From mgiglio at SOM.UMARYLAND.EDU Mon Mar 3 10:46:07 2008 From: mgiglio at SOM.UMARYLAND.EDU (Gwinn Giglio, Michelle) Date: Mon, 03 Mar 2008 13:46:07 -0500 Subject: [Go] New GO people from JCVI Message-ID: Hello everyone, I'd like to introduce you to Scott Durkin and Ramana Madupu. They have taken over the GO-related activities that I did at TIGR/JCVI. I have worked with both of them for many years on the prokaryotic annotation team and they come to the consortium with lots of experience in GO annotation. I am happy to have them carrying on the work I started at TIGR. I tried to pass on to them as much knowledge as I could about my GO work at TIGR, unfortunately, mostly I just left them with a huge "to do" list. :) Scott and Ramana will be coming to the April meeting to learn more of the ropes and take on their new roles as the JCVI representatives. I hope you will join me in welcoming them. Michelle From keilbeck at genetics.utah.edu Mon Mar 3 10:55:59 2008 From: keilbeck at genetics.utah.edu (Karen Eilbeck) Date: Mon, 3 Mar 2008 11:55:59 -0700 Subject: [Go] Please register for GOC meeting Message-ID: Hi all, This is a reminder to all of those people who are intending on coming to the GO/reference genome meetings in Salt Lake City next month to register at the website: http://wiki.geneontology.org/index.php/Register Thanks Karen From suzi at berkeleybop.org Mon Mar 3 11:05:24 2008 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Mon, 3 Mar 2008 11:05:24 -0800 Subject: [Go] New GO people from JCVI In-Reply-To: References: Message-ID: <42CCD6E8-B8F0-4183-AD1E-F7C124B9424B@berkeleybop.org> Thanks Michelle for the introduction. Scott and Ramana, welcome, looking forward to meeting you in April (and seeing Michelle again too). -Suzi On Mar 3, 2008, at 10:46 AM, Gwinn Giglio, Michelle wrote: > > > Hello everyone, > > I'd like to introduce you to Scott Durkin and Ramana Madupu. They > have > taken over the GO-related activities that I did at TIGR/JCVI. I > have worked > with both of them for many years on the prokaryotic annotation team > and they > come to the consortium with lots of experience in GO annotation. I > am happy > to have them carrying on the work I started at TIGR. I tried to > pass on to > them as much knowledge as I could about my GO work at TIGR, > unfortunately, > mostly I just left them with a huge "to do" list. :) > > Scott and Ramana will be coming to the April meeting to learn more > of the > ropes and take on their new roles as the JCVI representatives. I > hope you > will join me in welcoming them. > > Michelle > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From jane at ebi.ac.uk Tue Mar 4 01:59:14 2008 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 4 Mar 2008 09:59:14 +0000 (GMT) Subject: [Go] I'm back! Message-ID: Hi everyone - I'm finally back from maternity leave and have started to dredge through the mountain of email. I think I'm probably going to have to delete most of them unread if I ever want to do any work ever again, so if there's anything you think I should see, please email me to draw it to my attention! cheers, Jane Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From midori at ebi.ac.uk Tue Mar 4 02:26:31 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 4 Mar 2008 10:26:31 +0000 (GMT) Subject: [Go] Ontology development - February highlights Message-ID: Dear GO, The most recent monthly report on ontology content, for February 2008, is now available at: http://gocwiki.geneontology.org/index.php/Feb2008_ontology_report Ontology development highlights from Febuary: * David and Tanya have continued to clean up errors reported by Chris' QC script. The 'regulates' relationship itself is still on target for March 25th (http://wiki.geneontology.org/index.php/Regulation_Main_Page). * Work on sporulation will finish the revamp of 'sensu' terms (http://wiki.geneontology.org/index.php/Sporulation_Meeting_Notes). * Reorganization of electron transport terms continues. The working group will note where links between function and process terms can be made (http://wiki.geneontology.org/index.php/Electron_transport). * Disjoint violations in the process ontology have been corrected. In March, Jen will tackle the area of signal transduction, to identify both expert biologists and specific areas in GO that can be addressed. We will also continue work on links between function and process ontologies, which has begun with two pilot projects (one looking at one or a few biochemical pathways that are well curated in Reactome, and the other accompanying the electron transport work). We also still intend to turn attention to cross-products with the Cell ontology after the regulation work is secure. As usual, details of small- and medium-scale changes are available in the SourceForge Curator Requests tracker. Please contact us if you want to help out with ontology work in a particular area, or if you have any comments or questions about what's going on. Midori & David on behalf of GO's ontology developers From midori at ebi.ac.uk Tue Mar 4 02:42:54 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 4 Mar 2008 10:42:54 +0000 (GMT) Subject: [Go] Ontology development - February highlights (fwd) Message-ID: this time with the correct link ... ---------- Forwarded message ---------- Date: Tue, 4 Mar 2008 10:26:31 +0000 (GMT) From: Midori Harris To: GO Mailing List Subject: [Go] Ontology development - February highlights Dear GO, The most recent monthly report on ontology content, for February 2008, is now available at: http://wiki.geneontology.org/index.php?title=Feb2008_report Ontology development highlights from Febuary: * David and Tanya have continued to clean up errors reported by Chris' QC script. The 'regulates' relationship itself is still on target for March 25th (http://wiki.geneontology.org/index.php/Regulation_Main_Page). * Work on sporulation will finish the revamp of 'sensu' terms (http://wiki.geneontology.org/index.php/Sporulation_Meeting_Notes). * Reorganization of electron transport terms continues. The working group will note where links between function and process terms can be made (http://wiki.geneontology.org/index.php/Electron_transport). * Disjoint violations in the process ontology have been corrected. In March, Jen will tackle the area of signal transduction, to identify both expert biologists and specific areas in GO that can be addressed. We will also continue work on links between function and process ontologies, which has begun with two pilot projects (one looking at one or a few biochemical pathways that are well curated in Reactome, and the other accompanying the electron transport work). We also still intend to turn attention to cross-products with the Cell ontology after the regulation work is secure. As usual, details of small- and medium-scale changes are available in the SourceForge Curator Requests tracker. Please contact us if you want to help out with ontology work in a particular area, or if you have any comments or questions about what's going on. Midori & David on behalf of GO's ontology developers _______________________________________________ Go mailing list Go at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go From jblake at informatics.jax.org Tue Mar 4 07:48:08 2008 From: jblake at informatics.jax.org (jblake at informatics.jax.org) Date: Tue, 4 Mar 2008 10:48:08 -0500 (EST) Subject: [Go] I'm back! In-Reply-To: References: Message-ID: <3213.66.237.78.139.1204645688.squirrel@webmail.informatics.jax.org> whoopee Jane's back. Hi Jane, glad to hear your voice again. Judy > Hi everyone - I'm finally back from maternity leave and have started to > dredge through the mountain of email. I think I'm probably going to have > to delete most of them unread if I ever want to do any work ever again, so > if > there's anything you think I should see, please email me to draw it to my > attention! > > cheers, > > Jane > > > Dr Jane Lomax > GO Editorial Office > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridgeshire, UK > CB10 1SD > > p: +44 1223 492516 > f: +44 1223 494468 > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From tberardi at acoma.stanford.edu Thu Mar 6 16:16:11 2008 From: tberardi at acoma.stanford.edu (Tanya Berardini) Date: Thu, 6 Mar 2008 16:16:11 -0800 Subject: [Go] Alert: proposal to obsolete GO:0047859 (no annotations impacted) Message-ID: <8e22ab960803061616r134cb212uabdb133976c538a9@mail.gmail.com> The proposal has been made to obsolete dihydroxyphenylalanine ammonia-lyase activity ; GO:0047859 This term appears in the ec2go and metacyc2go mapping files. The reason for this proposal is that the corresponding EC reaction has been deleted from the EC. http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/3/1/11.html *** Unless objections are received by March 14, we will assume that you agree to this change. *** Thanks, Tanya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080306/c8138ac6/attachment.html From midori at ebi.ac.uk Thu Mar 13 01:46:32 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 13 Mar 2008 08:46:32 +0000 (GMT) Subject: [Go] March 12 managers call - minutes available Message-ID: Hello, The minutes from yesterday's GO Managers conference call are now on the wiki: http://wiki.geneontology.org/index.php/Managers_12March If you would like a particular issue to be discussed at the next managers' call, please contact the relevant manager(s): Reference Genomes: Pascale User Advocacy and Outreach: Jennifer and Jane Content Development: Midori and David Software: Chris For general management and budget issues, contact the GO PIs . Midori From keilbeck at genetics.utah.edu Thu Mar 13 11:55:45 2008 From: keilbeck at genetics.utah.edu (Karen Eilbeck) Date: Thu, 13 Mar 2008 12:55:45 -0600 Subject: [Go] GOC meeting fee update Message-ID: Hi all, For those of you attending the GOC and Ref Genome meetings in SLC next month, checks are to be made payable to the 'Department of Human Genetics'. Cheers, Karen From jimhu at tamu.edu Thu Mar 13 12:09:35 2008 From: jimhu at tamu.edu (Jim Hu) Date: Thu, 13 Mar 2008 14:09:35 -0500 Subject: [Go] GOC meeting fee update In-Reply-To: References: Message-ID: <7FECE58A-96FF-46D7-9310-CE53D6E1AE77@tamu.edu> Checks? How much? Did I miss this on the wiki? Jim On Mar 13, 2008, at 1:55 PM, Karen Eilbeck wrote: > Hi all, > For those of you attending the GOC and Ref Genome meetings in SLC next > month, checks are to be made payable to the 'Department of Human > Genetics'. > > Cheers, > Karen > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080313/8dcf6c01/attachment.html From jimhu at tamu.edu Thu Mar 13 12:10:25 2008 From: jimhu at tamu.edu (Jim Hu) Date: Thu, 13 Mar 2008 14:10:25 -0500 Subject: [Go] GOC meeting fee update In-Reply-To: References: Message-ID: Never mind, found it. On Mar 13, 2008, at 1:55 PM, Karen Eilbeck wrote: > Hi all, > For those of you attending the GOC and Ref Genome meetings in SLC next > month, checks are to be made payable to the 'Department of Human > Genetics'. > > Cheers, > Karen > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080313/6cf52040/attachment.html From jdeegan at ebi.ac.uk Fri Mar 14 04:41:58 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Fri, 14 Mar 2008 11:41:58 +0000 Subject: [Go] Muscle Biology Content Meeting Publication Message-ID: <47DA6486.6030104@ebi.ac.uk> Hi, Erika Feltrin and I have written a paper about the Muscle Biology Content Meeting, to be sent to BMC Medical Genomics. We would really appreciate any comments on the manuscript: http://www.ebi.ac.uk/~jdeegan/stored/musclepaper/muscle_paper_ver_1.doc We are also offering a small prize for anyone who can come up with a suitably cheezy title, including a bad pun on the word 'GO'. Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From cherry at stanford.edu Mon Mar 17 10:59:52 2008 From: cherry at stanford.edu (Mike Cherry) Date: Mon, 17 Mar 2008 10:59:52 -0700 Subject: [Go] daily SF digest emails References: Message-ID: <1B2D75AF-9EE1-47F8-A84C-14A8E8DB03AC@stanford.edu> With the change in the mailing lists I see a slight issue. In the past posts to the go-curator-tracker list were also sent to the full go list. I believe I can subscribe the go list to go-curator-tracker, or those that want to receive the SourceForge message can subscribe to that specific list. Reply to me and I'll summarize the results to the question, should the full GO list continue to receive the go-curator-tracker emails. -Mike Begin forwarded message: > From: Rama Balakrishnan > Date: March 17, 2008 10:40:38 AM PDT > To: SGD curators > Subject: daily SF digest emails > > Hi, > > I haven't received emails from the SF curator request tracker in the > last week (Julie hasn't either). Anybody else notice this? > > Thanks, > Rama From midori at ebi.ac.uk Mon Mar 17 11:42:40 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 17 Mar 2008 18:42:40 +0000 (GMT) Subject: [Go] daily SF digest emails In-Reply-To: <1B2D75AF-9EE1-47F8-A84C-14A8E8DB03AC@stanford.edu> References: <1B2D75AF-9EE1-47F8-A84C-14A8E8DB03AC@stanford.edu> Message-ID: Hi Mike, Unless you get a storm of opposition from others, I'd be inclined to continue sending the go-curator-tracker messages to the GO list -- the original reason for doing the digest emails was to provide some means, briefer and saner than sending *all* of the SF tracker-generated mail, of alerting anyone in GO to SF items that they might want to watch. m On Mon, 17 Mar 2008, Mike Cherry wrote: > With the change in the mailing lists I see a slight issue. In the > past posts to the go-curator-tracker list were also sent to the full > go list. > > I believe I can subscribe the go list to go-curator-tracker, or those > that want to receive the SourceForge message can subscribe to that > specific list. > > Reply to me and I'll summarize the results to the question, should the > full GO list continue to receive the go-curator-tracker emails. > > -Mike > > Begin forwarded message: > >> From: Rama Balakrishnan >> Date: March 17, 2008 10:40:38 AM PDT >> To: SGD curators >> Subject: daily SF digest emails >> >> Hi, >> >> I haven't received emails from the SF curator request tracker in the >> last week (Julie hasn't either). Anybody else notice this? >> >> Thanks, >> Rama > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From jimhu at tamu.edu Mon Mar 17 17:11:04 2008 From: jimhu at tamu.edu (Jim Hu) Date: Mon, 17 Mar 2008 19:11:04 -0500 Subject: [Go] Automated function prediction meeting at ISMB References: <47DED904.4060009@burnham.org> Message-ID: In case anyone is interested: Begin forwarded message: > From: Iddo Friedberg > Date: March 17, 2008 3:48:04 PM CDT > To: jimhu at tamu.edu > Subject: Thanks for the visit (and a request) > > Hi Jim, > > Thank you for taking the time to meet with me during my visit to > TAMU, and to show me your community annotation efforts. I was very > impressed, and it is my belief that community efforts teamed with > strong prediction algorithms are the way to make sense of the > increasing inundation of genomic material. > > > I would appreciate it if you could forward the following to any > interested people you might know, including relevant mailing lists. > It is a call for abstracts and participation at the Automated > Function Prediciton / Biospaiens meeting that will be held alongside > ISMB 2008. We are accepting abstracts fro contributed talks, posters > and mini tutorials by march 31. Of course, if you feel you or > someone in your lab has something to contribute, please do send it > in! > > Best, > > Iddo > > =============================== CUT HERE ============================= > Please feel free to forward this as necessary to the appropriate > people and lists. > > LOCALE: Toronto, Canada (ISMB 2008) > DATES: July 18-19, 2008 > > The Automated Function Prediction (AFP) SIG and the Biosapiens > European network of excellence are teaming up to hold a two-day > Special Interest Group (SIG) alongside ISMB 2008. > > The deluge of genomic information is challenging biologists to > annotate this data, from locating genes in the raw data through > predicting the function from protein sequence and structure. AFP and > Biosapiens share many common goals, and this year we have decided to > join forces for a SIG that will deal with a wide scope of gene, > protein, and genomic annotations. > > Abstracts for talks and posters will be accepted by March 31, 2008. > This year we are also considering mini-tutorial submissions. Please > see the AFP / Biosapiens site for more information. > > IMPORTANT DATES: > Talk, tutorial and poster abstracts due: March 31, 2008 > Notification of acceptance: April 20, 2008 > Final abstracts due: May 5, 2008 > AFP-Biosapiens SIG : July 18-19, 2008 > > FOR MORE INFORMATION: > http://2008.BioFunctionPrediction.org/ > > For inquiries, including sponsorship opportunities, please email: afpbiosap2008 at gmail.com > > > -- > Iddo Friedberg, Ph.D. > CALIT2, mail code 0440 > University of California, San Diego > 9500 Gilman Drive > La Jolla, CA 92093-0440, USA > T: +1 (858) 534-0570 > T: +1 (858) 646-3100 x3516 > http://iddo-friedberg.org ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080317/c09de1df/attachment-0001.html From jdeegan at ebi.ac.uk Tue Mar 18 03:24:55 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 18 Mar 2008 10:24:55 +0000 Subject: [Go] Ontology Editing Freeze Message-ID: <47DF9877.5080901@ebi.ac.uk> Hi, There is going to be an ontology editing freeze this week while we implement the following: - The new regulates relationships - Information at http://wiki.geneontology.org/index.php/Image:Regulates_documentation.doc - Questions to David Hill, Tanya Berardini, Chris Mungall dph at informatics.jax.org, tberardi at acoma.stanford.edu, cjm at fruitfly.org - The electron transport changes, including obsoletion of electron transport ; GO:0006118 - Information at http://wiki.geneontology.org/index.php/Changes_committed_on_25th_March%2C_2008 - Questions to Jennifer Deegan - jdeegan at ebi.ac.uk - The changes to the structure of the go/ontology directory - Information at http://wiki.geneontology.org/index.php/Ontology_CVS_Directory_Layout_Overhaul#Proposed_new_layout - Questions to Chris Mungall - cjm at fruitfly.org The ontology editing freeze will start at: Midnight PST, Tuesday, March 18th, 1 a.m. MST, Wednesday, March 19th, 2 a.m. CST, Wednesday, March 19th, 3 am EST, Wednesday, March 19th, 8 am GMT, Wednesday, March 19th, 9 a.m. CET, Wednesday, March 19th. The freeze will end at some point on Tuesday, March 25th, and Chris will mail to announce this. After the freeze, all edits must be on the .obo file in the new cvs 'editors' directory. Chris will send further details when he ends the freeze. Thanks, Jennifer From midori at ebi.ac.uk Tue Mar 18 03:29:45 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 18 Mar 2008 10:29:45 +0000 (GMT) Subject: [Go] Ontology Editing Freeze In-Reply-To: <47DF9877.5080901@ebi.ac.uk> References: <47DF9877.5080901@ebi.ac.uk> Message-ID: Time corrections (the US has gone onto daylight/summer time, but the UK and continental Europe have not): The ontology editing freeze will start at: Midnight PDT, Tuesday, March 18th, 1 a.m. MDT, Wednesday, March 19th, 2 a.m. CDT, Wednesday, March 19th, 3 am EDT, Wednesday, March 19th, 7 am GMT, Wednesday, March 19th, 8 a.m. CET, Wednesday, March 19th. On Tue, 18 Mar 2008, Jennifer Deegan (nee Clark) wrote: > Hi, > > There is going to be an ontology editing freeze this week while we > implement the following: > > - The new regulates relationships > - Information at > http://wiki.geneontology.org/index.php/Image:Regulates_documentation.doc > - Questions to David Hill, Tanya Berardini, Chris Mungall > dph at informatics.jax.org, tberardi at acoma.stanford.edu, cjm at > fruitfly.org > > - The electron transport changes, including obsoletion of electron > transport ; GO:0006118 > - Information at > http://wiki.geneontology.org/index.php/Changes_committed_on_25th_March%2C_2008 > - Questions to Jennifer Deegan - jdeegan at ebi.ac.uk > > - The changes to the structure of the go/ontology directory > - Information at > > http://wiki.geneontology.org/index.php/Ontology_CVS_Directory_Layout_Overhaul#Proposed_new_layout > - Questions to Chris Mungall - cjm at fruitfly.org > > The ontology editing freeze will start at: > Midnight PST, Tuesday, March 18th, > 1 a.m. MST, Wednesday, March 19th, > 2 a.m. CST, Wednesday, March 19th, > 3 am EST, Wednesday, March 19th, > 8 am GMT, Wednesday, March 19th, > 9 a.m. CET, Wednesday, March 19th. > > The freeze will end at some point on Tuesday, March 25th, and Chris > will mail to announce this. After the freeze, all edits must be on the > .obo file in the new cvs 'editors' directory. Chris will send further > details when he ends the freeze. > > Thanks, > > Jennifer > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From val at sanger.ac.uk Tue Mar 18 03:36:16 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Tue, 18 Mar 2008 10:36:16 +0000 Subject: [Go] Ontology Editing Freeze In-Reply-To: <47DF9877.5080901@ebi.ac.uk> References: <47DF9877.5080901@ebi.ac.uk> Message-ID: <47DF9B20.8050401@sanger.ac.uk> We currently still use the old AmiGO within GeneDB.Will the new regulates relationship be compatible with the old AmiGO.? We were waiting for the new AmiGO release to update, but I guess we would need to do this sooner. thanks val Jennifer Deegan (nee Clark) wrote: > Hi, > > There is going to be an ontology editing freeze this week while we >implement the following: > > - The new regulates relationships > - Information at >http://wiki.geneontology.org/index.php/Image:Regulates_documentation.doc > - Questions to David Hill, Tanya Berardini, Chris Mungall > dph at informatics.jax.org, tberardi at acoma.stanford.edu, cjm at >fruitfly.org > > - The electron transport changes, including obsoletion of electron >transport ; GO:0006118 > - Information at >http://wiki.geneontology.org/index.php/Changes_committed_on_25th_March%2C_2008 > - Questions to Jennifer Deegan - jdeegan at ebi.ac.uk > > - The changes to the structure of the go/ontology directory > - Information at > >http://wiki.geneontology.org/index.php/Ontology_CVS_Directory_Layout_Overhaul#Proposed_new_layout > - Questions to Chris Mungall - cjm at fruitfly.org > > The ontology editing freeze will start at: > Midnight PST, Tuesday, March 18th, > 1 a.m. MST, Wednesday, March 19th, > 2 a.m. CST, Wednesday, March 19th, > 3 am EST, Wednesday, March 19th, > 8 am GMT, Wednesday, March 19th, > 9 a.m. CET, Wednesday, March 19th. > > The freeze will end at some point on Tuesday, March 25th, and Chris >will mail to announce this. After the freeze, all edits must be on the >.obo file in the new cvs 'editors' directory. Chris will send further >details when he ends the freeze. > > Thanks, > > Jennifer > >_______________________________________________ >Go mailing list >Go at geneontology.org >http://fafner.stanford.edu/mailman/listinfo/go > > > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From cherry at stanford.edu Tue Mar 18 07:23:15 2008 From: cherry at stanford.edu (Mike Cherry) Date: Tue, 18 Mar 2008 07:23:15 -0700 Subject: [Go] Major shutdown of Geneontology.Org In-Reply-To: References: <47DF9877.5080901@ebi.ac.uk> Message-ID: The GO CVS will be down from 6am Wednesday to 6pm Pacific time. This is so the A/C in our computer rooom can be fixed. So the freeze will extend the freeze. The GO www.geneontology.org site will also be