From FMcCarthy at cvm.msstate.edu Fri Jan 4 06:17:29 2008 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Fri, 04 Jan 2008 08:17:29 -0600 Subject: [gofriends] Announcement: Delivering Value from Avian Genomics Message-ID: This is the first announcement for the upcoming international meeting ?Delivering Value from Avian Genomics? May 19-20, 2008 and "Avian Gene Ontology (GO) and Microarray Data Modeling Workshop", immediately following on May 21-22, 2008. Both events will be held at Mississippi State University (fly to Atlanta and then to our local airport at GTR). The meeting theme is to identify how value can be derived from past and future investments in and from genomics research in aves. This theme is in response to the recently released "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008?2017", the sequencing of the zebra finch genome and the high profile importance of aves in human disease. We are inviting interested representatives of USDA, NIH and CDC. We are now negotiating to have invited and selected manuscripts published in a special issue of a genomics journal. The Avian Gene Ontology (GO) and Microarray Data Modeling Workshop will provide education about the Gene Ontology, advice on the ways that you may have annotated or annotate your own datasets and education on the tools available to use the GO to model your microarray (and other) functional genomics datasets to derive biological meaning. Graduate student travel awards will be available. Further details will be made available via this newsgroup and anyone interested can send an email to agbase at cse.msstate.edu and also be added to the conference and/or workshop mailing list. regards, Shane Burgess Susan Bridges Fiona McCarthy -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From eurie at genome.Stanford.EDU Mon Jan 7 11:35:48 2008 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Mon, 7 Jan 2008 11:35:48 -0800 Subject: [gofriends] Downtime for GO FTP and CVS services Message-ID: The following services will be unavailable Monday, January 7th starting at 12:00 noon PST (3:00 PM EST, 8:00 PM GMT, and 5:00 AM January 8th JST) for emergency maintenance: FTP server (ftp://ftp.geneontology.org/pub/go/) GO database archive site (http://archive.godatabase.org) Web access to the CVS repository (http://cvsweb.geneontology.org/cgi- bin/cvsweb.cgi/) Anonymous access to the GO CVS During this time, the AmiGO database (http://www.godatabase.org/) and GO web pages (http://www.geneontology.org/) will be available. We expect the work to take approximately 5 hours but we will make every attempt to keep it as short as possible. We apologize for short notice and for any inconvenience this may cause. -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From parkinson at ebi.ac.uk Wed Jan 9 00:14:45 2008 From: parkinson at ebi.ac.uk (Helen Parkinson) Date: Wed, 9 Jan 2008 08:14:45 -0000 (GMT) Subject: [gofriends] Message-ID: <58301.84.41.190.196.1199866485.squirrel@webmail.ebi.ac.uk> Dear Colleagues, I'd like to draw your attention to the ISMB call for papers: ISCB ANNOUNCEMENTS AND U P D A T E S :: ISMB 2008, July 19-23, Toronto, Canada Call for Papers Closing in One Week www.iscb.org/ismb2008/sub_papers.php Paper Submission Deadline: January 16, 2008 Robert Stevens and I are co-chairing the databases and ontologies session and we invite you to submit papers on these themes to help us build a stimulating session. We look forward to seeing you in Toronto http://www.iscb.org/ismb2008/ best regards Helen Parkinson and Robert Stevens -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From huntley at ebi.ac.uk Thu Jan 10 05:46:52 2008 From: huntley at ebi.ac.uk (Rachael Huntley) Date: Thu, 10 Jan 2008 13:46:52 +0000 Subject: [gofriends] GO visualisation tool? Message-ID: <478621CC.3060003@ebi.ac.uk> Dear all, I have had this query from a user, does anyone know of a tool that can do this? >Do you know of any GO viewer that allows you to visualise the GO structure and place genes with a specific annotation under that branch of the tree? < Thanks, Rachael. -- Rachael Huntley Ph.D. European Bioinformatics Institute-EMBL Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 492515 Fax: +44 (0)1223 494468 E-mail: huntley at ebi.ac.uk URL: http://www.ebi.ac.uk/GOA -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From sgoetz at ochoa.fib.es Thu Jan 10 07:07:14 2008 From: sgoetz at ochoa.fib.es (Stefan Goetz) Date: Thu, 10 Jan 2008 16:07:14 +0100 Subject: [gofriends] Message-ID: <380-2200814101571411@ochoa.fib.es> Dear Rachael, Blast2GO allows you to easily import your GO annotations and visualize them as a so called "combined graph" DAG with color highlighting for gene or annotation counts. Pie charts can also be created and all images exported as SVG or PNG files. Here a screenshot: http://blast2go.bioinfo.cipf.es/screenshots/combinedGraph.html ...and some easy tutorial: http://bioinfo.cipf.es/blast2go/b2gdata/blast2goTutorial.pdf Regards, Stefan Goetz Blast2GO Team Rachael Huntley wrote: > Dear all, > > I have had this query from a user, does anyone know of a tool that can do this? > > >Do you know of any GO viewer that allows you to visualise the GO structure and place genes with a specific annotation under that branch of the tree? > < > > Thanks, > Rachael. > -- -------------------------------------------- Stefan G?tz Bioinformatics Department Centro de Investigaci?n Pr?ncipe Felipe (CIPF) C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanogr?fico) 46013 Valencia, Spain Tel: +34 963289680 Ext. 1011 Fax: +34 963289574 E-Mail: sgoetz at cipf.es http://bioinfo.cipf.es -------------------------------------------- -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From jimhu at tamu.edu Thu Jan 10 07:52:35 2008 From: jimhu at tamu.edu (Jim Hu) Date: Thu, 10 Jan 2008 09:52:35 -0600 Subject: [gofriends] GO visualisation tool? In-Reply-To: <478621CC.3060003@ebi.ac.uk> References: <478621CC.3060003@ebi.ac.uk> Message-ID: <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> Hi Rachael, I'm not sure I understand what the user wants to do. Doesn't AmiGO place genes under the appropriate branches based on annotations? Is this not the desired kind of visualization? Or do they want something different? Jim On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: > Dear all, > > I have had this query from a user, does anyone know of a tool that > can do this? > > >Do you know of any GO viewer that allows you to visualise the GO > structure and place genes with a specific annotation under that > branch of the tree? > < > > Thanks, > Rachael. > > -- > Rachael Huntley Ph.D. > > European Bioinformatics Institute-EMBL > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Tel: +44 (0)1223 492515 > Fax: +44 (0)1223 494468 > > E-mail: huntley at ebi.ac.uk > URL: http://www.ebi.ac.uk/GOA > > > -- > This message is from the GOFriends moderated mailing list. A list > of public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: owner-gofriends at geneontology.org > Subscribing send "subscribe" to gofriends-request at geneontology.org > Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org > Web: http://www.geneontology.