From dhowe at cs.uoregon.edu Thu Nov 1 12:11:36 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Thu, 01 Nov 2007 12:11:36 -0700 Subject: [gofriends] google Document-comments please Message-ID: <472A24E8.9040607@cs.uoregon.edu> Sue and I have begun commenting on the Google doc outline for the Biocuration Meeting Review. Please visit the document and insert your comments as soon as possible. This is going to be a fairly expedited production process! We would like to send an outline or rough draft to Phil Campbell, the Editor at Nature, on Friday, Nov. 9th. Thanks, Doug -- 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 dhowe at cs.uoregon.edu Thu Nov 1 12:16:10 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Thu, 01 Nov 2007 12:16:10 -0700 Subject: [gofriends] Re: google Document-comments please In-Reply-To: <472A24E8.9040607@cs.uoregon.edu> References: <472A24E8.9040607@cs.uoregon.edu> Message-ID: <472A25FA.7090705@cs.uoregon.edu> My apologies...this post was directed to an incorrect email list. Please disregard. -Doug Doug howe wrote: > Sue and I have begun commenting on the Google doc outline for the > Biocuration Meeting Review. Please visit the document and insert your > comments as soon as possible. This is going to be a fairly expedited > production process! > > We would like to send an outline or rough draft to Phil Campbell, the > Editor at Nature, on Friday, Nov. 9th. > > Thanks, > Doug > -- 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 dhowe at cs.uoregon.edu Thu Nov 1 12:26:15 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Thu, 01 Nov 2007 12:26:15 -0700 Subject: [gofriends] google Document-comments please Message-ID: <472A2857.5060701@cs.uoregon.edu> Again, my apologies. The following was posted to an incorrect distribution list. Please disregard. -Doug Sue and I have begun commenting on the Google doc outline for the Biocuration Meeting Review. Please visit the document and insert your comments as soon as possible. This is going to be a fairly expedited production process! We would like to send an outline or rough draft to Phil Campbell, the Editor at Nature, on Friday, Nov. 9th. Thanks, Doug -- 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 Tue Nov 6 08:51:38 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Tue, 6 Nov 2007 08:51:38 -0800 Subject: [gofriends] Some GO services unavailable Message-ID: <95465556-7C74-4ECF-AB5F-3B400B29BE2A@genome.stanford.edu> Hello, Due to an unexpected electrical problems, we will need to shut down the GO FTP server, CVS, and all wikis temporarily. As of now, AmiGO and the GO database will remain online. We apologize for the short notice and for the inconvenience this may cause. Cheers, Eurie -- 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 Wed Nov 14 06:46:10 2007 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Wed, 14 Nov 2007 14:46:10 +0000 Subject: [gofriends] November 2007 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <473B0A32.1010908@ebi.ac.uk> GOA releases: November 2007 ============================ 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. GOA News Update: ***************** New Subcellular Location2GO mapping (spsl2go) The GOA group are pleased to announce that in collaboration with Serenella Ferro Rojas of the Swiss Institute of Bioinformatics, we are able to offer a new external database mapping file. So far, 269 Subcellular Location terms from the Comment (CC) lines of UniProtKB entries have been manually mapped to GO terms. The new mapping has been applied electronically to enhance the electronic (IEA coded) GO annotation in our latest GOA release. This mapping has provided 418,185 new associations with 396,734 proteins. The spsl2go mapping file is available from the GOA ftp site (ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/spsl2go) and the Gene Ontology Consortium website (http://www.geneontology.org/external2go/spsl2go). The GO reference for this mapping is GO_REF:0000023. PRSF2GO mapping file now available This month, the GOA group has created a PRSF2GO mapping file. This file is a subset of the InterPro2GO mapping, with PRSF identifiers used instead of InterPro