down. We hope to keep AmiGO, FTP and Web CVS up. This is a major shutdown so we're unsure how much will work as the whole machine room will have its cooling and power turned off. -Mike On Mar 18, 2008, at 3:29 AM, Midori Harris wrote: > Time corrections (the US has gone onto daylight/summer time, but the > UK > and continental Europe have not): > > The ontology editing freeze will start at: > Midnight PDT, Tuesday, March 18th, > 1 a.m. MDT, Wednesday, March 19th, > 2 a.m. CDT, Wednesday, March 19th, > 3 am EDT, Wednesday, March 19th, > 7 am GMT, Wednesday, March 19th, > 8 a.m. CET, Wednesday, March 19th. > > On Tue, 18 Mar 2008, Jennifer Deegan (nee Clark) wrote: > >> Hi, >> >> There is going to be an ontology editing freeze this week while we >> implement the following: >> >> - The new regulates relationships >> - Information at >> http://wiki.geneontology.org/index.php/Image:Regulates_documentation.doc >> - Questions to David Hill, Tanya Berardini, Chris Mungall >> dph at informatics.jax.org, tberardi at acoma.stanford.edu, cjm at >> fruitfly.org >> >> - The electron transport changes, including obsoletion of electron >> transport ; GO:0006118 >> - Information at >> http://wiki.geneontology.org/index.php/Changes_committed_on_25th_March%2C_2008 >> - Questions to Jennifer Deegan - jdeegan at ebi.ac.uk >> >> - The changes to the structure of the go/ontology directory >> - Information at >> >> http://wiki.geneontology.org/index.php/Ontology_CVS_Directory_Layout_Overhaul#Proposed_new_layout >> - Questions to Chris Mungall - cjm at fruitfly.org >> >> The ontology editing freeze will start at: >> Midnight PST, Tuesday, March 18th, >> 1 a.m. MST, Wednesday, March 19th, >> 2 a.m. CST, Wednesday, March 19th, >> 3 am EST, Wednesday, March 19th, >> 8 am GMT, Wednesday, March 19th, >> 9 a.m. CET, Wednesday, March 19th. >> >> The freeze will end at some point on Tuesday, March 25th, and Chris >> will mail to announce this. After the freeze, all edits must be on >> the >> .obo file in the new cvs 'editors' directory. Chris will send further >> details when he ends the freeze. >> >> Thanks, >> >> Jennifer >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From jdeegan at ebi.ac.uk Tue Mar 18 07:28:42 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 18 Mar 2008 14:28:42 +0000 Subject: [Go] Major shutdown of Geneontology.Org In-Reply-To: References: <47DF9877.5080901@ebi.ac.uk> Message-ID: <47DFD19A.4000305@ebi.ac.uk> Hi Mike, Thanks for the warning on the machine room shutdown. We should be able to work round this, as our ontology freeze can just be extended by a few hours if needed. Thanks, Jen From cherry at stanford.edu Tue Mar 18 09:28:30 2008 From: cherry at stanford.edu (Mike Cherry) Date: Tue, 18 Mar 2008 09:28:30 -0700 Subject: [Go] Fwd: Calling all Curators References: <29DEEF3E-C3B9-4488-A68A-73DAB1287FF8@stanford.edu> Message-ID: <59E19E7A-B4CC-4B20-A268-DE4424F2BE57@stanford.edu> Below are two messages for Scientific Curators that do manual curation. The first call is this Thursday at 9AM pacific time. -Mike Begin forwarded message: > From: Mike Cherry > Date: March 17, 2008 9:57:09 AM PDT > To: GO Annotation list > Subject: First Curator Call > > In light of spring/easter vacations I'd like to hold our first > teleconference this Thursday (March 20) noon-1PM Eastern (9-10A > Pacific & 4-5P UK). I know everyone cannot make that time. > > It seems that Tuesday from noon-1P might be generally a good time > for the future. > > Anyway, this first call will be more organizational in nature than > future calls. Please call into the following numbers with the > listed access code. > > US: 1-866-365-4406 > access number: 7237541 > > UK: 08004960580 > access number: 7237541 > > I look forward to our discussions. > > -Mike > Begin forwarded message: > From: Mike Cherry > Date: March 14, 2008 8:00:04 AM PDT > To: annotation at geneontology.org > Cc: refgenome at geneontology.org > Subject: Calling all Curators > > This is to all scientific curators at all model organism databases > (MOD). I would like to begin a monthly teleconference, which could > also include a video conference later this year. There are several > forms of interaction between individual curators and between MODs > already however a regular frequent forum is needed to continue > making progress. In particular, we need to continually work to > reduce variability between the annotations created by different > MODs, and by different curators. This is NOT for just the GOC and > those that normally are involved in GOC conferences. This is for > all MOD curators. The MODs are become closer in their procedures as > a result of the discussions occurring as part of the GOC. However, > there is a lot more than can be done to unify all curators at all > the MODs. Thus this call will not be a GOC call on picking the best > GO term -- that may happen a little but the intent is to include > broader curation activities. > > While this meeting will be started by the Gene Ontology Consortium I > want this to grow to all scientific curators that create manual > annotations. This conference call is not about making software that > does annotation, but would include discussions of software to assist > curators. This is not a conference discussion of software > practices, there are enough venues for these discussions. > > The video part will be a future addition as I feel that these > meetings will be more productive if we can see each other, we are > discussing the human activity of curation and a discussion works > better face to face. I am very interested in having a video > component as I believe this will help the meetings provide an even > better connection. We will be able to use WebEx to share slides and > web screens. This monthly conference will start as a conference > call and with time we can work out the technical details for the > video and/or Skype. As you'll see below we could have greater than > 50 people on these calls. > > The biggest issue is scheduling. I would like to propose that two > regular times are schedule switch monthly between the two times. > Its obvious that it is difficult to get California and the UK on a > call at the same time during normal business hours. Requiring > folks, at least initially, to call in from home is a big negative. > Thus I have created a doodle pool. Please ignore the dates, rather > use this as just days of the week. All times in the poll should be > stated as Eastern time. The result of this pool is to identify two > different times that would work for the most people. This assumes > that most will only connect once every two months. > > http://www.doodle.ch/eambfifz3ip5v2sv > > While a core number of the participants will be from the GOC. I want > the group include a diverse number of curators. Other topics like > sequence annotation both DNA and protein, phenotype annotation, and > of course general topics appropriate for any curation group for > example how do you prioritize the literature and how do we work with > journals in a more productive manner. > > The intension is for ALL MOD curators to be involved, not just the > one or two people that currently represent a group at the GOC. I > feel it will be a failure if this is just for the usual crowd. If > this can get a diverse group interacting then perhaps we will need > to have additional regular calls. The goal is to foster interactions > between the community of curators that exist around the world. GO > already has mechanisms for communication that work, but could always > be better. There are many others that are not connected either > because they don't belong to the GO club (some people feel this way) > or they personally don't connect with GO because their project > already has others participating in the GOC. We already have a > start on a broader group. The Annotation email list has 106 > addresses, something about 45 are addresses of people that have > attended a GOC meeting. That leaves 61 addresses that are either > not connected to GOC or are other curators at GOC projects but have > not attended one of the Consortium meetings. > > After each teleconf there will be a brief summary sent out (not sure > which lists to include yet) and that email may get even more people > interacting and interested in the next call. > > Because scientific curators are professional staff members we need > to raise the requirement for interactions with the goal of being > more efficient, have less variability between the annotations, and > to have more understanding of what others do. Interacting with > other groups to promote an exchange of information will result in > more effective operations and more standardized results. This goes > beyond GOC and the MODs as the curation profession needs to work > together and decrease the amount of isolation that I believe exists. > I certainly do not believe that this is done on purpose but rather > the interaction has not been made simpler. For sure there are lots > of interactions already, but I believe there could be many more. The > GOC is a great example of how things change when people talk to each > other. The hope is that curators from projects funded by NIH, NSF, > USDA, DOE, BBSRC, EBI, ... and industry will come together at least > every two months. Curators already, by definition, have a lot of > interaction with the communities they server. We need to add a > reward system where they are also judged by the amount of > interaction with other curators. Some already do a lot of this, many > don't do as much as they should -- we can help this happen. I'm > thinking of contacting the PIs of the MODs and strongly encourage > their staff to participate. > > Please fill out the doodle poll (URL above). I propose that the annotation at geneontology.org > list can be used for this new interaction. That list already has > many curators subscribed plus it is not a very heavily used list at > the moment. After a week or two I'll get back to you with the time > of our first conference. > > -Mike > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080318/db3c3b4e/attachment-0001.html From midori at ebi.ac.uk Tue Mar 18 09:00:19 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 18 Mar 2008 16:00:19 UT Subject: [Go] [Go-curator-tracker] SourceForge Update Message-ID: <200803181600.m2IG0JX1557317@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080318/8d6f2054/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080318/8d6f2054/attachment.pl -------------- next part -------------- _______________________________________________ Go-curator-tracker mailing list Go-curator-tracker at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go-curator-tracker From mgiglio at som.umaryland.edu Tue Mar 18 12:38:39 2008 From: mgiglio at som.umaryland.edu (Gwinn Giglio, Michelle) Date: Tue, 18 Mar 2008 15:38:39 -0400 Subject: [Go] new documentation for ISS and its subcodes Message-ID: Hello all, Attached you will find a draft of the new documentation for ISS and its subcodes (ISA, ISO, and ISM). This document has been discussed and approved by the evidence committee. Please take a look. Any comments or suggestions you have should be sent no later then Wednesday March 26th. This will then give us enough time to make changes and get the final version on the GO website by April 1st (which is the date we put in the newsletter for these codes to go live). Thanks very much, Michelle -------------- next part -------------- A non-text attachment was scrubbed... Name: new_ISS_documentation.doc Type: application/msword Size: 60928 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20080318/1a847446/attachment-0001.doc From jdeegan at ebi.ac.uk Wed Mar 19 02:55:01 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Wed, 19 Mar 2008 09:55:01 +0000 Subject: [Go] ontology freeze Message-ID: <47E0E2F5.8090405@ebi.ac.uk> Hi, Just a quick reminder that an ontology editing freeze is now in force. Please do not edit the ontologies until Chris writes with further information. Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From cherry at stanford.edu Wed Mar 19 04:46:11 2008 From: cherry at stanford.edu (Mike Cherry) Date: Wed, 19 Mar 2008 04:46:11 -0700 Subject: [Go] ontology freeze In-Reply-To: <47E0E2F5.8090405@ebi.ac.uk> References: <47E0E2F5.8090405@ebi.ac.uk> Message-ID: <0FE42383-2118-4D5F-96F8-D3095C79669B@stanford.edu> Also the Stanford servers will be down starting in about 90 minutes. We will be able to keep AmiGO, FTP, and CVS Web up. However, the writable CVS, www.geneontology.org and all the GO email lists will be down. You can continue to send emails to the lists, they will be delivered after the mailserver is online. We anticipate this downtime to potentially last until 6PM Pacific/9PM Eastern this evening. -MIke On Mar 19, 2008, at 2:55 AM, Jennifer Deegan (nee Clark) wrote: > Hi, > > Just a quick reminder that an ontology editing freeze is now in force. > Please do not edit the ontologies until Chris writes with further > information. > > Thanks, > > Jen > > -- > Jennifer Deegan (nee Clark) > EMBL-European Bioinformatics Institute > Gene Ontology Consortium > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From rhee at acoma.stanford.edu Tue Mar 18 22:23:01 2008 From: rhee at acoma.stanford.edu (Sue Rhee) Date: Tue, 18 Mar 2008 22:23:01 -0700 Subject: [Go] [Fwd: book invitation] Message-ID: <47E0A335.7040405@acoma.stanford.edu> Is anyone interested in writing a book chapter on GO? I don't have the time nor energy to do it this year. Sue -------- Original Message -------- Subject: book invitation Date: Tue, 18 Mar 2008 14:44:41 -0500 From: Xu, Dong (UMC) To: CC: Popescu, Mihail Dear Sue, We are editing a book entitled "Data mining applications using ontologies in biomedicine", to be published by Artech House. Given your expertise on the subject, we would like to invite you and/or your co-workers to contribute a chapter to the book. A possible title of your chapter may be "Gene Ontology (GO)", especially given your role in the GO consortium. The goal of this book is to introduce the cutting-edge developments and applications of bio-ontologies, including the theoretical foundations and examples of ontologies, applications of ontologies in biomedicine (from molecular levels to clinical levels), and technological infrastructure for bio-ontologies. We have selected the topics carefully (see the proposed chapters in the attachment) so that the book would be useful to a broad readership, including students, postdoctoral fellows, professional practitioners, as well as bioinformatics/medical informatics experts. We expect that the book can be used as a textbook for upper undergraduate-level or beginning graduate-level bioinformatics/medical informatics courses. We do not assume extensive prior knowledge for reading this book. A dedicated reader with a college degree in computational, biological or physical science should be able to follow the book without much difficulty. Chapters should be written according to the guideline of the publisher (see attached Author's guide). We expect that your chapter is around 7,000 words, together with figures and tables. On the other hand, we have some flexibility in terms of the length of your chapter. Completed manuscripts should be returned to us by the end of September 2008. If you are interested in contributing to the book, please reply as soon as possible, and we can discuss the title and what your contribution may consists of in more detail. Feel free to suggest alternatives or new chapters/authors if you believe an important area has been omitted. Best wishes, Mihail Popescu and Dong Xu -- Sue Rhee Staff Scientist Carnegie Institution, Department of Plant Biology 260 Panama Street, Stanford, CA 94305 Email: (650) 325-1521 x251 Fax: (650) 325-6857 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080318/10bb39e6/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: chapters.DOC Type: application/msword Size: 44032 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20080318/10bb39e6/attachment-0001.dot -------------- next part -------------- A non-text attachment was scrubbed... Name: AHAuGuide.pdf Type: application/octet-stream Size: 1326739 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20080318/10bb39e6/attachment-0001.obj From midori at ebi.ac.uk Wed Mar 19 07:34:09 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 19 Mar 2008 14:34:09 +0000 (GMT) Subject: [Go] Muscle Biology Content Meeting Publication In-Reply-To: <47DA6486.6030104@ebi.ac.uk> References: <47DA6486.6030104@ebi.ac.uk> Message-ID: Hi, The manuscript looks well organized and summarizes the changes nicely. I've made some comments and suggestions in the attached version. m On Fri, 14 Mar 2008, Jennifer Deegan (nee Clark) wrote: > Hi, > > Erika Feltrin and I have written a paper about the Muscle Biology > Content Meeting, to be sent to BMC Medical Genomics. > We would really appreciate any comments on the manuscript: > http://www.ebi.ac.uk/~jdeegan/stored/musclepaper/muscle_paper_ver_1.doc > > We are also offering a small prize for anyone who can come up with a > suitably cheezy title, including a bad pun on the word 'GO'. > > Thanks, > > Jen > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: muscle_paper_ver_1a.doc Type: application/msword Size: 64512 bytes Desc: Url : http://fafner.stanford.edu/pipermail/go/attachments/20080319/c366c086/attachment-0001.doc From cjm at fruitfly.org Wed Mar 19 23:09:08 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 19 Mar 2008 23:09:08 -0700 Subject: [Go] Muscle Biology Content Meeting Publication In-Reply-To: References: <47DA6486.6030104@ebi.ac.uk> Message-ID: <0C3104F4-14C5-4369-AB93-47E82BF1900D@fruitfly.org> hmm, seem to have lost my edits.. ah well > Our revised ontology structure should facilitate the interpretation > of high-throughput experiments (e.g. gene expression microarrays) > in the area of muscle science and muscular disease. Such studies > yield a very large number of data points and this makes it a > challenge to determine which genes specifically contribute to a > disease phenotype [17]. However the use of GO ontologies and > annotations within GO-related statistical analysis tools [18] > should greatly simplify this analysis . So I think this is very true, but what would make this highly compelling would be some examples. Perhaps: * A reference genome gene that is muscle related, graphs before and after the ontology change * Some actual high throughput experimental results, enriched, before and after Of course changes will only be reflected in the upper level grouping of results, as people may not have time to annotate to the newer more specific terms I can help with this, given a gene list. On Mar 19, 2008, at 7:34 AM, Midori Harris wrote: > Hi, > > The manuscript looks well organized and summarizes the changes > nicely. I've made some comments and suggestions in the attached > version. > > m > > On Fri, 14 Mar 2008, Jennifer Deegan (nee Clark) wrote: > >> Hi, >> >> Erika Feltrin and I have written a paper about the Muscle Biology >> Content Meeting, to be sent to BMC Medical Genomics. >> We would really appreciate any comments on the manuscript: >> http://www.ebi.ac.uk/~jdeegan/stored/musclepaper/ >> muscle_paper_ver_1.doc >> >> We are also offering a small prize for anyone who can come up with a >> suitably cheezy title, including a bad pun on the word 'GO'. >> >> Thanks, >> >> Jen >> >> >> > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From midori at ebi.ac.uk Wed Mar 19 09:00:18 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 19 Mar 2008 16:00:18 UT Subject: [Go] [Go-curator-tracker] SourceForge Update Message-ID: <200803191600.m2JG0I61285148@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080319/ee696a26/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080319/ee696a26/attachment.ksh -------------- next part -------------- _______________________________________________ Go-curator-tracker mailing list Go-curator-tracker at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go-curator-tracker From midori at ebi.ac.uk Thu Mar 20 03:15:48 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 20 Mar 2008 10:15:48 +0000 (GMT) Subject: [Go] new documentation for ISS and its subcodes In-Reply-To: References: Message-ID: Hi Michelle, This looks really good; thanks! In the attached, I've made some tiny corrections (typos and the like). Midori On Tue, 18 Mar 2008, Gwinn Giglio, Michelle wrote: > > > Hello all, > > Attached you will find a draft of the new documentation for ISS and its > subcodes (ISA, ISO, and ISM). > > This document has been discussed and approved by the evidence committee. > Please take a look. Any comments or suggestions you have should be sent no > later then Wednesday March 26th. This will then give us enough time to make > changes and get the final version on the GO website by April 1st (which is > the date we put in the newsletter for these codes to go live). > > Thanks very much, > > Michelle > > -------------- next part -------------- A non-text attachment was scrubbed... Name: new_ISS_documentation-mah.doc Type: application/msword Size: 71680 bytes Desc: Url : http://fafner.stanford.edu/pipermail/go/attachments/20080320/21e65e7d/attachment-0001.doc From adiehl at informatics.jax.org Thu Mar 20 04:30:45 2008 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Thu, 20 Mar 2008 11:30:45 +0000 Subject: [Go] Muscle Biology Content Meeting Publication In-Reply-To: <0C3104F4-14C5-4369-AB93-47E82BF1900D@fruitfly.org> References: <47DA6486.6030104@ebi.ac.uk> <0C3104F4-14C5-4369-AB93-47E82BF1900D@fruitfly.org> Message-ID: <47E24AE5.8040907@informatics.jax.org> Jen and Erika, Starting with Midori's revision, I made some changes of my own, indicated by the track changes. I removed a number of superfluous commas and added some too, converting all series to the "Oxford comma," since about half were and half were not using it. I also changed a few words to eliminate repetitive use of some words in particular paragraphs and made a few other changes as well. One idea to address Chris' comment regarding adding an example of concrete improvement would be to take the set of muscle genes (from the 172 you identified) that overlap with the Reference Genome genes and ask Mary Dolan to graph their annotations before and after the muscle biology changes to the ontologies were implemented. You don't even have to mention that these are Reference Genome genes (or just provide a URL reference to the RGG project page), but since they are, they should have a good bit of annotation already. Even if this annotation is not to new terms introduced in this revision, it should (hopefully) illustrate the improved structure of the ontology. You could prune off not muscle biology annotation to simplify the graphs as well. Thanks, Alex Chris Mungall wrote: > hmm, seem to have lost my edits.. ah well > > >> Our revised ontology structure should facilitate the interpretation >> of high-throughput experiments (e.g. gene expression microarrays) >> in the area of muscle science and muscular disease. Such studies >> yield a very large number of data points and this makes it a >> challenge to determine which genes specifically contribute to a >> disease phenotype [17]. However the use of GO ontologies and >> annotations within GO-related statistical analysis tools [18] >> should greatly simplify this analysis . >> > > > So I think this is very true, but what would make this highly > compelling would be some examples. Perhaps: > > * A reference genome gene that is muscle related, graphs before and > after the ontology change > * Some actual high throughput experimental results, enriched, before > and after > > Of course changes will only be reflected in the upper level grouping > of results, as people may not have time to annotate to the newer more > specific terms > > I can help with this, given a gene list. > > On Mar 19, 2008, at 7:34 AM, Midori Harris wrote: > > >> Hi, >> >> The manuscript looks well organized and summarizes the changes >> nicely. I've made some comments and suggestions in the attached >> version. >> >> m >> >> On Fri, 14 Mar 2008, Jennifer Deegan (nee Clark) wrote: >> >> >>> Hi, >>> >>> Erika Feltrin and I have written a paper about the Muscle Biology >>> Content Meeting, to be sent to BMC Medical Genomics. >>> We would really appreciate any comments on the manuscript: >>> http://www.ebi.ac.uk/~jdeegan/stored/musclepaper/ >>> muscle_paper_ver_1.doc >>> >>> We are also offering a small prize for anyone who can come up with a >>> suitably cheezy title, including a bad pun on the word 'GO'. >>> >>> Thanks, >>> >>> Jen >>> >>> >>> >>> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 -------------- next part -------------- A non-text attachment was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080320/43cd501f/attachment.pl From midori at ebi.ac.uk Thu Mar 20 09:00:19 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 20 Mar 2008 16:00:19 UT Subject: [Go] [Go-curator-tracker] SourceForge Update Message-ID: <200803201600.m2KG0Ja1537100@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080320/43cd501f/attachment-0001.