expanded version of what Jen is doing at PAG. We have run this course on campus here twice and we have it pretty well ironed out. We have trained about 12 annotators across various species. We have not had any issues with annotations sent by these people to GOA via AgBase. I have recently been asked if we can do the same course for others outside of MSU. I said, that yes we could (in theory). Fiona is speaking about this at the 1st annual Biocurator meeting. At AgBase we are acting at the moment as a kind of buffer for GOA so that we can answer a lot (all?) of the Agriculture beginners questions in GO and save the GOA folks for answering our hard questions. 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 ]http://www.ark-genomics.org 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. 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 Thu Dec 8 08:40:40 2005 From: burgess at cvm.msstate.edu (Shane Burgess) Date: Thu, 08 Dec 2005 10:40:40 -0600 Subject: Farm Animal - GO applications In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45102192FF2@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45102192FF2@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: "dave burt \(RI\)" on Wednesday, December 07, 2005 at 5:01 AM +0000 wrote: >5. GO applications > >- databases {Ensembl, NCBI, GO, etc] >- tools [Affymetrix, GenMAPP, OntoExpress, etc] >- other ontology groups [phenotypes, chick Atlas, etc] All of the proteomics companies. The companies making the network/pathway modeling programs (such as "Ingenuity") > > >- The idea here - is to identify the databases/tool providers who will >use the chickGO annotations >- I assume they would also be interested in this mail list > >- and then get letters of support for grants to support the annotation >process > >OK that's enough > >Looking forward to the discussion and ideas > >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 ]http://www.ark-genomics.org From burgess at cvm.msstate.edu Thu Dec 8 08:45:37 2005 From: burgess at cvm.msstate.edu (Shane Burgess) Date: Thu, 08 Dec 2005 10:45:37 -0600 Subject: GO annotation [the search for annotators, grants, letters of support for g In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45102192FF0@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45102192FF0@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: "dave burt \(RI\)" on Wednesday, December 07, 2005 at 4:53 AM +0000 wrote: >3. GO annotation [the search for annotators, grants, letters of support >for grants, etc] > >- AgBase and GOA will be the focus for entry of GO annotation, info etc >which can then me stored in the master database at AgBase No problem here. Note also that we have the PMID database (you just can't see it on AgBase yet) so we don't continually reannotate the same papers. > > >- I think increasing our profile will bring in new contacts for GO >annotation Yes, I am noticing this alraedy. > >- but we can also target meetings (e.g. immunologists at Avian >Immunoglogy meeting, or Developmental Biologists at SDB, etc) Yes, again we do this because GO is a critical part of what we do, it natually comes up. > > >- what about a few short overview tagetted at specific journals? >Developmental Biology, Animals Genetics, etc I agree. How do you suggest we do this. Fi is about to submit the paper on AgBase, though we have been out of touch and I am not sure where se plans to submit it. > >- again we need letter of support for the project (grants) Yes and please email me if you can help me such for a grant due in to NIH Feb 1. I don't want to bug you all with emails begging letters so please reply if you would be willing to. I am willing to write letters for anyone involved in this. Shane > > >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 ]http://www.ark-genomics.org 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 Thu Dec 8 08:52:57 2005 From: burgess at cvm.msstate.edu (Shane Burgess) Date: Thu, 08 Dec 2005 10:52:57 -0600 Subject: Gene names/descriptions/nomenclature [based on HGNC] In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45102192FF1@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45102192FF1@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: "dave burt \(RI\)" on Wednesday, December 07, 2005 at 4:56 AM +0000 wrote: >4. Gene names/descriptions/nomenclature [based on HGNC] > >As far as chicken gene nomenclature we decided years ago to adopt the >human system, if possible > >Crittenden LB, Bitgood JJ, Burt DW. (1995). In: Genetic Nomenclature >Guide - Chick. (Ed. A. Stewart). Trends in Genetics 11 (Suppl.), 33-34. > >Crittenden LB, Bitgood JJ, Burt DW, Ponce de Leon FA, Tixier-Boichard