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/gofriends/attachments/20080110/ae7034ed/attachment.html From huntley at ebi.ac.uk Thu Jan 10 08:00:23 2008 From: huntley at ebi.ac.uk (Rachael Huntley) Date: Thu, 10 Jan 2008 16:00:23 +0000 Subject: [gofriends] GO visualisation tool? In-Reply-To: <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> Message-ID: <47864117.30207@ebi.ac.uk> Hi Jim, He has done a microarray experiment and wants to cluster the genes according to GO, so he wants to see the GO tree with the genes displayed under the GO terms they are annotated to. I don't think AmiGO does this sort of thing. Rachael. Jim Hu wrote: > Hi Rachael, > > I'm not sure I understand what the user wants to do. Doesn't AmiGO > place genes under the appropriate branches based on annotations? Is > this not the desired kind of visualization? Or do they want something > different? > > Jim > > > On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: > >> Dear all, >> >> I have had this query from a user, does anyone know of a tool that >> can do this? >> >> >Do you know of any GO viewer that allows you to visualise the GO >> structure and place genes with a specific annotation under that >> branch of the tree? >> < >> >> Thanks, >> Rachael. >> >> -- >> Rachael Huntley Ph.D. >> >> European Bioinformatics Institute-EMBL >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel: +44 (0)1223 492515 >> Fax: +44 (0)1223 494468 >> >> E-mail: huntley at ebi.ac.uk >> URL: http://www.ebi.ac.uk/GOA >> >> >> -- >> This message is from the GOFriends moderated mailing list. A list of >> public >> announcements and discussion of the Gene Ontology (GO) project. >> Problems with the list? E-mail: >> owner-gofriends at geneontology.org >> >> Subscribing send "subscribe" to >> gofriends-request at geneontology.org >> >> Unsubscribing send "unsubscribe" to >> gofriends-request at geneontology.org >> >> Web: http://www.geneontology.org/ > > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > -- Do you need any additional GO annotation resources? Which proteins would you like annotated with GO? Let us know in the GOA User Survey, available at http://www.ebi.ac.uk/GOA/contactus.html ************************************* Rachael Huntley Ph.D. European Bioinformatics Institute-EMBL Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 492515 Fax: +44 (0)1223 494468 E-mail: huntley at ebi.ac.uk URL: http://www.ebi.ac.uk/GOA -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From jimhu at tamu.edu Thu Jan 10 08:24:40 2008 From: jimhu at tamu.edu (Jim Hu) Date: Thu, 10 Jan 2008 10:24:40 -0600 Subject: [gofriends] GO visualisation tool? In-Reply-To: <47864117.30207@ebi.ac.uk> References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> <47864117.30207@ebi.ac.uk> Message-ID: Hi Rachael, On Jan 10, 2008, at 10:00 AM, Rachael Huntley wrote: > Hi Jim, > > He has done a microarray experiment and wants to cluster the genes > according to GO, so he wants to see the GO tree with the genes > displayed under the GO terms they are annotated to. I don't think > AmiGO does this sort of thing. Ah, that makes sense. So, if I understand this right, a general tool would be something where you give a program the ontology, a gene association file, and a list of genes, and get the appropriate display. This has to be filtered for statistically enriched associations to be useful, I think. I'm interested to see what others suggest. I think that various projects have their own organism- specific versions of this, and I think it's built into commercial packages like GeneSpring. But I'd like to see a list and discussion of what's available as open source... especially for things that can be displayed as web tools. Jim > > > Rachael. > > Jim Hu wrote: > >> Hi Rachael, >> >> I'm not sure I understand what the user wants to do. Doesn't AmiGO >> place genes under the appropriate branches based on annotations? >> Is this not the desired kind of visualization? Or do they want >> something different? >> >> Jim >> >> >> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >> >>> Dear all, >>> >>> I have had this query from a user, does anyone know of a tool that >>> can do this? >>> >>> >Do you know of any GO viewer that allows you to visualise the GO >>> structure and place genes with a specific annotation under that >>> branch of the tree? >>> < >>> >>> Thanks, >>> Rachael. >>> >>> -- >>> Rachael Huntley Ph.D. >>> >>> European Bioinformatics Institute-EMBL >>> Wellcome Trust Genome Campus >>> Hinxton >>> Cambridge CB10 1SD >>> United Kingdom Tel: +44 (0)1223 492515 >>> Fax: +44 (0)1223 494468 >>> >>> E-mail: huntley at ebi.ac.uk >>> URL: http://www.ebi.ac.uk/GOA >>> >>> >>> -- >>> This message is from the GOFriends moderated mailing list. A list >>> of public >>> announcements and discussion of the Gene Ontology (GO) project. >>> Problems with the list? E-mail: owner-gofriends at geneontology.org >>> >>> Subscribing send "subscribe" to gofriends-request at geneontology.org >>> >>> Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org >>> >>> Web: http://www.geneontology.org/ >> >> >> ===================================== >> >> Jim Hu >> >> Associate Professor >> >> Dept. of Biochemistry and Biophysics >> >> 2128 TAMU >> >> Texas A&M Univ. >> >> College Station, TX 77843-2128 >> >> 979-862-4054 >> >> >> > > > -- > > Do you need any additional GO annotation resources? > Which proteins would you like annotated with GO? > > Let us know in the GOA User Survey, available at http://www.ebi.ac.uk/GOA/contactus.html > > > ************************************* > > Rachael Huntley Ph.D. > > European Bioinformatics Institute-EMBL > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Tel: +44 (0)1223 492515 > Fax: +44 (0)1223 494468 > > E-mail: huntley at ebi.ac.uk > URL: http://www.ebi.ac.uk/GOA > ===================================== 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/gofriends/attachments/20080110/1917abb1/attachment.html From gillespm at cshl.edu Thu Jan 10 08:35:53 2008 From: gillespm at cshl.edu (Marc Gillespie) Date: Thu, 10 Jan 2008 11:35:53 -0500 Subject: [gofriends] GO visualisation tool? In-Reply-To: References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> <47864117.30207@ebi.ac.uk> Message-ID: <08F57C53-F552-48C6-96F2-D591311C2328@cshl.edu> Hi All, I wasn't going to post back (laziness?), but your unabashed interest got me started. We have been looking at DAVID to get students going on microarray work, it is free, it parses microarray data, and it seems to have a nice GO term clustering facility. I haven't delved into it yet, but will in about two months, when I have to write up a formal microarray lab for undergrads. Hope this helps, Marc Marc Gillespie Ph.D. Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724 USA Office (718) 990-5249 email gillespm at cshl.edu On Jan 10, 2008, at 11:24 AM, Jim Hu wrote: > Hi Rachael, > > On Jan 10, 2008, at 10:00 AM, Rachael Huntley wrote: > >> Hi Jim, >> >> He has done a microarray experiment and wants to cluster the genes >> according to GO, so he wants to see the GO tree with the genes >> displayed under the GO terms they are annotated to. I don't think >> AmiGO does this sort of thing. > > Ah, that makes sense. So, if I understand this right, a general > tool would be something where you give a program the ontology, a > gene association file, and a list of genes, and get the appropriate > display. This has to be filtered for statistically enriched > associations to be useful, I think. I'm interested to see what > others suggest. I think that various projects have their own > organism-specific versions of this, and I think it's built into > commercial packages like GeneSpring. But I'd like to see a list and > discussion of what's available as open source... especially for > things that can be displayed as web tools. > > Jim > >> >> >> Rachael. >> >> Jim Hu wrote: >> >>> Hi Rachael, >>> >>> I'm not sure I understand what the user wants to do. Doesn't >>> AmiGO place genes under the appropriate branches based on >>> annotations? Is this not the desired kind of visualization? Or >>> do they want something different? >>> >>> Jim >>> >>> >>> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >>> >>>> Dear all, >>>> >>>> I have had this query from a user, does anyone know of a tool >>>> that can do this? >>>> >>>> >Do you know of any GO viewer that allows you to visualise the >>>> GO structure and place genes with a specific annotation under >>>> that branch of the tree? >>>> < >>>> >>>> Thanks, >>>> Rachael. >>>> >>>> -- >>>> Rachael Huntley Ph.D. >>>> >>>> European Bioinformatics Institute-EMBL >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD >>>> United Kingdom Tel: +44 (0)1223 492515 >>>> Fax: +44 (0)1223 494468 >>>> >>>> E-mail: huntley at ebi.ac.uk >>>> URL: http://www.ebi.ac.uk/GOA >>>> >>>> >>>> -- >>>> This message is from the GOFriends moderated mailing list. A >>>> list of public >>>> announcements and discussion of the Gene Ontology (GO) project. >>>> Problems with the list? E-mail: owner-gofriends at geneontology.org >>>> >>>> Subscribing send "subscribe" to gofriends-request at geneontology.org >>>> >>>> Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org >>>> >>>> Web: http://www.geneontology.org/ >>> >>> >>> ===================================== >>> >>> Jim Hu >>> >>> Associate Professor >>> >>> Dept. of Biochemistry and Biophysics >>> >>> 2128 TAMU >>> >>> Texas A&M Univ. >>> >>> College Station, TX 77843-2128 >>> >>> 979-862-4054 >>> >>> >>> >> >> >> -- >> >> Do you need any additional GO annotation resources? >> Which proteins would you like annotated with GO? >> >> Let us know in the GOA User Survey, available at http://www.ebi.ac.uk/GOA/contactus.html >> >> >> ************************************* >> >> Rachael Huntley Ph.D. >> >> European Bioinformatics Institute-EMBL >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel: +44 (0)1223 492515 >> Fax: +44 (0)1223 494468 >> >> E-mail: huntley at ebi.ac.uk >> URL: http://www.ebi.ac.uk/GOA >> > > ===================================== > 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/gofriends/attachments/20080110/77becc24/attachment.html From peter.robinson at charite.de Thu Jan 10 08:48:11 2008 From: peter.robinson at charite.de (Peter Robinson) Date: Thu, 10 Jan 2008 17:48:11 +0100 Subject: [gofriends] GO visualisation tool? In-Reply-To: References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> <47864117.30207@ebi.ac.uk> Message-ID: <47864C4B.7050509@charite.de> I am not sure I understand the requirement, but The Ontologizer provides a visualization of significant terms and their anscestors within the Ontology. Users can click on each term to display a list of all genes annotated (directly or by inheritance) to the term within the table browser. http://www.charite.de/ch/medgen/ontologizer Depending on the analysis being done, it is unlikely to be helpful to actually display the lists of genes in the graphic itself because of information overload. Take care, Peter Jim Hu wrote: > Hi Rachael, > > On Jan 10, 2008, at 10:00 AM, Rachael Huntley wrote: > >> Hi Jim, >> >> He has done a microarray experiment and wants to cluster the genes >> according to GO, so he wants to see the GO tree with the genes >> displayed under the GO terms they are annotated to. I don't think >> AmiGO does this sort of thing. > > Ah, that makes sense. So, if I understand this right, a general tool > would be something where you give a program the ontology, a gene > association file, and a list of genes, and get the appropriate display. > This has to be filtered for statistically enriched associations to be > useful, I think. I'm interested to see what others suggest. I think > that various projects have their own organism-specific versions of this, > and I think it's built into commercial packages like GeneSpring. But > I'd like to see a list and discussion of what's available as open > source... especially for things that can be displayed as web tools. > > Jim > >> >> >> Rachael. >> >> Jim Hu wrote: >> >>> Hi Rachael, >>> >>> I'm not sure I understand what the user wants to do. Doesn't AmiGO >>> place genes under the appropriate branches based on annotations? Is >>> this not the desired kind of visualization? Or do they want >>> something different? >>> >>> Jim >>> >>> >>> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >>> >>>> Dear all, >>>> >>>> I have had this query from a user, does anyone know of a tool that >>>> can do this? >>>> >>>> >Do you know of any GO viewer that allows you to visualise the GO >>>> structure and place genes with a specific annotation under that >>>> branch of the tree? >>>> < >>>> >>>> Thanks, >>>> Rachael. >>>> >>>> -- >>>> Rachael Huntley Ph.D. >>>> >>>> European Bioinformatics Institute-EMBL >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD >>>> United Kingdom Tel: +44 (0)1223 492515 >>>> Fax: +44 (0)1223 494468 >>>> >>>> E-mail: huntley at ebi.ac.uk >>>> URL: http://www.ebi.ac.uk/GOA >>>> >>>> >>>> -- >>>> This message is from the GOFriends moderated mailing list. A list >>>> of public >>>> announcements and discussion of the Gene Ontology (GO) project. >>>> Problems with the list? E-mail: >>>> owner-gofriends at geneontology.org >>>> >>>> Subscribing send "subscribe" to >>>> gofriends-request at geneontology.org >>>> >>>> Unsubscribing send "unsubscribe" to >>>> gofriends-request at geneontology.org >>>> >>>> Web: http://www.geneontology.org/ >>> >>> >>> ===================================== >>> >>> Jim Hu >>> >>> Associate Professor >>> >>> Dept. of Biochemistry and Biophysics >>> >>> 2128 TAMU >>> >>> Texas A&M Univ. >>> >>> College Station, TX 77843-2128 >>> >>> 979-862-4054 >>> >>> >>> >> >> >> -- >> >> Do you need any additional GO annotation resources? >> Which proteins would you like annotated with GO? >> >> Let us know in the GOA User Survey, available at >> http://www.ebi.ac.uk/GOA/contactus.html >> >> >> ************************************* >> >> Rachael Huntley Ph.D. >> >> European Bioinformatics Institute-EMBL >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel: +44 (0)1223 492515 >> Fax: +44 (0)1223 494468 >> >> E-mail: huntley at ebi.ac.uk >> URL: http://www.ebi.ac.uk/GOA >> > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > -- Dr. med. Peter N. Robinson, MSc. Institut f?r Medizinische Genetik Universit?tsklinikum Charite Humboldt-Universit?t Augustenburger Platz 1 13353 Berlin Germany voice: 49-30-450569124 fax: 49-30-450569915 email: peter.robinson at charite.de http://www.charite.de/ch/medgen/robinson -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From arnaudm at genome.Stanford.EDU Thu Jan 10 08:49:14 2008 From: arnaudm at genome.Stanford.EDU (Martha Arnaud) Date: Thu, 10 Jan 2008 08:49:14 -0800 Subject: [gofriends] GO visualisation tool? In-Reply-To: References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> <47864117.30207@ebi.ac.uk> Message-ID: <3B76B127-CD8B-4F67-9083-0C16B27C2C82@genome.stanford.edu> Hi Jim, Rachael-- > a general tool would be something where you give a program the > ontology, a gene association file, and a list of genes, and get the > appropriate display. This has to be filtered for statistically > enriched associations to be useful, I think. I'm interested to see > what others suggest. I think that various projects have their own > organism-specific versions of this, and I think it's built into > commercial packages like GeneSpring. But I'd like to see a list > and discussion of what's available as open source... especially for > things that can be displayed as web tools. How about GO Term Finder? The folks at Princeton have a nice, very flexible implementation of it available on their web site: http://go.princeton.edu/cgi-bin/GOTermFinder You can try it out with the list of S. cerevisiae genes they provide (the "SGD sample gene list"). Scroll down the results page to see the graph; it is displayed below the results table. It's open source; see http://www.ncbi.nlm.nih.gov/pubmed/15297299?dopt=Abstract Martha On Jan 10, 2008, at 8:24 AM, Jim Hu wrote: > Hi Rachael, > > On Jan 10, 2008, at 10:00 AM, Rachael Huntley wrote: > >> Hi Jim, >> >> He has done a microarray experiment and wants to cluster the genes >> according to GO, so he wants to see the GO tree with the genes >> displayed under the GO terms they are annotated to. I don't think >> AmiGO does this sort of thing. > > Ah, that makes sense. So, if I understand this right, a general > tool would be something where you give a program the ontology, a > gene association file, and a list of genes, and get the appropriate > display. This has to be filtered for statistically enriched > associations to be useful, I think. I'm interested to see what > others suggest. I think that various projects have their own > organism-specific versions of this, and I think it's built into > commercial packages like GeneSpring. But I'd like to see a list > and discussion of what's available as open source... especially for > things that can be displayed as web tools. > > Jim > >> >> >> Rachael. >> >> Jim Hu wrote: >> >>> Hi Rachael, >>> >>> I'm not sure I understand what the user wants to do. Doesn't >>> AmiGO place genes under the appropriate branches based on >>> annotations? Is this not the desired kind of visualization? Or >>> do they want something different? >>> >>> Jim >>> >>> >>> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >>> >>>> Dear all, >>>> >>>> I have had this query from a user, does anyone know of a tool >>>> that can do this? >>>> >>>> >Do you know of any GO viewer that allows you to visualise the >>>> GO structure and place genes with a specific annotation under >>>> that branch of the tree? >>>> < >>>> >>>> Thanks, >>>> Rachael. >>>> >>>> -- >>>> Rachael Huntley Ph.D. >>>> >>>> European Bioinformatics Institute-EMBL >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD >>>> United Kingdom Tel: +44 (0)1223 492515 >>>> Fax: +44 (0)1223 494468 >>>> >>>> E-mail: huntley at ebi.ac.uk >>>> URL: http://www.ebi.ac.uk/GOA >>>> >>>> >>>> -- >>>> This message is from the GOFriends moderated mailing list. A >>>> list of public >>>> announcements and discussion of the Gene Ontology (GO) project. >>>> Problems with the list? E-mail: owner- >>>> gofriends at geneontology.org >>> gofriends at geneontology.org> >>>> Subscribing send "subscribe" to gofriends- >>>> request at geneontology.org >>> request at geneontology.org> >>>> Unsubscribing send "unsubscribe" to gofriends- >>>> request at geneontology.org >>> request at geneontology.org> >>>> Web: http://www.geneontology.org/ >>> >>> >>> ===================================== >>> >>> Jim Hu >>> >>> Associate Professor >>> >>> Dept. of Biochemistry and Biophysics >>> >>> 2128 TAMU >>> >>> Texas A&M Univ. >>> >>> College Station, TX 77843-2128 >>> >>> 979-862-4054 >>> >>> >>> >> >> >> -- >> >> Do you need any additional GO annotation resources? >> Which proteins would you like annotated with GO? >> >> Let us know in the GOA User Survey, available at http:// >> www.ebi.ac.uk/GOA/contactus.html >> >> >> ************************************* >> >> Rachael Huntley Ph.D. >> >> European Bioinformatics Institute-EMBL >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel: +44 (0)1223 492515 >> Fax: +44 (0)1223 494468 >> >> E-mail: huntley at ebi.ac.uk >> URL: http://www.ebi.ac.uk/GOA >> > > ===================================== > Jim Hu > Associate Professor > Dept. of Biochemistry and Biophysics > 2128 TAMU > Texas A&M Univ. > College Station, TX 77843-2128 > 979-862-4054 > > ********************************************************** Martha B. Arnaud, Ph.D. Senior Scientific Curator, Candida Genome Database Department of Genetics Stanford University School of Medicine Stanford, CA 94305-5120 arnaudm at genome.stanford.edu http://www.candidagenome.org ********************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080110/68acde0e/attachment.html From vlee at ebi.ac.uk Thu Jan 10 09:04:15 2008 From: vlee at ebi.ac.uk (Vivian Lee) Date: Thu, 10 Jan 2008 17:04:15 -0000 (GMT) Subject: [gofriends] GO visualisation tool? In-Reply-To: References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> <47864117.30207@ebi.ac.uk> Message-ID: <52948.87.81.240.110.1199984655.squirrel@webmail.ebi.ac.uk> Hi Rachael and Jim, Ive been asked the same question when I was in a conference giving the GOA presentation. I am sure that a number of the tools at GO consortium website (http://www.geneontology.org/GO.tools.microarray.shtml) will do the visualization in addition to statistic analysis/annotation. I have got a recommendation from a friend who used gosurfer (http://bioinformatics.bioen.uiuc.edu/gosurfer/applications.htm) to present their microarray data with the GO tree pic which then was published in a journal (Mol Psychiatry. 