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080320/43cd501f/attachment-0001.pl -------------- next part -------------- _______________________________________________ Go-curator-tracker mailing list Go-curator-tracker at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go-curator-tracker From rama at genome.stanford.edu Thu Mar 20 12:24:11 2008 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Thu, 20 Mar 2008 12:24:11 -0700 Subject: [Go] new documentation for ISS and its subcodes In-Reply-To: References: Message-ID: <549D68A1-4539-4674-888E-939A8F6A89BF@genome.stanford.edu> Hi Michelle, This looks very good. I have one minor comment. I am not sure if the following belongs to the evidence code documentation or if it shd be added to the GO annotation file format page. Up to you. For ISA and ISO- Entry in the 'with' column is mandatory for ISA/ISO. Annotations in the gene_associations file using ISA/ISO evidence codes and with out identifiers in the 'with' column will be filtered out by the Annotation File Format Quality Control script. Thanks, Rama On Mar 20, 2008, at 3:15 AM, Midori Harris wrote: > Hi Michelle, > > This looks really good; thanks! In the attached, I've made some tiny > corrections (typos and the like). > > Midori > > On Tue, 18 Mar 2008, Gwinn Giglio, Michelle wrote: > >> >> >> Hello all, >> >> Attached you will find a draft of the new documentation for ISS and >> its >> subcodes (ISA, ISO, and ISM). >> >> This document has been discussed and approved by the evidence >> committee. >> Please take a look. Any comments or suggestions you have should be >> sent no >> later then Wednesday March 26th. This will then give us enough >> time to make >> changes and get the final version on the GO website by April 1st >> (which is >> the date we put in the newsletter for these codes to go live). >> >> Thanks very much, >> >> Michelle >> > mah.doc>_______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From midori at ebi.ac.uk Fri Mar 21 09:00:20 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 21 Mar 2008 16:00:20 UT Subject: [Go] SourceForge Update Message-ID: <200803211600.m2LG0Ks1264873@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080321/f39a49cb/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080321/f39a49cb/attachment.pl From midori at ebi.ac.uk Sat Mar 22 09:00:17 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 22 Mar 2008 16:00:17 UT Subject: [Go] SourceForge Update Message-ID: <200803221600.m2MG0HO1062206@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080322/f54c00dd/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080322/f54c00dd/attachment.pl From ma11 at gen.cam.ac.uk Sun Mar 23 07:44:09 2008 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Sun, 23 Mar 2008 14:44:09 +0000 Subject: [Go] Muscle Biology Content Meeting Publication In-Reply-To: <47E24AE5.8040907@informatics.jax.org> References: <47DA6486.6030104@ebi.ac.uk> <0C3104F4-14C5-4369-AB93-47E82BF1900D@fruitfly.org> <47E24AE5.8040907@informatics.jax.org> Message-ID: <6CDC1903-C8FD-40FF-BBBF-A165A6CB3B3A@gen.cam.ac.uk> Hi all I attach further edits on top of Alex's version. Mostly linguistic. I suggest that all GO terms and relationships are in courier font without quotes. Makes them easy to distinguish from text Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: muscle_paper_ver_1a_addMA.doc Type: application/applefile Size: 387 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20080323/a0f155bd/attachment-0001.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: muscle_paper_ver_1a_addMA.doc Type: application/octet-stream Size: 78848 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20080323/a0f155bd/attachment-0001.obj From midori at ebi.ac.uk Mon Mar 24 09:00:17 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 24 Mar 2008 16:00:17 UT Subject: [Go] SourceForge Update Message-ID: <200803241600.m2OG0Ik1559010@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080324/af889898/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080324/af889898/attachment.pl From cjm at fruitfly.org Mon Mar 24 13:41:48 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Mon, 24 Mar 2008 13:41:48 -0700 Subject: [Go] Attn DB admins : Introduction of New Relationship Types in GO (March 25, 2008) References: <8e22ab960802261404r517f7f27hdba941e10c432ee4@mail.gmail.com> Message-ID: <3BE4AC46-8B55-4DF9-AE9D-5D59CCA7C34B@fruitfly.org> Hi all I'm contacting you because your name is listed as being one of the technical contacts for a database that is affiliated with the GO consortium[*]. As previously announced on the gofriends list, the Gene Ontology is introducing 3 new relations: regulates, negatively_regulates and positively_regulates. This requires no changes to the logic of any software or databases that use the GO. However, any special purpose code or configurations for rendering relations as icons, images or short symbols may need changed. If you wish to use the same SVGs as oboedit or the same pngs/gifs as AmiGO, you can download any of the icons here: http://obofoundry.org/ro/icons/ See the email below for full details If you had not previously received notice of this change and need more time to test let me know, otherwise the new relations will go live this week. Let me know if you have any other questions -- Chris [*] See: http://wiki.geneontology.org/index.php/External_Database_Contact_Info Begin forwarded message: > From: "Tanya Berardini" > Date: February 26, 2008 2:04:24 PM PST > To: "GO LIST" , gofriends at genome.stanford.edu > Subject: [gofriends] SECOND ANNOUNCEMENT: Introduction of New > Relationship Types in GO (March 25, 2008) > > Please note that the name of the file to be used for testing has > been updated. > > GO Consortium members: Please let us know when you have > successfully tested loading the new files. > > ------------- > > We are pleased to announce that The Gene Ontology Consortium will > introduce three new relationship types -- regulates, > negatively_regulates and positively_regulates -- into the Biological > Process ontology. > > For some time now, the GO content developers have been aware that > regulatory processes are not necessarily integral to the processes (as > previously indicated by the use of the 'part_of' relation) that they > regulate. Nevertheless, regulatory processes have been represented as > part_of the processes they regulate. We have long intended to replace > these part_of relationships with a new relationship type called > 'regulates'. We are now in a position to make this replacement. > > Ontology developers have thoroughly reviewed the relationships > involving regulatory processes and their targets to ensure internal > consistency. If a term 'regulation of process X' exists in the > ontology, it must be a valid subtype of 'regulation of biological > process', and must have a part_of relationship (which will be > transformed into one of the 'regulates' relationships) with 'process > X' or be a valid subtype of another regulatory process. > > We have also introduced two new high-level regulation terms, > 'regulation of molecular function' (for example, 'regulation of > cyclase activity') and 'regulation of biological quality' (for > example, 'regulation of blood pressure'), to represent processes that > regulate the activity of gene products and processes that regulate > measurable biological attributes, respectively. Regulation of > molecular function terms have been aligned with the corresponding > terms in the molecular function ontology. > > WE PLAN TO REPLACE THE CURRENT 'part_of' RELATIONSHIPS IN THE ONTOLOGY > WITH THE NEW 'regulates' RELATIONSHIP ON MARCH 25,2008. > > Software developers should ensure that their procedures for loading > the ontologies into their resources are compatible with these changes > by this date. Below is an example of a current OBO 1.2 stanza for a > regulates term and a new stanza with the regulates relationship in > place. > > EXAMPLES OF CURRENT STANZAS > > [Term] > id: GO:0000019 > name: regulation of mitotic recombination > namespace: biological_process > def: "Any process that modulates the frequency, rate or extent of DNA > recombination during mitosis." [GOC:go_curators] > narrow_synonym: "regulation of recombination within rDNA repeats" [] > is_a: GO:0000018 ! regulation of DNA recombination > relationship: part_of GO:0006312 ! mitotic recombination > > [Term] > id: GO:0045596 > name: negative regulation of cell differentiation > namespace: biological_process > def: "Any process that stops, prevents or reduces the frequency, > rate or extent of cell differentiation." [GOC:go_curators] > subset: gosubset_prok > synonym: "down regulation of cell differentiation" EXACT [] > synonym: "down-regulation of cell differentiation" EXACT [] > synonym: "downregulation of cell differentiation" EXACT [] > synonym: "inhibition of cell differentiation" NARROW [] > is_a: GO:0045595 ! regulation of cell differentiation > is_a: GO:0048523 ! negative regulation of cellular process > is_a: GO:0051093 ! negative regulation of developmental process > EXAMPLES OF NEW STANZAS > > [Term] > id: GO:0000019 > name: regulation of mitotic recombination > namespace: biological_process > def: "Any process that modulates the frequency, rate or extent of DNA > recombination during mitosis." [GOC:go_curators] > synonym: "regulation of recombination within rDNA repeats" NARROW [] > is_a: GO:0000018 ! regulation of DNA recombination > relationship: regulates GO:0006312 ! mitotic recombination > [Term] > id: GO:0045596 > name: negative regulation of cell differentiation > namespace: biological_process > def: "Any process that stops, prevents or reduces the frequency, > rate or extent of cell differentiation." [GOC:go_curators] > subset: gosubset_prok > synonym: "down regulation of cell differentiation" EXACT [] > synonym: "down-regulation of cell differentiation" EXACT [] > synonym: "downregulation of cell differentiation" EXACT [] > synonym: "inhibition of cell differentiation" NARROW [] > is_a: GO:0045595 ! regulation of cell differentiation > is_a: GO:0048523 ! negative regulation of cellular process > is_a: GO:0051093 ! negative regulation of developmental process > relationship: negatively_regulates GO:0030154 ! cell differentiation > > The regulates relationship is transitive over both the is_a and > part_of relationships. > > is_a transitivity: If process B exists in the GO biological process > ontology and it is an is_a child of process A then any process that > regulates process B also regulates process A. > > part_of transitivity: If process Y exists in the GO biological > process ontology and it is a part_of child of process X then any > process that regulates process Y also regulates process X. > > We strongly suggest that you test your loading scripts to ensure that > your database loads execute correctly. There is a test OBO 1.2 file > available at: > > /go/scratch/regulates_relations_examples/ > go_regtest_withPosNeg_noPF_noXP.obo > > Please feel free to contact us with any questions or concerns about > this change. > > Sincerely, > > Tanya Berardini > David Hill > Chris Mungall > on behalf of the GO Consortium From midori at ebi.ac.uk Tue Mar 25 04:25:13 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 25 Mar 2008 11:25:13 +0000 (GMT) Subject: [Go] Muscle Biology Content Meeting Publication Message-ID: further edits in attached ... and a note to check whether the journal will allow Michael's suggestion about fonts I've also incremented the file name to '1b'; this has my first round, then Alex's, Michael's, and my second round of edits. m -------------- next part -------------- A non-text attachment was scrubbed... Name: muscle_paper_ver_1b.doc Type: application/octet-stream Size: 71680 bytes Desc: Url : http://fafner.stanford.edu/pipermail/go/attachments/20080325/c68e9e71/attachment-0001.obj -------------- next part -------------- On 25 Mar 2008, at 11:05 am, Midori Harris wrote: > > > ---------- Forwarded message ---------- > Date: Sun, 23 Mar 2008 14:44:09 +0000 > From: Michael Ashburner > To: Alexander Diehl > Cc: go list > Subject: Re: [Go] Muscle Biology Content Meeting Publication > > Hi all > > I attach further edits on top of Alex's version. Mostly linguistic. > I suggestthat all GO terms > and relationships are in courier font without quotes. Makes them > easy todistinguish from text > > Michael________________________________ > _______________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From pgaudet at northwestern.edu Tue Mar 25 05:39:26 2008 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Tue, 25 Mar 2008 08:39:26 -0400 Subject: [Go] Muscle Biology Content Meeting Publication In-Reply-To: References: Message-ID: <47E8F27E.60708@northwestern.edu> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080325/9e0c82b4/attachment.html From midori at ebi.ac.uk Tue Mar 25 06:08:57 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 25 Mar 2008 13:08:57 +0000 (GMT) Subject: [Go] secretory pathway (SF 1912842) Message-ID: Dear GO, Questions have arisen about the process term 'secretory pathway' (GO:0045045). At first the aim was to improve the definition, but upon further discussion we're now leaningtowards making the term obsolete. Could people take a look at the SourceForge item and let us know if there's a case for keeping the term? If no arguments in its favor emerge, I'll send the formal obsoletion warning email in a few days. https://sourceforge.net/tracker/index.php?func=detail&aid=1912842&group_id=36855&atid=440764 Thanks, Midori From midori at ebi.ac.uk Tue Mar 25 09:00:17 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 25 Mar 2008 16:00:17 UT Subject: [Go] SourceForge Update Message-ID: <200803251600.m2PG0HD1328039@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080325/19bb8e5f/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080325/19bb8e5f/attachment.pl From jdeegan at ebi.ac.uk Tue Mar 25 09:09:05 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 25 Mar 2008 16:09:05 +0000 Subject: [Go] ontology editing freeze lifted Message-ID: <47E923A1.6060906@ebi.ac.uk> Hi, The 'regulates' relationships, the electron transport changes, and the new cvs layout have been implemented, and the ontology editing freeze is now over. For those who edit the ontologies, please now only edit the ontology file go/ontology/editors/gene_ontology_write.obo See this page for further details of the cvs layout changes: http://wiki.geneontology.org/index.php/Thaw_Mail Please do not use the gene_ontology_write.obo unless you are editing the ontologies. File users should use gene_ontology.1_2.obo, which is the stable version. The script is not yet in place to handle the file conversions between the write file and the other formats, but we will receive a mail from SGD via the GO list when it is. This means that the changes will not yet have filtered through to all users, but they should do so in a day or two. (Thank you to those who spotted this and asked.) Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From jdeegan at ebi.ac.uk Tue Mar 25 09:35:16 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 25 Mar 2008 16:35:16 +0000 Subject: [Go] ontology editing freeze lifted In-Reply-To: <47E923A1.6060906@ebi.ac.uk> References: <47E923A1.6060906@ebi.ac.uk> Message-ID: <47E929C4.7020704@ebi.ac.uk> Hi, So that everybody can start to enjoy the new improvements to the file, the changes have now been manually propagated through to gene_ontology_edit.obo. This means that they will reach the ftp server in half an hour, and gene_ontology.obo tomorrow. Midori is going to keep propagating the changes like this using a manual commit once a day until the scripts are in place at SGD. Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From pj37 at cornell.edu Tue Mar 25 09:59:18 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 25 Mar 2008 12:59:18 -0400 Subject: [Go] secretory pathway (SF 1912842) In-Reply-To: References: Message-ID: <47E92F66.4070100@cornell.edu> Ask the group developing SecretomeP http://www.cbs.dtu.dk/services/SecretomeP/output.php and SiglaP/TargetP http://www.cbs.dtu.dk/services/TargetP/output.php They have often used this term in the results of their analysis tool. Pankaj Midori Harris wrote: > Dear GO, > > Questions have arisen about the process term 'secretory pathway' > (GO:0045045). At first the aim was to improve the definition, but > upon further discussion we're now leaningtowards making the term obsolete. > Could people take a look at the SourceForge item and let us know if > there's a case for keeping the term? If no arguments in its favor emerge, > I'll send the formal obsoletion warning email in a few days. > > https://sourceforge.net/tracker/index.php?func=detail&aid=1912842&group_id=36855&atid=440764 > > Thanks, > Midori > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From pj37 at cornell.edu Tue Mar 25 10:10:46 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 25 Mar 2008 13:10:46 -0400 Subject: [Go] secretory pathway (SF 1912842) In-Reply-To: <47E92F66.4070100@cornell.edu> References: <47E92F66.4070100@cornell.edu> Message-ID: <47E93216.3070907@cornell.edu> Correcting my self. The tools do not use the GO term, but the predicted results can be translated to associate with the GO term for annotation and analysis by users, if the proteins are predicted to have 'secretory pathway' annotations from these tools. Pankaj Pankaj Jaiswal wrote: > Ask the group developing SecretomeP > http://www.cbs.dtu.dk/services/SecretomeP/output.php > and SiglaP/TargetP > http://www.cbs.dtu.dk/services/TargetP/output.php > > They have often used this term in the results of their analysis tool. > > Pankaj > > Midori Harris wrote: >> Dear GO, >> >> Questions have arisen about the process term 'secretory pathway' >> (GO:0045045). At first the aim was to improve the definition, but >> upon further discussion we're now leaningtowards making the term obsolete. >> Could people take a look at the SourceForge item and let us know if >> there's a case for keeping the term? If no arguments in its favor emerge, >> I'll send the formal obsoletion warning email in a few days. >> >> https://sourceforge.net/tracker/index.php?func=detail&aid=1912842&group_id=36855&atid=440764 >> >> Thanks, >> Midori From pgaudet at northwestern.edu Tue Mar 25 10:46:32 2008 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Tue, 25 Mar 2008 13:46:32 -0400 Subject: [Go] secretory pathway (SF 1912842) In-Reply-To: <47E93216.3070907@cornell.edu> References: <47E92F66.4070100@cornell.edu> <47E93216.3070907@cornell.edu> Message-ID: <47E93A78.6020409@northwestern.edu> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080325/c61965ee/attachment.html From cjm at fruitfly.org Wed Mar 26 08:42:42 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 26 Mar 2008 08:42:42 -0700 Subject: [Go] help required: database contacts Message-ID: <2FD191E2-CA46-4F17-92FB-3421D9D23F4E@fruitfly.org> (apologies if you've seen this already) I'm trying to build a comprehensive list of contacts for databases that are involved with the GOC. If you don't see your organization below, can you add it, along with a contact? Thanks! http://wiki.geneontology.org/index.php/External_Database_Contact_Info From jimhu at tamu.edu Wed Mar 26 11:00:36 2008 From: jimhu at tamu.edu (Jim Hu) Date: Wed, 26 Mar 2008 13:00:36 -0500 Subject: [Go] help required: database contacts In-Reply-To: <2FD191E2-CA46-4F17-92FB-3421D9D23F4E@fruitfly.org> References: <2FD191E2-CA46-4F17-92FB-3421D9D23F4E@fruitfly.org> Message-ID: <3AEC49FE-EE60-45C9-9C25-740FC3D8D815@tamu.edu> Hi Chris, I just edited the page. http://wiki.geneontology.org/index.php/External_Database_Contact_Info#E._coli Not sure if the additional info is helpful or just confusing! But it's a wiki, so people can reedit it. Jim On Mar 26, 2008, at 10:42 AM, Chris Mungall wrote: > (apologies if you've seen this already) > > I'm trying to build a comprehensive list of contacts for databases > that are involved with the GOC. If you don't see your organization > below, can you add it, along with a contact? Thanks! > > http://wiki.geneontology.org/index.php/External_Database_Contact_Info > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080326/30596d14/attachment-0001.html From cjm at fruitfly.org Wed Mar 26 13:29:53 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 26 Mar 2008 13:29:53 -0700 Subject: [Go] help required: database contacts In-Reply-To: <2FD191E2-CA46-4F17-92FB-3421D9D23F4E@fruitfly.org> References: <2FD191E2-CA46-4F17-92FB-3421D9D23F4E@fruitfly.org> Message-ID: <38E7DD32-DBA7-45B4-B899-7A323DDBE858@fruitfly.org> Thanks all, I think I have all your changes. On Mar 26, 2008, at 8:42 AM, Chris Mungall wrote: > (apologies if you've seen this already) > > I'm trying to build a comprehensive list of contacts for databases > that are involved with the GOC. If you don't see your organization > below, can you add it, along with a contact? Thanks! > > http://wiki.geneontology.org/index.php/External_Database_Contact_Info > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From kchris at genome.stanford.edu Wed Mar 26 15:11:04 2008 From: kchris at genome.stanford.edu (Karen Christie) Date: Wed, 26 Mar 2008 15:11:04 -0700 (PDT) Subject: [Go] ontology editing freeze lifted In-Reply-To: <47E929C4.7020704@ebi.ac.uk> References: <47E923A1.6060906@ebi.ac.uk> <47E929C4.7020704@ebi.ac.uk> Message-ID: Hi, In light of the fact that Chris's recent email to go-friends says that the CVS changes "will go into effect within the next few weeks, and will be announced on this list." and that the README for the go/ontology/editors/ directory says this: "The current contents are frozen, and should be treated as a placeholder/test