M. >(1996). Nomenclature for naming loci, alleles, linkage groups and >chromosomes to be used in poultry genome publications and databases. >Genetics, Selection Evol. 28, 289-297. > >Burt DW. (1999). In: Genetic Nomenclature Guide. Trends in Genetics, >November Supplement. > > > > >Also on a www link > >HGNC: [ http://www.gene.ucl.ac.uk/nomenclature/guidelines.html >]http://www.gene.ucl.ac.uk/nomenclature/guidelines.html > >Chicken: [ http://poultry.mph.msu.edu/about/NOME1195.html >]http://poultry.mph.msu.edu/about/NOME1195.html > >I think we should link up with HGNC? > >This process is best linked to the GO process? > >dave OK, so Fiona has been dealing specifically with this and has met with the HGNC folks, we have PhD student working on this with them now. I don't know much more than that I am afraid. It's probably best if we wait for Fiona's in put here. At AgBase have already adopted the Human system (based on the above tow publications) because we have already had to deal with the problem. Again Fiona already has the (rudimentary) database setup (you just can't see it yet) and we can we can help as the clearing house here as needed. As for genes with no human ortholog, the paradigm in mouse (as with new genes in human) is that the investigators with the vested interest work with HGNC to make sure their name fits the format and isn't already used. Again though for details we need to wait on Fiona. > >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 ]http://www.ark-genomics.org 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 jclark at ebi.ac.uk Thu Dec 8 08:59:58 2005 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 08 Dec 2005 16:59:58 +0000 Subject: How to increase profile [meetings, workshops, software, training, etc] In-Reply-To: References: <84DA9D8AC9B05F4B889E7C70238CB45102192FEF@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <4398668E.90008@ebi.ac.uk> Hi Shane, Thanks for this update on AgBase below. It's really hard for us to know how much buffering of questions you're doing so it's good to hear about that. I didn't realise that you were getting funding related to corn. Are you annotating that then? I've had real trouble getting groups with money to annotate corn (you mean Zea mays right?). In response to your point about GO and PAG, we have had talks there every year for several years but this is our first full day session. The plant ontology consortium also do a lot there. I think that as long as there is demand we will be welcome to have a long session like this. There were no problems at all when I wrote and asked for the space. Would you perhaps like to explore the idea of having an Agriculture/Farm animal GO session? I think it may not be too late to set one up if the group feel the need more airtime. It took all of about 20 minutes to get my GO session organised and it would be great publicity. Thanks, Jen > > - Plant & Animal Genome (San Diego) - we should make a concerted effort to > spread the idea > > I am speaking in the Chicken genome section of this meeting specifically > on ChickGO at AgBase and Fiona is speaking in the Ruminant Section on > CowGO and SheepGO. I am also invited to the speak at the general > proteomics section and GO will be mentioned there as the fundamental > basis for our Modeling. Of course Jen has her very own GO session. Jen and > I are discussing how we can best integrate this whole thing. Do you all > think that we could/should push to have a specific GO/Ontology/Annotation > session session at PAG every year? Certainly, given the fundamental nature > of GO (and other ontologies) for modeling functional genomics data (and > even structurally annotating genomes to some degrees), there is a strong > argument here. Especially as proteomics, with a much smaller interest > group, has its own session. Also I plan to speak with the USDA genome > administrators at PAG. > > - so what would be useful would be to share powerpoint slides, make a > common poster - other ideas? > Yes. Susan Fi and I do this routinely send each other our ppts and, > speaking for Fi and I at least, I am very happy to send these to be > archived somewhere "on the www" if it helps all involved. > > A common poster would be great. If we hurry I can put it up at PAG. > > - as part of our grant proposals we will have - travel, training, sharing > of software > Yes we really need to generate a lot of support , and letters of support, > from the animal and plant communities (in addition of letters of support > from each other). I mention plants here because Dawn Luthe (corn) has been > greatly involved in the money for AgBase and, in the USA at least, plants > have MUCH