2004 Jul;9(7):684-97, 643.) Also heard that some tools provide options of colour scheme and shape of nodes:-) (so you can personalise the layout). It is worthy noting that using a tool with regular updates of GO annotation will give a better result. Hope this helps. Vivian > Hi Rachael, > > On Jan 10, 2008, at 10:00 AM, Rachael Huntley wrote: > >> Hi Jim, >> >> He has done a microarray experiment and wants to cluster the genes >> according to GO, so he wants to see the GO tree with the genes >> displayed under the GO terms they are annotated to. I don't think >> AmiGO does this sort of thing. > > Ah, that makes sense. So, if I understand this right, a general tool > would be something where you give a program the ontology, a gene > association file, and a list of genes, and get the appropriate > display. This has to be filtered for statistically enriched > associations to be useful, I think. I'm interested to see what others > suggest. I think that various projects have their own organism- > specific versions of this, and I think it's built into commercial > packages like GeneSpring. But I'd like to see a list and discussion > of what's available as open source... especially for things that can > be displayed as web tools. > > Jim > >> >> >> Rachael. >> >> Jim Hu wrote: >> >>> Hi Rachael, >>> >>> I'm not sure I understand what the user wants to do. Doesn't AmiGO >>> place genes under the appropriate branches based on annotations? >>> Is this not the desired kind of visualization? Or do they want >>> something different? >>> >>> Jim >>> >>> >>> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >>> >>>> Dear all, >>>> >>>> I have had this query from a user, does anyone know of a tool that >>>> can do this? >>>> >>>> >Do you know of any GO viewer that allows you to visualise the GO >>>> structure and place genes with a specific annotation under that >>>> branch of the tree? >>>> < >>>> >>>> Thanks, >>>> Rachael. >>>> >>>> -- >>>> Rachael Huntley Ph.D. >>>> >>>> European Bioinformatics Institute-EMBL >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD >>>> United Kingdom Tel: +44 (0)1223 492515 >>>> Fax: +44 (0)1223 494468 >>>> >>>> E-mail: huntley at ebi.ac.uk >>>> URL: http://www.ebi.ac.uk/GOA >>>> >>>> >>>> -- >>>> This message is from the GOFriends moderated mailing list. A list >>>> of public >>>> announcements and discussion of the Gene Ontology (GO) project. >>>> Problems with the list? E-mail: >>>> owner-gofriends at geneontology.org >>>> >>>> Subscribing send "subscribe" to >>>> gofriends-request at geneontology.org >>>> >>>> Unsubscribing send "unsubscribe" to >>>> gofriends-request at geneontology.org >>>> >>>> Web: http://www.geneontology.org/ >>> >>> >>> ===================================== >>> >>> Jim Hu >>> >>> Associate Professor >>> >>> Dept. of Biochemistry and Biophysics >>> >>> 2128 TAMU >>> >>> Texas A&M Univ. >>> >>> College Station, TX 77843-2128 >>> >>> 979-862-4054 >>> >>> >>> >> >> >> -- >> >> Do you need any additional GO annotation resources? >> Which proteins would you like annotated with GO? >> >> Let us know in the GOA User Survey, available at >> http://www.ebi.ac.uk/GOA/contactus.html >> >> >> ************************************* >> >> Rachael Huntley Ph.D. >> >> European Bioinformatics Institute-EMBL >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel: +44 (0)1223 492515 >> Fax: +44 (0)1223 494468 >> >> E-mail: huntley at ebi.ac.uk >> URL: http://www.ebi.ac.uk/GOA >> > > ===================================== > Jim Hu > Associate Professor > Dept. of Biochemistry and Biophysics > 2128 TAMU > Texas A&M Univ. > College Station, TX 77843-2128 > 979-862-4054 > > > -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From huntley at ebi.ac.uk Fri Jan 11 08:19:52 2008 From: huntley at ebi.ac.uk (huntley at ebi.ac.uk) Date: Fri, 11 Jan 2008 16:19:52 -0000 (GMT) Subject: [gofriends] GO visualisation tool? In-Reply-To: <47878DC4.2090307@cipf.es> References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> <47864117.30207@ebi.ac.uk> <47878DC4.2090307@cipf.es> Message-ID: <47895.81.98.242.1.1200068392.squirrel@webmail.ebi.ac.uk> Thanks to all who responded on this! I have passed all suggestions to the user. Rachael. >>>> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >>>> >>>>> Dear all, >>>>> >>>>> I have had this query from a user, does anyone know of a tool that >>>>> can do this? >>>>> >>>>> >Do you know of any GO viewer that allows you to visualise the GO >>>>> structure and place genes with a specific annotation under that >>>>> branch of the tree? >>>>> < >>>>> >>>>> Thanks, >>>>> Rachael. >>>>> >>>>> -- >>>>> Rachael Huntley Ph.D. >>>>> >>>>> European Bioinformatics Institute-EMBL >>>>> Wellcome Trust Genome Campus >>>>> Hinxton >>>>> Cambridge CB10 1SD >>>>> United Kingdom Tel: +44 (0)1223 492515 >>>>> Fax: +44 (0)1223 494468 >>>>> >>>>> E-mail: huntley at ebi.ac.uk >>>>> URL: http://www.ebi.ac.uk/GOA >>>>> -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From sod at cs.wayne.edu Sun Jan 13 20:28:57 2008 From: sod at cs.wayne.edu (Sorin Draghici) Date: Sun, 13 Jan 2008 23:28:57 -0500 Subject: [gofriends] In-Reply-To: <380-2200814101571411@ochoa.fib.es> References: <380-2200814101571411@ochoa.fib.es> Message-ID: <478AE509.4010700@cs.wayne.edu> Rachel, I think both Onto-Express (OE) and its stand alone version, OE2GO, allow you to use arbitrary annotations and visualize the GO DAG. Regards, Sorin Sorin Draghici, Ph.D. Director of the Bioinformatics Core, Karmanos Cancer Institute Associate Professor Tel: (313) 577-5484 Dept. of Computer Science Fax: (313) 577-6868 Wayne State University 5143 Cass Ave, Room 431 State Hall, Detroit, MI, 48202 WWW: http://vortex.cs.wayne.edu/Sorin/index.htm (personal) WWW: http://vortex.cs.wayne.edu/Projects.htm (lab) Check out my recent book: Data Analysis Tools for Microarrays: http://www.crcpress.com/shopping_cart/products/product_detail.asp?sku=C3154&parent_id=&pc= Stefan Goetz wrote: > Dear Rachael, > Blast2GO allows you to easily import your GO annotations and > visualize them as a so called "combined graph" DAG with color > highlighting for gene or annotation counts. Pie charts can also be > created and all images exported as SVG or PNG files. Here a > screenshot: > http://blast2go.bioinfo.cipf.es/screenshots/combinedGraph.html > ...and some easy tutorial: > http://bioinfo.cipf.es/blast2go/b2gdata/blast2goTutorial.pdf > Regards, > Stefan Goetz > Blast2GO Team > > Rachael Huntley wrote: >> Dear all, >> >> I have had this query from a user, does anyone know of a tool that > can do this? >>> Do you know of any GO viewer that allows you to visualise the GO > structure and place genes with a specific annotation under that > branch of the tree? >> < >> >> Thanks, >> Rachael. >> > > -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From sod at cs.wayne.edu Sun Jan 13 20:38:46 2008 From: sod at cs.wayne.edu (Sorin Draghici) Date: Sun, 13 Jan 2008 23:38:46 -0500 Subject: [gofriends] GO visualisation tool? In-Reply-To: References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> <47864117.30207@ebi.ac.uk> Message-ID: <478AE756.7080609@cs.wayne.edu> Hi, A list of such tools together with an extensive discussion is available in: Purvesh Khatri and Sorin Draghici. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics, 21(18):3587-95, September 2005. The paper is available here: http://vortex.cs.wayne.edu/papers/Ontological_analysis.pdf Regards, Sorin Draghici, Ph.D. Director of the Bioinformatics Core, Karmanos Cancer Institute Associate Professor Tel: (313) 577-5484 Dept. of Computer Science Fax: (313) 577-6868 Wayne State University 5143 Cass Ave, Room 431 State Hall, Detroit, MI, 48202 WWW: http://vortex.cs.wayne.edu/Sorin/index.htm (personal) WWW: http://vortex.cs.wayne.edu/Projects.htm (lab) Check out my recent book: Data Analysis Tools for Microarrays: http://www.crcpress.com/shopping_cart/products/product_detail.asp?sku=C3154&parent_id=&pc= Jim Hu wrote: > Hi Rachael, > > On Jan 10, 2008, at 10:00 AM, Rachael Huntley wrote: > >> Hi Jim, >> >> He has done a microarray experiment and wants to cluster the genes >> according to GO, so he wants to see the GO tree with the genes >> displayed under the GO terms they are annotated to. I don't think >> AmiGO does this sort of thing. > > Ah, that makes sense. So, if I understand this right, a general tool > would be something where you give a program the ontology, a gene > association file, and a list of genes, and get the appropriate display. > This has to be filtered for statistically enriched associations to be > useful, I think. I'm interested to see what others suggest. I think > that various projects have their own organism-specific versions of this, > and I think it's built into commercial packages like GeneSpring. But > I'd like to see a list and discussion of what's available as open > source... especially for things that can be displayed as web tools. > > Jim > >> >> >> Rachael. >> >> Jim Hu wrote: >> >>> Hi Rachael, >>> >>> I'm not sure I understand what the user wants to do. Doesn't AmiGO >>> place genes under the appropriate branches based on annotations? Is >>> this not the desired kind of visualization? Or do they want >>> something different? >>> >>> Jim >>> >>> >>> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >>> >>>> Dear all, >>>> >>>> I have had this query from a user, does anyone know of a tool that >>>> can do this? >>>> >>>> >Do you know of any GO viewer that allows you to visualise the GO >>>> structure and place genes with a specific annotation under that >>>> branch of the tree? >>>> < >>>> >>>> Thanks, >>>> Rachael. >>>> >>>> -- >>>> Rachael Huntley Ph.D. >>>> >>>> European Bioinformatics Institute-EMBL >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD >>>> United Kingdom Tel: +44 (0)1223 492515 >>>> Fax: +44 (0)1223 494468 >>>> >>>> E-mail: huntley at ebi.ac.uk >>>> URL: http://www.ebi.ac.uk/GOA >>>> >>>> >>>> -- >>>> This message is from the GOFriends moderated mailing list. A list >>>> of public >>>> announcements and discussion of the Gene Ontology (GO) project. >>>> Problems with the list? E-mail: >>>> owner-gofriends at geneontology.org >>>> >>>> Subscribing send "subscribe" to >>>> gofriends-request at geneontology.org >>>> >>>> Unsubscribing send "unsubscribe" to >>>> gofriends-request at geneontology.org >>>> >>>> Web: http://www.geneontology.org/ >>> >>> >>> ===================================== >>> >>> Jim Hu >>> >>> Associate Professor >>> >>> Dept. of Biochemistry and Biophysics >>> >>> 2128 TAMU >>> >>> Texas A&M Univ. >>> >>> College Station, TX 77843-2128 >>> >>> 979-862-4054 >>> >>> >>> >> >> >> -- >> >> Do you need any additional GO annotation resources? >> Which proteins would you like annotated with GO? >> >> Let us know in the GOA User Survey, available at >> http://www.ebi.ac.uk/GOA/contactus.html >> >> >> ************************************* >> >> Rachael Huntley Ph.D. >> >> European Bioinformatics Institute-EMBL >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel: +44 (0)1223 492515 >> Fax: +44 (0)1223 494468 >> >> E-mail: huntley at ebi.ac.uk >> URL: http://www.ebi.ac.uk/GOA >> > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From FMcCarthy at cvm.msstate.edu Wed Jan 16 11:30:43 2008 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Wed, 16 Jan 2008 13:30:43 -0600 Subject: [gofriends] array analysis tools: request to developers Message-ID: Hi All, We will be running a 1 1/2 day GO Training course at Mississippi State on 21-22 May, 2008. This will be in conjunction with the international conference ?Delivering Value from Avian Genomics? (May 19-20, 2008). Many of the conference attendees have array datasets that they will be using GO to functionally model. I would like to extend to tool developers the opportunity to attend this workshop and demo your tool for the avian community. Naturally not everyone will be able to attend but if your tool can be used for gene expression/microarray analysis of avian datasets (eg. includes avian GO annotations) then please contact me and I will do my best to ensure that attendees have a list of potential tools that they can use. Please contact me if you are interested. thanks, Fiona The AgBase Databases Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031 http://www.agbase.msstate.edu/ -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From dbarrell at ebi.ac.uk Mon Jan 21 05:20:15 2008 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Mon, 21 Jan 2008 13:20:15 +0000 Subject: [gofriends] January 2008 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <47949C0F.3070104@ebi.ac.uk> GOA releases: January 2008 ============================ GOA (GO Annotation at EBI) is a project run by the European Bioinformatics Institute that aims to provide assignments of gene products to the Gene Ontology (GO) resource. The data can be obtained via: EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ EBI SRS: http://srs.ebi.ac.uk. Search GOA data library GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/ GO CVS: http://www.geneontology.org/GO.CVS.help.html (the last two will be updated overnight) For further information read: http://www.ebi.ac.uk/GOA or contact goa at ebi.ac.uk. Regards The UniProt GOA Team -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From akivela at gripstudios.com Wed Jan 23 03:13:43 2008 From: akivela at gripstudios.com (=?ISO-8859-1?Q?Aki_Kivel=E4?