and NOT USED in production" I have a question: Which file is currently the one to be edited? the old one at go/ontology/gene_ontology_edit.obo OR the new one at go/ontology/editors/gene_ontology_write.obo If it's the latter then the README in the editors directory needs to be edited to contain up-to-date info, and also a correct file name (currently lists "gene_ontology_live.obo" but not "gene_ontology_write.obo". confusedly yours, -Karen On Tue, 25 Mar 2008, Jennifer Deegan (nee Clark) wrote: > Hi, > > So that everybody can start to enjoy the new improvements to the file, > the changes have now been manually propagated through to > gene_ontology_edit.obo. This means that they will reach the ftp server > in half an hour, and gene_ontology.obo tomorrow. > > Midori is going to keep propagating the changes like this using a manual > commit once a day until the scripts are in place at SGD. > > Thanks, > > Jen > > > > > > > -- > Jennifer Deegan (nee Clark) > EMBL-European Bioinformatics Institute > Gene Ontology Consortium > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From jdeegan at ebi.ac.uk Wed Mar 26 15:14:15 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Wed, 26 Mar 2008 22:14:15 +0000 Subject: [Go] ontology editing freeze lifted In-Reply-To: References: <47E923A1.6060906@ebi.ac.uk> <47E929C4.7020704@ebi.ac.uk> Message-ID: <47EACAB7.9020508@ebi.ac.uk> Hi Karen, > > Which file is currently the one to be edited? > It's this one: > the new one at go/ontology/editors/gene_ontology_write.obo > > If it's the latter then the README in the editors directory needs to > be edited to contain up-to-date info, and also a correct file name > (currently lists "gene_ontology_live.obo" but not > "gene_ontology_write.obo". > We will update the README. Thanks for pointing it out. Jen From erika at cribi.unipd.it Thu Mar 27 02:36:19 2008 From: erika at cribi.unipd.it (Erika Feltrin) Date: Thu, 27 Mar 2008 10:36:19 +0100 Subject: [Go] help required: database contacts In-Reply-To: <2FD191E2-CA46-4F17-92FB-3421D9D23F4E@fruitfly.org> References: <2FD191E2-CA46-4F17-92FB-3421D9D23F4E@fruitfly.org> Message-ID: <1206610579.4563.17.camel@sophie.cribi.unipd.it> Dear Chris, I edit the wiki page and insert the link to my group. Peopple who are interested in contact one of us find email addresses at that web page. Thanks Erika Il giorno mer, 26/03/2008 alle 08.42 -0700, Chris Mungall ha scritto: > (apologies if you've seen this already) > > I'm trying to build a comprehensive list of contacts for databases > that are involved with the GOC. If you don't see your organization > below, can you add it, along with a contact? Thanks! > > http://wiki.geneontology.org/index.php/External_Database_Contact_Info > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From midori at ebi.ac.uk Thu Mar 27 09:00:16 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 27 Mar 2008 16:00:16 UT Subject: [Go] SourceForge Update Message-ID: <200803271600.m2RG0Gw1309372@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080327/893c4a0b/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080327/893c4a0b/attachment.pl From ma11 at gen.cam.ac.uk Fri Mar 28 03:23:31 2008 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Fri, 28 Mar 2008 10:23:31 +0000 Subject: [Go] GO Web Services Message-ID: Should we have a page on GO for GO web services ? GoPubMed Andreas Schlicker (MPI-INF) functional similarity is another M From jblake at informatics.jax.org Fri Mar 28 04:17:15 2008 From: jblake at informatics.jax.org (Judith Blake) Date: Fri, 28 Mar 2008 07:17:15 -0400 Subject: [Go] GO Web Services In-Reply-To: References: Message-ID: <47ECD3BB.6080008@informatics.jax.org> I think this is an excellent idea... I particularly like these services that would be useful to our users but that don't require that we set up toolshops. judy Michael Ashburner wrote: > Should we have a page on GO for GO web services ? > > GoPubMed > Andreas Schlicker (MPI-INF) functional similarity is another > > M > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From midori at ebi.ac.uk Fri Mar 28 09:00:18 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 28 Mar 2008 16:00:18 UT Subject: [Go] SourceForge Update Message-ID: <200803281600.m2SG0IM1566257@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080328/41ad1d20/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080328/41ad1d20/attachment.pl From tberardi at acoma.stanford.edu Fri Mar 28 10:34:33 2008 From: tberardi at acoma.stanford.edu (Tanya Berardini) Date: Fri, 28 Mar 2008 10:34:33 -0700 Subject: [Go] Look! We made the blogosphere too! Message-ID: <8e22ab960803281034k32c755b9tfe4776eb1a893c35@mail.gmail.com> 'Regulates' relationships in the news: http://www.openhelix.com/blog/?p=245 Tanya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080328/8eab3792/attachment.html From midori at ebi.ac.uk Sat Mar 29 09:00:20 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 29 Mar 2008 16:00:20 UT Subject: [Go] SourceForge Update Message-ID: <200803291600.m2TG0Kc1292364@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080329/bcd967f4/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080329/bcd967f4/attachment.pl From suzi at fruitfly.org Fri Mar 28 05:01:11 2008 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 28 Mar 2008 13:01:11 +0100 Subject: [Go] GO Web Services In-Reply-To: <47ECD3BB.6080008@informatics.jax.org> References: <47ECD3BB.6080008@informatics.jax.org> Message-ID: <6842C21D-992D-486C-ADAF-370C738142A1@fruitfly.org> 2 pages perhaps? One for those services that we (already) offer, and a second for those from others. -S On Mar 28, 2008, at 12:17 PM, Judith Blake wrote: > I think this is an excellent idea... > > I particularly like these services that would be useful to our users > but > that don't require that we set up toolshops. > > judy > > > Michael Ashburner wrote: >> Should we have a page on GO for GO web services ? >> >> GoPubMed >> Andreas Schlicker (MPI-INF) functional similarity is another >> >> M >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From rama at genome.stanford.edu Sun Mar 30 09:49:52 2008 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Sun, 30 Mar 2008 09:49:52 -0700 Subject: [Go] GO Web Services In-Reply-To: <6842C21D-992D-486C-ADAF-370C738142A1@fruitfly.org> References: <47ECD3BB.6080008@informatics.jax.org> <6842C21D-992D-486C-ADAF-370C738142A1@fruitfly.org> Message-ID: <3682B998-64DF-45E6-9433-562AA2B50404@genome.stanford.edu> Hi, May be I am missing the obvious here. We already have a page for GO tools-http://www.geneontology.org/ GO.tools.shtml and this page is organized by what is web-based, downloadable, provided by GO etc. What will the proposed GO web services page include? Thanks, Rama On Mar 28, 2008, at 5:01 AM, Suzanna Lewis wrote: > 2 pages perhaps? One for those services that we (already) offer, and a > second for those from others. > > -S > > On Mar 28, 2008, at 12:17 PM, Judith Blake wrote: > >> I think this is an excellent idea... >> >> I particularly like these services that would be useful to our users >> but >> that don't require that we set up toolshops. >> >> judy >> >> >> Michael Ashburner wrote: >>> Should we have a page on GO for GO web services ? >>> >>> GoPubMed >>> Andreas Schlicker (MPI-INF) functional similarity is another >>> >>> M >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From jimhu at tamu.edu Sun Mar 30 10:08:45 2008 From: jimhu at tamu.edu (Jim Hu) Date: Sun, 30 Mar 2008 12:08:45 -0500 Subject: [Go] GO Web Services In-Reply-To: <3682B998-64DF-45E6-9433-562AA2B50404@genome.stanford.edu> References: <47ECD3BB.6080008@informatics.jax.org> <6842C21D-992D-486C-ADAF-370C738142A1@fruitfly.org> <3682B998-64DF-45E6-9433-562AA2B50404@genome.stanford.edu> Message-ID: <42136EBE-A634-4243-B158-57E899D4E301@tamu.edu> Hi Rama, I'm not sure what the others are talking about, but formally, web services are not the same as web-based tools. Web services in my usage is stuff where a structured query dynamically returns something like an XML file that is readable by a computer. For example, EcoliWiki is a web-based tool, and I've been working on implementing a web service that takes a gene identifier and returns a structured XML document with the GO associations for that gene. The distinction between web services and frequently updated downloads is a bit blurry in my mind. Other examples include the E-Utils at PubMed, DAS for gbrowse, and the stuff you don't see in the background that updates Amazon pages from different publishers. See http://en.wikipedia.org/wiki/Web_service Jim On Mar 30, 2008, at 11:49 AM, Rama Balakrishnan wrote: > Hi, > > May be I am missing the obvious here. > > We already have a page for GO tools-http://www.geneontology.org/ > GO.tools.shtml > and this page is organized by what is web-based, downloadable, > provided by GO etc. > > What will the proposed GO web services page include? > > Thanks, > > Rama > > > > On Mar 28, 2008, at 5:01 AM, Suzanna Lewis wrote: > >> 2 pages perhaps? One for those services that we (already) offer, >> and a >> second for those from others. >> >> -S >> >> On Mar 28, 2008, at 12:17 PM, Judith Blake wrote: >> >>> I think this is an excellent idea... >>> >>> I particularly like these services that would be useful to our users >>> but >>> that don't require that we set up toolshops. >>> >>> judy >>> >>> >>> Michael Ashburner wrote: >>>> Should we have a page on GO for GO web services ? >>>> >>>> GoPubMed >>>> Andreas Schlicker (MPI-INF) functional similarity is another >>>> >>>> M >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>> >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080330/f1cb1b32/attachment-0001.html From rama at genome.stanford.edu Sun Mar 30 21:48:04 2008 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Sun, 30 Mar 2008 21:48:04 -0700 Subject: [Go] GO Web Services In-Reply-To: <42136EBE-A634-4243-B158-57E899D4E301@tamu.edu> References: <47ECD3BB.6080008@informatics.jax.org> <6842C21D-992D-486C-ADAF-370C738142A1@fruitfly.org> <3682B998-64DF-45E6-9433-562AA2B50404@genome.stanford.edu> <42136EBE-A634-4243-B158-57E899D4E301@tamu.edu> Message-ID: <064E4B47-D363-41FF-B835-B3635FE988FE@genome.stanford.edu> Jim, Thanks for clarifying. Rama On Mar 30, 2008, at 10:08 AM, Jim Hu wrote: > Hi Rama, > > I'm not sure what the others are talking about, but formally, web > services are not the same as web-based tools. > Web services in my usage is stuff where a structured query > dynamically returns something like an XML file that is readable by > a computer. For example, EcoliWiki is a web-based tool, and I've > been working on implementing a web service that takes a gene > identifier and returns a structured XML document with the GO > associations for that gene. The distinction between web services > and frequently updated downloads is a bit blurry in my mind. > > Other examples include the E-Utils at PubMed, DAS for gbrowse, and > the stuff you don't see in the background that updates Amazon pages > from different publishers. See > > http://en.wikipedia.org/wiki/Web_service > > Jim > > > On Mar 30, 2008, at 11:49 AM, Rama Balakrishnan wrote: >> Hi, >> >> May be I am missing the obvious here. >> >> We already have a page for GO tools-http://www.geneontology.org/ >> GO.tools.shtml >> and this page is organized by what is web-based, downloadable, >> provided by GO etc. >> >> What will the proposed GO web services page include? >> >> Thanks, >> >> Rama >> >> >> >> On Mar 28, 2008, at 5:01 AM, Suzanna Lewis wrote: >> >>> 2 pages perhaps? One for those services that we (already) offer, >>> and a >>> second for those from others. >>> >>> -S >>> >>> On Mar 28, 2008, at 12:17 PM, Judith Blake wrote: >>> >>>> I think this is an excellent idea... >>>> >>>> I particularly like these services that would be useful to our >>>> users >>>> but >>>> that don't require that we set up toolshops. >>>> >>>> judy >>>> >>>> >>>> Michael Ashburner wrote: >>>>> Should we have a page on GO for GO web services ? >>>>> >>>>> GoPubMed >>>>> Andreas Schlicker (MPI-INF) functional similarity is another >>>>> >>>>> M >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>> >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > ===================================== > Jim Hu > Associate Professor > Dept. of Biochemistry and Biophysics > 2128 TAMU > Texas A&M Univ. > College Station, TX 77843-2128 > 979-862-4054 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080330/a2c2832e/attachment.html From erika at cribi.unipd.it Mon Mar 31 05:20:47 2008 From: erika at cribi.unipd.it (Erika Feltrin) Date: Mon, 31 Mar 2008 14:20:47 +0200 Subject: [Go] Title for the Muscle Biology Publication Message-ID: <1206966047.4648.12.camel@sophie.cribi.unipd.it> Dear all, I would like to thank all of you for the help and suggestions on Muscle Paper. Finally Jen and I are almost ready to submit the manuscript to BMC Medical Genomics but we need more help from you...one thing is missing: the TITLE. Below are possible titles but any further ideas are very very welcome. 