more access to money. This one of the reasons why it's "agBase" > and not "LivestockBase". Though having said at AgBase, money earmarked for > a species is spent on that species. This is why chicken is the most > advanced animal, followed by cow. > > - In addition we should be proactive and enlist those we think will be > interested in this project (either as annotators, users?). > Yes I agree. > > The paradigm that we have here at AgBase is that we provide a service and > port of call for people who are interested in using GO in Ag species. > Also, at AgBase, we think that the communities are too small and poorly > funded to replicate what is happening at , for example, MGI in mouse. So > we are encouraging those PIs who need GO annotations for their genes of > interest, and in situations were we haven't already done the manual > annotations, to manually annotate their genes of interest as experts in > their area of interest. We also hold a database of all papers PMID numbers > that we manually annotate (you just can?t see it on AgBase yet) so that 1. > people don?t have to re-annotate the same papers over and over again > (believe me, no wants to annotate more papers than they need to) and 2. we > can identify papers that can be used in annotation QC. Christine at TAMU > will hold a database for her bovine manual GO annotations and Christine > and AgBase will swap these with each other.Of course we have come full > circle here because people will need to know how to GO annotate. > > So here at AgBase we have a 12 hour long course (we developed this after > Fiona spent two weeks at MGI with Judy Blake?s group). This course is kind > of an expanded version of what Jen is doing at PAG. > > We have run this course on campus here twice and we have it pretty well > ironed out. We have trained about 12 annotators across various species. We > have not had any issues with annotations sent by these people to GOA via > AgBase. I have recently been asked if we can do the same course for others > outside of MSU. I said, that yes we could (in theory). Fiona is speaking > about this at the 1st annual Biocurator meeting. > > At AgBase we are acting at the moment as a kind of buffer for GOA so that > we can answer a lot (all?) of the Agriculture beginners questions in GO > and save the GOA folks for answering our hard questions. > From pruitt at ncbi.nlm.nih.gov Thu Dec 8 09:22:13 2005 From: pruitt at ncbi.nlm.nih.gov (Pruitt, Kim (NIH/NLM/NCBI) [E]) Date: Thu, 8 Dec 2005 12:22:13 -0500 Subject: Introduction - GO at NCBI Message-ID: Hi, I'm monitoring this new list so that NCBI can be informed as GO data becomes available for more organisms. We don't curate GO terms ourselves, but do process GO information that is provided on the GO FTP site. We integrate this data into Entrez Gene and RefSeq sequence records (citing GO as the data source and linking to the GO browser). This adds descriptive information in the context of other information available in Gene and RefSeq, and supports retrieval of records based on GO terms. For example: "enzyme binding"[GO] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=PureSearch&db=gene&det ails_term=%22enzyme%20binding%22%5BGO%5D%20AND%20alive%5Bprop%5D Regards, Kim Pruitt ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Kim D. Pruitt, Ph.D DHHS/NIH/NLM/NCBI 45 Center Drive, MSC 6510 Building 45; Rm 6AN12J Bethesda, MD 20892-6510 phone: (301)435-5898 email: pruitt at ncbi.nlm.nih.gov ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From jclark at ebi.ac.uk Mon Dec 12 03:28:32 2005 From: jclark at ebi.ac.uk (J Clark) Date: Mon, 12 Dec 2005 11:28:32 +0000 Subject: list members Message-ID: <439D5EE0.20503@ebi.ac.uk> Hi, I'm compiling a list of all the people on this mailing list that will show in what capacity we have all joined thie discussion. The list I have is pasted below. If there are any names or pieces of information missing can people let me know? The information will ultimately go on the Gene Ontology interest group webpage. http://www.geneontology.org/GO.interests.shtml#curr Thanks, Jen Susan Bridges - AgBase (Agricultural species) Shane Burgess - AgBase (Agricultural species) Dave Burt - Chicken and all avian genomes, ARK-genomics www.ARK-genomics.org, AvianNET www.chicken-genome.org, Arkdb http://www.thearkdb.org/browser?species=chicken QTLdb (BBSRC with Andy Law), Ensembl-chick (BBSRC project with Ewan B, Dave B, Andy Law, Simon Hubbard) Evelyn Camon - Coordinates the GO annotation (GOA) group (http://www.ebi.ac.uk/GOA) at the EBI. Jennifer Clark - Gene Ontology Editorial Office Christian Diot - Animal Genetic Joint Resarch Unit, INRA-Agrocampus