=) Date: Wed, 23 Jan 2008 13:13:43 +0200 Subject: [gofriends] Announcement: General OBO to Topic Maps conversion available Message-ID: <47973D87.11244.4E425C@localhost> Hello I would like to announce we have specified and implemented general OBO flat file to Topic Maps (ISO 13250) conversion. Conversion feature is a part of Wandora application. Application is free for non- commercial and research use. As a demonstration we have converted The Gene Ontology to a topic map. The application and the topic map conversion of GO are downloadable at http://www.wandora.org http://www.wandora.org/wandora/wiki/index.php?title=Topic_map_conversi on_of_Gene_Ontology I would appreciate feedback and suggestions for improvements. Best Regards, Aki Kivel? Grip Studios Interactive Inc. Kristianinkatu 15 FIN-00170 Helsinki Finland -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From tberardi at acoma.Stanford.EDU Wed Jan 23 11:18:44 2008 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Wed, 23 Jan 2008 11:18:44 -0800 Subject: [gofriends] Introduction of new relationship types in GO Message-ID: <8e22ab960801231118u322a20bekb066c6ace8a499d@mail.gmail.com> Dear GO Community: 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, and we are working to align regulation of biological quality terms with PATO. WE PLAN TO REPLACE THE CURRENT 'part_of' RELATIONSHIPS IN THE ONTOLOGY WITH THE NEW 'regulates' RELATIONSHIPS ON MARCH 25,2008. Concurrent with this replacement, we will also introduce new 'intersection_of' tags into the OBO stanzas of the regulation terms; these tags can be safely ignored by software with no negative consequences. 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. CURRENT STANZA [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 NEW STANZA [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 intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006312 ! mitotic recombination relationship: regulates GO:0006312 ! mitotic recombination 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/gene_ontology_with_regulates_relations_test.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 -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From hu at animalgenome.org Thu Jan 10 08:21:30 2008 From: hu at animalgenome.org (Zhiliang Hu) Date: Thu, 10 Jan 2008 10:21:30 -0600 (CST) Subject: [gofriends] GO visualisation tool? Message-ID: Rachael, For the purpose you describe, perhaps you may like to try this tool out: http://www.animalgenome.org/bioinfo/tools/countgo/ Zhiliang On Thu, 10 Jan 2008, Rachael Huntley wrote: > Date: Thu, 10 Jan 2008 16:00:23 +0000 > From: Rachael Huntley > To: Jim Hu > Cc: go-friends at genome.stanford.edu > Subject: Re: [gofriends] GO visualisation tool? > > Hi Jim, > > He has done a microarray experiment and wants to cluster the genes > according to GO, so he wants to see the GO tree with the genes displayed > under the GO terms they are annotated to. I don't think AmiGO does this > sort of thing. > > Rachael. > > Jim Hu wrote: > >> Hi Rachael, >> >> I'm not sure I understand what the user wants to do. Doesn't AmiGO >> place genes under the appropriate branches based on annotations? Is >> this not the desired kind of visualization? Or do they want something >> different? >> >> Jim >> >> >> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >> >>> Dear all, >>> >>> I have had this query from a user, does anyone know of a tool that >>> can do this? >>> >>>> Do you know of any GO viewer that allows you to visualise the GO >>> structure and place genes with a specific annotation under that >>> branch of the tree? >>> < >>> >>> Thanks, >>> Rachael. >>> >>> -- >>> Rachael Huntley Ph.D. >>> >>> European Bioinformatics Institute-EMBL >>> Wellcome Trust Genome Campus >>> Hinxton >>> Cambridge CB10 1SD >>> United Kingdom >>> Tel: +44 (0)1223 492515 >>> Fax: +44 (0)1223 494468 >>> >>> E-mail: huntley at ebi.ac.uk >>> URL: http://www.ebi.ac.uk/GOA -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From aconesa at cipf.es Fri Jan 11 07:39:48 2008 From: aconesa at cipf.es (Ana Conesa) Date: Fri, 11 Jan 2008 16:39:48 +0100 Subject: [gofriends] GO visualisation tool? In-Reply-To: References: <478621CC.3060003@ebi.ac.uk> <521BF6B1-E70E-4142-9E21-192958959D30@tamu.edu> <47864117.30207@ebi.ac.uk> Message-ID: <47878DC4.2090307@cipf.es> Blast2GO is a free available tool (http://www.blast2go.org) that does exactly that. You can upload your GO annotation file (or generate it with the tool), select the genes you want to visualize and using the "Combined Graph" functionality create the corresponding DAG. Seeing the genes annotated at the GO term is an option of the Combined Graph function. Besides this, B2G also makes enrichment analysis, so you can visualize and highlight only enriched terms. Blast2GO is a desktop application you can download and run form your computer. We are now working on the integration of this tool within the Babelomics suite (http://www.babelomics.org), which will be available very soon on the web. Babelomics has a wide repertoire of statistical methods for functional analysis. This integration will provide an annotation and a high performance visualization engines to the Babelomics suite. Ana Jim Hu wrote: > Hi Rachael, > > On Jan 10, 2008, at 10:00 AM, Rachael Huntley wrote: > >> Hi Jim, >> >> He has done a microarray experiment and wants to cluster the genes >> according to GO, so he wants to see the GO tree with the genes >> displayed under the GO terms they are annotated to. I don't think >> AmiGO does this sort of thing. > > Ah, that makes sense. So, if I understand this right, a general tool > would be something where you give a program the ontology, a gene > association file, and a list of genes, and get the appropriate > display. This has to be filtered for statistically enriched > associations to be useful, I think. I'm interested to see what others > suggest. I think that various projects have their own > organism-specific versions of this, and I think it's built into > commercial packages like GeneSpring. But I'd like to see a list and > discussion of what's available as open source... especially for things > that can be displayed as web tools. Jim > >> >> >> Rachael. >> >> Jim Hu wrote: >> >>> Hi Rachael, >>> >>> I'm not sure I understand what the user wants to do. Doesn't AmiGO >>> place genes under the appropriate branches based on annotations? Is >>> this not the desired kind of visualization? Or do they want >>> something different? >>> >>> Jim >>> >>> >>> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote: >>> >>>> Dear all, >>>> >>>> I have had this query from a user, does anyone know of a tool that >>>> can do this? >>>> >>>> >Do you know of any GO viewer that allows you to