1. Improving muscle vocabulary: Here we GO! 2. Ready, Steady, GO, for Muscle! 3. Ontologists GO native in the muscle community. 4. Muscle community: Breakthrough to GO! 5. Muscle community: Break in to GO! 6. Muscle community: GO native. 7. Muscle Biology: break into GO. 8. Muscle Research to GO into the Future. 9. Muscle Research to GO in leaps and bounds. Thank you very much, Erika From adiehl at informatics.jax.org Mon Mar 31 05:40:02 2008 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Mon, 31 Mar 2008 12:40:02 +0000 Subject: [Go] Title for the Muscle Biology Publication In-Reply-To: <1206966047.4648.12.camel@sophie.cribi.unipd.it> References: <1206966047.4648.12.camel@sophie.cribi.unipd.it> Message-ID: <47F0DBA2.7090005@informatics.jax.org> I'm not too wild about overly cutesy names when it comes to the serious academic endeavor that this work represents, but at least number 1 actually suggests what was done and is described in the paper. Number 3 is perhaps the most clever but potentially demeaning to the authors. -- Alex Erika Feltrin wrote: > Dear all, > > I would like to thank all of you for the help and suggestions on Muscle > Paper. > Finally Jen and I are almost ready to submit the manuscript to BMC > Medical Genomics but we need more help from you...one thing is missing: > the TITLE. > Below are possible titles but any further ideas are very very welcome. > > 1. Improving muscle vocabulary: Here we GO! > 2. Ready, Steady, GO, for Muscle! > 3. Ontologists GO native in the muscle community. > 4. Muscle community: Breakthrough to GO! > 5. Muscle community: Break in to GO! > 6. Muscle community: GO native. > 7. Muscle Biology: break into GO. > 8. Muscle Research to GO into the Future. > 9. Muscle Research to GO in leaps and bounds. > > Thank you very much, > > Erika > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From jblake at informatics.jax.org Mon Mar 31 07:14:06 2008 From: jblake at informatics.jax.org (Judith Blake) Date: Mon, 31 Mar 2008 10:14:06 -0400 Subject: [Go] Title for the Muscle Biology Publication In-Reply-To: <47F0DBA2.7090005@informatics.jax.org> References: <1206966047.4648.12.camel@sophie.cribi.unipd.it> <47F0DBA2.7090005@informatics.jax.org> Message-ID: <47F0F1AE.9030005@informatics.jax.org> I suggest... Improving Muscle Research with Advanced Terminologies: Muscle Research and Gene Ontology: New standards for improved data integration and aggregation. Judy Alexander Diehl wrote: > I'm not too wild about overly cutesy names when it comes to the serious > academic endeavor that this work represents, but at least number 1 > actually suggests what was done and is described in the paper. Number 3 > is perhaps the most clever but potentially demeaning to the authors. > > -- Alex > > > Erika Feltrin wrote: > >> Dear all, >> >> I would like to thank all of you for the help and suggestions on Muscle >> Paper. >> Finally Jen and I are almost ready to submit the manuscript to BMC >> Medical Genomics but we need more help from you...one thing is missing: >> the TITLE. >> Below are possible titles but any further ideas are very very welcome. >> >> 1. Improving muscle vocabulary: Here we GO! >> 2. Ready, Steady, GO, for Muscle! >> 3. Ontologists GO native in the muscle community. >> 4. Muscle community: Breakthrough to GO! >> 5. Muscle community: Break in to GO! >> 6. Muscle community: GO native. >> 7. Muscle Biology: break into GO. >> 8. Muscle Research to GO into the Future. >> 9. Muscle Research to GO in leaps and bounds. >> >> Thank you very much, >> >> Erika >> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> >> > > > From jblake at informatics.jax.org Mon Mar 31 07:17:41 2008 From: jblake at informatics.jax.org (Judith Blake) Date: Mon, 31 Mar 2008 10:17:41 -0400 Subject: [Go] Title for the Muscle Biology Publication In-Reply-To: <47F0F1AE.9030005@informatics.jax.org> References: <1206966047.4648.12.camel@sophie.cribi.unipd.it> <47F0DBA2.7090005@informatics.jax.org> <47F0F1AE.9030005@informatics.jax.org> Message-ID: <47F0F285.2020203@informatics.jax.org> actually, there are two titles here...I like the second on better Judy Judith Blake wrote: > I suggest... > > Improving Muscle Research with Advanced Terminologies: > > Muscle Research and Gene Ontology: New standards for improved data > integration and aggregation. > > Judy > > Alexander Diehl wrote: > >> I'm not too wild about overly cutesy names when it comes to the serious >> academic endeavor that this work represents, but at least number 1 >> actually suggests what was done and is described in the paper. Number 3 >> is perhaps the most clever but potentially demeaning to the authors. >> >> -- Alex >> >> >> Erika Feltrin wrote: >> >> >>> Dear all, >>> >>> I would like to thank all of you for the help and suggestions on Muscle >>> Paper. >>> Finally Jen and I are almost ready to submit the manuscript to BMC >>> Medical Genomics but we need more help from you...one thing is missing: >>> the TITLE. >>> Below are possible titles but any further ideas are very very welcome. >>> >>> 1. Improving muscle vocabulary: Here we GO! >>> 2. Ready, Steady, GO, for Muscle! >>> 3. Ontologists GO native in the muscle community. >>> 4. Muscle community: Breakthrough to GO! >>> 5. Muscle community: Break in to GO! >>> 6. Muscle community: GO native. >>> 7. Muscle Biology: break into GO. >>> 8. Muscle Research to GO into the Future. >>> 9. Muscle Research to GO in leaps and bounds. >>> >>> Thank you very much, >>> >>> Erika >>> >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> >>> >> >> > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From midori at ebi.ac.uk Mon Mar 31 09:00:17 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 31 Mar 2008 16:00:17 UT Subject: [Go] SourceForge Update Message-ID: <200803311600.m2VG0HX1263999@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080331/cb05d5d4/attachment-0001.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20080331/cb05d5d4/attachment-0001.pl From midori at ebi.ac.uk Mon Mar 31 05:23:56 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 31 Mar 2008 13:23:56 +0100 (BST) Subject: [Go] Title for the Muscle Biology Publication In-Reply-To: <1206965928.4648.10.camel@sophie.cribi.unipd.it> References: <1206965928.4648.10.camel@sophie.cribi.unipd.it> Message-ID: "GO flexes its muscles"? Seems too flippant ... but I felt clever for a moment. More seriously, I like 8 and 9. m On Mon, 31 Mar 2008, Erika Feltrin wrote: > Dear all, > > I would like to thank all of you for the help and suggestions on Muscle > Paper. > Finally Jen and I are almost ready to submit the manuscript to BMC > Medical Genomics but we need more help from you...one thing is missing: > the TITLE. > Below are possible titles but any further ideas are very very welcome. > > 1. Improving muscle vocabulary: Here we GO! > 2. Ready, Steady, GO, for Muscle! > 3. Ontologists GO native in the muscle community. > 4. Muscle community: Breakthrough to GO! > 5. Muscle community: Break in to GO! > 6. Muscle community: GO native. > 7. Muscle Biology: break into GO. > 8. Muscle Research to GO into the Future. > 9. Muscle Research to GO in leaps and bounds. > > Thank you very much, > > Erika > > From rknoell at med.uni-goettingen.de Mon Mar 31 05:33:14 2008 From: rknoell at med.uni-goettingen.de (=?iso-8859-1?Q?Kn=F6ll=2C_Ralph?=) Date: Mon, 31 Mar 2008 14:33:14 +0200 Subject: [Go] Title for the Muscle Biology Publication In-Reply-To: <1206965928.4648.10.camel@sophie.cribi.unipd.it> References: <1206965928.4648.10.camel@sophie.cribi.unipd.it> Message-ID: <157C901DF1BB9348A39E79990B58B0940B84AE@UMGEXC-VS1.umgexc.med.uni-goettingen.de> Dear Erika, I like most: # 1 Regards Ralph Prof. Dr. Ralph Kn?ll Head Cardiovascular Molecular Genetics NGFN - Coordinator Heart Centre G?ttingen Georg August University 37099 G?ttingen Germany -----Urspr?ngliche Nachricht----- Von: Erika Feltrin [mailto:erika at cribi.unipd.it] Gesendet: Montag, 31. M?rz 2008 14:19 An: GOlist; Jennifer Clark; Elisabeth Ehler; Jennifer Fordham; Midori Harris; Kn?ll, Ralph; Sorrentino Vincenzo; Chiara Gardin; Paolo Laveder; lorimitt at cribi.unipd.it; Alessandra Nori; Pompeo Volpe; zarivan at cribi.unipd.it; stefano.campanaro at unipd.it; Georgine Faulkner; Carlo Reggiani; giorgio.valle at unipd.it Betreff: Title for the Muscle Biology Publication Dear all, I would like to thank all of you for the help and suggestions on Muscle Paper. Finally Jen and I are almost ready to submit the manuscript to BMC Medical Genomics but we need more help from you...one thing is missing: the TITLE. Below are possible titles but any further ideas are very very welcome. 1. Improving muscle vocabulary: Here we GO! 2. Ready, Steady, GO, for Muscle! 3. Ontologists GO native in the muscle community. 4. Muscle community: Breakthrough to GO! 5. Muscle community: Break in to GO! 6. Muscle community: GO native. 7. Muscle Biology: break into GO. 8. Muscle Research to GO into the Future. 9. Muscle Research to GO in leaps and bounds. Thank you very much, Erika From faulkner at icgeb.org Mon Mar 31 05:50:04 2008 From: faulkner at icgeb.org (Georgine Faulkner) Date: Mon, 31 Mar 2008 14:50:04 +0200 Subject: [Go] Title for the Muscle Biology Publication In-Reply-To: <1206965928.4648.10.camel@sophie.cribi.unipd.it> References: <1206965928.4648.10.camel@sophie.cribi.unipd.it> Message-ID: <20080331124918.5F482127A038@helix.icgeb.org> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20080331/b8c8dc86/attachment.html From erika at cribi.unipd.it Mon Mar 31 05:18:48 2008 From: erika at cribi.unipd.it (Erika Feltrin) Date: Mon, 31 Mar 2008 14:18:48 +0200 Subject: [Go] Title for the Muscle Biology Publication Message-ID: <1206965928.4648.10.camel@sophie.cribi.unipd.it> Dear all, I would like to thank all of you for the help and suggestions on Muscle Paper. Finally Jen and I are almost ready to submit the manuscript to BMC Medical Genomics but we need more help from you...one thing is missing: the TITLE. Below are possible titles but any further ideas are very very welcome. 1. Improving muscle vocabulary: Here we GO! 2. Ready, Steady, GO, for Muscle! 3. Ontologists GO native in the muscle community. 4. Muscle community: Breakthrough to GO! 5. Muscle community: Break in to GO! 6. Muscle community: GO native. 7. Muscle Biology: break into GO. 8. Muscle Research to GO into the Future. 9. Muscle Research to GO in leaps and bounds. Thank you very much, Erika