Rennes, France. Genomic analyses in poultry, including genetic variability and gene expression (transcriptomics) analyses and linkage to adiposity and more generally to production traits. Christine Elsik - Bovine Genome Database Alex Evans - Reproductive tissues, growth, and the immune system of cattle and sheep. Genomics of exercise in horses. Yann Guiguen Fran?ois Hatey - PigNet Andy Law - Bioinformatics (Roslin Institute) Patrice Martin - Fiona McCarthy - AgBase (Agricultural species) Dermot Morris, Richard Fitzpatrick, Sinead Waters - All part of the Animal Reproduction Department of Teagasc (the Irish Agriculture and Food Development Authority) with interests in all aspects of reproduction and nutition, particularly in cattle but also in sheep. Ivan Morrison - Ruminants Frank Panitz - Carl J. Schmidt - GoFigure: http://udgenome.ags.udel.edu/frm_go.html GallusKB: http://udgenome.ags.udel.edu/gallus/index.php From jclark at ebi.ac.uk Mon Dec 12 05:07:01 2005 From: jclark at ebi.ac.uk (J Clark) Date: Mon, 12 Dec 2005 13:07:01 +0000 Subject: list Message-ID: <439D75F5.8020304@ebi.ac.uk> Hi, I'm nearly there with the list now. I have edited a bit to make the information briefer. If anybody objects to any of the following going live on the website can they let me know? Thanks, Jen Susan Bridges - AgBase (Agricultural species) Mississippi State University, USA. Shane Burgess - AgBase (Agricultural species) Mississippi State University, USA. Dave Burt - Chicken and all avian genomes, ARK-genomics www.ARK-genomics.org, AvianNET www.chicken-genome.org, Arkdb http://www.thearkdb.org/browser?species=chicken QTLdb, Ensembl-chick Roslin Institute, UK Evelyn Camon - GOA Coordinator (http://www.ebi.ac.uk/GOA). EBI, UK Jennifer Clark - Gene Ontology Editorial Office EBI, UK Christian Diot - Adiposity and production traits (Poultry). INRA, France. Andr? Eggen - Bovine genome structure. INRA, France. Christine Elsik - Bovine Genome Database Texas A&M University, USA. Alex Evans - Reproductive tissues, growth, and the immune system (cattle and sheep). Genomics of exercise (horses). UCD, Ireland. Richard Fitzpatrick - Reproduction and nutition (cattle and sheep) Teagasc (Ireland) Yann Guiguen - Functional genomics (Trout) INRA, France. Fran?ois Hatey - Functional genomics of reproduction and meat quality (Trout) European Network for Pig Genomics "PigNet" (COST action 861) www.toulouse.inra.fr/pignet INRA, France. Andy Law - Bioinformatics Roslin Institute, UK Patrice Martin - Functional genomics (cow) INRA, France. Fiona McCarthy - AgBase (Agricultural species) Mississippi State University, USA. Dermot Morris - Reproduction and nutition (cattle and sheep) Teagasc (Ireland) Ivan Morrison - Ruminants Frank Panitz - Carl J. Schmidt - GoFigure http://udgenome.ags.udel.edu/frm_go.html GallusKB http://udgenome.ags.udel.edu/gallus/index.php University of Delaware, USA Sinead Waters - Reproduction and nutition (cattle and sheep) Teagasc (Ireland) From camon at ebi.ac.uk Mon Dec 12 06:09:45 2005 From: camon at ebi.ac.uk (Evelyn Camon) Date: Mon, 12 Dec 2005 14:09:45 +0000 Subject: Bovine GO annotations Message-ID: <439D84A9.8070502@ebi.ac.uk> Hi, The International Protein Index team at the EBI are currently working on the ensembl bovine release and will produce a non-redundant Bovine dataset for us in January. GOA releases follow directly after IPI release so we will be able to produce a Bovine specific non-redundant GO annotation file with many more annotations in our release in January 2006. Happy Christmas, Evelyn From jclark at ebi.ac.uk Wed Dec 14 05:04:52 2005 From: jclark at ebi.ac.uk (J Clark) Date: Wed, 14 Dec 2005 13:04:52 +0000 Subject: farm animal webpage Message-ID: <43A01874.9050605@ebi.ac.uk> Hi, There is now a full webpage dedicated to the GO farm animal interest group on the GO website. http://www.geneontology.org/GO.list.farmanimals.shtml If more people have joined and would like their details listed at the bottom of the page then please do send the information on to me. We currently have in excess of 35 members. Anyone you know with an interest in joining this group is welcome to do so. To join they should just follow the instructions on the webpage. Thanks, Jen From jclark at ebi.ac.uk Thu Dec 15 08:19:32 2005 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 15 Dec 2005 16:19:32 +0000 Subject: farm animal fliers Message-ID: <43A19794.1080200@ebi.ac.uk> Hi, Somebody suggested that we might get some fliers made to advertise the farm animal GO annotation effort that I could distribute at PAG. PAG is quite soon so I probably can't get anything terribly exotic set up. I'll make fliers with a small bit of info and the