visualise the GO >>>> structure and place genes with a specific annotation under that >>>> branch of the tree? >>>> < >>>> >>>> Thanks, >>>> Rachael. >>>> >>>> -- >>>> Rachael Huntley Ph.D. >>>> >>>> European Bioinformatics Institute-EMBL >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD >>>> United Kingdom Tel: +44 (0)1223 492515 >>>> Fax: +44 (0)1223 494468 >>>> >>>> E-mail: huntley at ebi.ac.uk >>>> URL: http://www.ebi.ac.uk/GOA >>>> >>>> >>>> -- >>>> This message is from the GOFriends moderated mailing list. A list >>>> of public >>>> announcements and discussion of the Gene Ontology (GO) project. >>>> Problems with the list? E-mail: >>>> owner-gofriends at geneontology.org >>>> >>>> Subscribing send "subscribe" to >>>> gofriends-request at geneontology.org >>>> >>>> Unsubscribing send "unsubscribe" to >>>> gofriends-request at geneontology.org >>>> >>>> Web: http://www.geneontology.org/ >>> >>> >>> ===================================== >>> >>> Jim Hu >>> >>> Associate Professor >>> >>> Dept. of Biochemistry and Biophysics >>> >>> 2128 TAMU >>> >>> Texas A&M Univ. >>> >>> College Station, TX 77843-2128 >>> >>> 979-862-4054 >>> >>> >>> >> >> >> -- >> >> Do you need any additional GO annotation resources? >> Which proteins would you like annotated with GO? >> >> Let us know in the GOA User Survey, available at >> http://www.ebi.ac.uk/GOA/contactus.html >> >> >> ************************************* >> >> Rachael Huntley Ph.D. >> >> European Bioinformatics Institute-EMBL >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel: +44 (0)1223 492515 >> Fax: +44 (0)1223 494468 >> >> E-mail: huntley at ebi.ac.uk >> URL: http://www.ebi.ac.uk/GOA >> > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > -- ------------------------------------------ Ana Conesa, PhD Bioinformatics Department Centro de Investigaci?n Pr?ncipe Felipe Avda. Autopista Saler, 16 46013 Valencia Spain http://bioinfo.cipf.es/aconesa ========================================== CAMDA2007 Conference @ CIPF http://camda.bioinfo.cipf.es ========================================== -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From asidhu at biomap.org Sat Jan 26 01:50:33 2008 From: asidhu at biomap.org (Amandeep Sidhu) Date: Sat, 26 Jan 2008 18:50:33 +0900 Subject: [gofriends] 3rd Special Track on Ontologies for Biomedical Systems for 21st CBMS 2008 Message-ID: <2dbc82b00801260150g2ea6aafdi578170c76fe85914@mail.gmail.com> 3rd Special Track on Ontologies for Biomedical Systems for 21st IEEE International Symposium on Computer-Based Medical Systems http://cbms08.biomap.org/ Call for Papers Biomedical Ontologies have developed in an uncoordinated way, often reflecting mere relations of 'association' between what are called 'concepts', and serving primarily the purposes of information extraction from on-line biomedical literature and databases. In recent years, we have learned a great deal about the criteria which must be satisfied if ontology is to allow true information integration and automatic reasoning across data and information derived from different sources. The goal of this track is to survey existing biomedical ontologies and reform them in such a way as to allow true information integration in biomedical domain. Authors are invited to submit original papers exploring the theories, techniques, and applications of biomedical ontologies. Papers are invited (but not limited) to the following themes: * Biomedical Ontologies for Genetics, Proteomics, Diseases, Privacy etc. * Conceptual Models for Biological and Medical Data * Semantics in Biological Data Modeling * Use of semantics to manage Interoperation in Biomedical Databases * Semantic Web technologies and formalisms for Biomedical Data * Ontology representation and exchange languages for bioinformatics * Biomedical Ontologies and OWL * Biological Data Integration and Management using Ontologies * Biomedical Data Engineering using Ontologies * Application of Biomedical Ontologies for Heterogeneous Database Access * Query Optimization Techniques for Biomedical Database using Ontologies * Support of Ontologies for Biological Information Retrieval and Web Services * Change Management in Biomedical Ontologies * Tools for Development and Management of Biomedical Ontologies Important Dates 04 February 2008 Paper Submission Due 28 February 2008 Notification of acceptance 28 March 2008 Final camera-ready paper due 28 March 2008 Pre-registration deadline Paper Submission Procedures Submitted papers have to be original, containing new and original results. Use a maximum of 6 pages IEEE two-column format, including figures and references. All submissions will be done electronically via the CBMS 2008 web submission system (http://www.easychair.org/conferences/?conf=CBMS2008). Submission implies the willingness of at least one of the authors to register and present the paper at the CBMS 2008 Symposium. All papers will be peer reviewed by at least two independent referees. All accepted papers will be included in the conference proceedings. High Quality submissions will be published in a special issue of Biomedical Ontologies Journal by Oxford University Press. Track Organizers Amandeep S. Sidhu Curtin University of Technology, Perth http://www.amandeep.org/ Tharam S. Dillon Curtin University of Technology, Perth Jake Chen Indiana University, USA http://informatics.iupui.edu/people/profile.php?id=74 Elizabeth Chang Curtin University of Technology, Australia http://www.fit.cbs.curtin.edu.au/~chang/docs/index.php Program Committee Alexey Tsymbal (Siemens, Germany) David Hansen (e-Health Research Centre, CSIRO, Australia) David Taniar (Monash University, Australia) Ernesto Damiani (Computer Science Department, Milan University, Italy) Fabio Porto (Database Laboratory, EPFL, Switzerland) Farookh K. Hussain (Curtin University of Technology, Australia) Fedja Hadzic (University of Technology Sydney, Australia) Huiru Zheng (University of Ulster, UK) Jake Chen (Indiana University, USA) James Geller (New Jersey Institute of Technology, USA) Jason Wang (New Jersey Institute of Technology, USA) Li Liao (University of Delaware, USA) Ling Feng (Tsinghua University, China) Maja Hadzic (Curtin University of Technology, Australia) Midori Harris (GO Consortium, European Bioinformatics Institute) Mustafa Jarrar (Vrije Universiteit Brussel, Belgium) Robert Meersman (Vrije Universiteit Brussel, Belgium) Silke Eckstein (Technical University of Braunschweig, Germany) Sourav S Bhowmick (Nanyang Technological University, Singapore) Sun Kim (School of Informatics, Indiana University, USA) Wenny Rahayu (La Trobe University, Australia) Werner Ceusters (New York State Center of Excellence in Bioinformatics & Life Sciences, USA) Yi Pan (Georgia State University, USA) -------------- next part -------------- An HTML attachment was scrubbed... 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