interest group e-mail on them. I just wanted to say that if anybody else has more time than me and is feeling creative then please do go ahead and design/send something. (I'm thinking particularly of individual database groups that may like to get some advertising for their efforts.) I can easily print other people's fliers and take them to PAG. Thanks, Jen From jreecy at iastate.edu Thu Dec 15 08:35:40 2005 From: jreecy at iastate.edu (James M Reecy) Date: Thu, 15 Dec 2005 10:35:40 -0600 Subject: farm animal fliers In-Reply-To: <43A19794.1080200@ebi.ac.uk> References: <43A19794.1080200@ebi.ac.uk> Message-ID: <6.1.2.0.2.20051215103338.027f1dd8@jreecy.mail.iastate.edu> Jen, I will send out a notice on the AnGen List serve later today. In addition, I will put in a plug for the farm animal GO annotation effort in all of the talks that I will give to the livestock species sections of NRSP-8. Jim At 10:19 AM 12/15/2005, J Clark wrote: >Hi, > >Somebody suggested that we might get some fliers made to advertise the >farm animal GO annotation effort that I could distribute at PAG. PAG is >quite soon so I probably can't get anything terribly exotic set up. I'll >make fliers with a small bit of info and the interest group e-mail on >them. I just wanted to say that if anybody else has more time than me and >is feeling creative then please do go ahead and design/send >something. (I'm thinking particularly of individual database groups that >may like to get some advertising for their efforts.) I can easily print >other people's fliers and take them to PAG. > >Thanks, > >Jen James Reecy NRSP-8 Database Coordinator National Beef Cattle Evaluation Consortium Dept. of Animal Science Iowa State University 2255 Kildee Hall Ames, IA 50011-3150 Tel. (515) 294-9269 fax: 515-294-2401 E-mail: jreecy at iastate.edu http://www.ans.iastate.edu/faculty/reecy.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/farmanimals/attachments/20051215/46576c3b/attachment.html From jclark at ebi.ac.uk Thu Dec 15 08:43:34 2005 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 15 Dec 2005 16:43:34 +0000 Subject: farm animal fliers In-Reply-To: <6.1.2.0.2.20051215103338.027f1dd8@jreecy.mail.iastate.edu> References: <43A19794.1080200@ebi.ac.uk> <6.1.2.0.2.20051215103338.027f1dd8@jreecy.mail.iastate.edu> Message-ID: <43A19D36.2030303@ebi.ac.uk> Hi Jim, Thanks for that. :-) That will really be an enormous help. Best wishes, Jen James M Reecy wrote: > Jen, > I will send out a notice on the AnGen List serve later today. > In addition, I will put in a plug for the farm animal GO annotation > effort in all of the talks that I will give to the livestock species > sections of NRSP-8. > > Jim > > > At 10:19 AM 12/15/2005, J Clark wrote: > >> Hi, >> >> Somebody suggested that we might get some fliers made to advertise the >> farm animal GO annotation effort that I could distribute at PAG. PAG >> is quite soon so I probably can't get anything terribly exotic set up. >> I'll make fliers with a small bit of info and the interest group >> e-mail on them. I just wanted to say that if anybody else has more >> time than me and is feeling creative then please do go ahead and >> design/send something. (I'm thinking particularly of individual >> database groups that may like to get some advertising for their >> efforts.) I can easily print other people's fliers and take them to PAG. >> >> Thanks, >> >> Jen > > James Reecy > NRSP-8 Database Coordinator > National Beef Cattle Evaluation Consortium > Dept. of Animal Science > Iowa State University > 2255 Kildee Hall > Ames, IA 50011-3150 > Tel. (515) 294-9269 > fax: 515-294-2401 > E-mail: jreecy at iastate.edu > http://www.ans.iastate.edu/faculty/reecy.html > From jclark at ebi.ac.uk Sat Dec 17 02:15:53 2005 From: jclark at ebi.ac.uk (Jennifer Clark) Date: Sat, 17 Dec 2005 10:15:53 +0000 Subject: farm animal fliers Message-ID: <43A3E559.4090805@ebi.ac.uk> Hi, I've just been talking to a few people about the idea of making some fliers for PAG. It seems like there are a lot of groups going to PAG who are starting to have annotation efforts or may have other GO-related work going on that they would like people to know about. We in the Consortium don't know the full list and I wouldn't like to be making fliers about some and accidentally missing others. If you are attending PAG and would like to bring fliers along then please feel free to do so. If anybody wants to send some and is not coming to PAG then you can send them to me there at this address: Jennifer Clark, Plant and Animal Genome Meeting delegate, Town and Country Resort & Convention Center, 500 Hotel Circle North, San Diego, California 92108. Thanks, Jen