identifiers. The prsf2go mapping file is available from the GOA ftp site (ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/prsf2go) and the Gene Ontology Consortium website (http://www.geneontology.org/external2go/prsf2go). Ensembl Compara pipeline This month, the Ensembl Compara electronic annotation pipeline will provide annotations to an increased set of species, including macaque, chimpanzee, guinea pig, Xenopus, Tetradon, Fugu, zebrafish and Aedes aegypti. For full details of this method, please see: http://www.ebi.ac.uk/goa/compara_go_annotations.html External Dates Annotation dates supplied in column 14 of the GOA gene association files have now been corrected for annotations integrated from external model organism databases. GOA Survey The GOA group now has added a short user survey to our website, which we invite you to complete, especially if: - you have set of proteins that you would like to suggest to be prioritized for manual annotation? - you would like to join our expert panel to review a specified set of fully manually-annotated proteins? - there are additional files that GOA could supply that you would find useful? The survey is available at: http://www.ebi.ac.uk/GOA/contactus.html 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 stacia at genome.Stanford.EDU Fri Nov 16 11:20:30 2007 From: stacia at genome.Stanford.EDU (Stacia Engel) Date: Fri, 16 Nov 2007 11:20:30 -0800 Subject: [gofriends] Gene Ontology Newsletter - November 2007 issue Message-ID: Gene Ontology Newsletter November 2007, Issue No. 7 In this issue: 1. Cardiovascular Physiology and Muscle Content Meetings 2. Cardiovascular Gene Ontology Annotation Initiative 3. How to Get Started with GO: Annotation SOPs 4. Evidence Code Update 5. With (or) From field 6. Subcellular Location to GO mapping (spsl2go) 7. Upcoming Meetings The text of the newsletter can be viewed online or downloaded: HTML: http://www.geneontology.org/newsletter/current-newsletter.shtml PDF: http://www.geneontology.org/newsletter/current-newsletter.pdf Please contact the Gene Ontology Consortium with any comments or suggestions at gohelp at geneontology.org. Frequently asked questions may appear as tutorials or tips in upcoming newsletters. -- 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 edimmer at ebi.ac.uk Thu Nov 22 02:20:53 2007 From: edimmer at ebi.ac.uk (E Dimmer) Date: Thu, 22 Nov 2007 10:20:53 +0000 Subject: [gofriends] GO tool required to create GO pie chart from set of GI numbers Message-ID: <47455805.3050007@ebi.ac.uk> Hi, Does anyone know of a tool that could help Mark's query (below)? If so, we would be grateful if you could send any details. Thanks, Emily contactName: Mark Ross contactEmail: mross7 at gmu.edu contactText: Can I enter protein database GI numbers, such as from the NCBI database, and retrieve GO annotations? If so, how can I do this? My goal is to produce the often seen pie chart representations of protein categorization from a broad protein analysis (biol. process, function or compartment). Thank you for your help. - Mark -- ************************************ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ -- 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 Fri Nov 23 14:57:07 2007 From: hu at animalgenome.org (Zhiliang Hu) Date: Fri, 23 Nov 2007 16:57:07 -0600 (CST) Subject: [gofriends] GO tool required to create GO pie chart from set of GI numbers Message-ID: >From ncbi GI match to GO, I am afraid you have to do blast. For GO classifications and drawing a pie chart, you may like to try: http://www.animalgenome.org/bioinfo/tools/countgo/ Zhiliang On Thu, 22 Nov 2007, E Dimmer wrote: > Date: Thu, 22 Nov 2007 10:20:53 +0000 > From: E Dimmer > To: gofriends at genome.stanford.edu > Cc: mross7 at gmu.edu > Subject: [gofriends] GO tool required to create GO pie chart from set of GI > numbers > > Hi, > > Does anyone know of a tool that could help Mark's query (below)? > If so, we would be grateful if you could send any details. > > Thanks, > Emily > > contactName: Mark Ross > contactEmail: mross7 at gmu.edu > contactText: Can I enter protein database GI numbers, such as from the > NCBI database, and retrieve GO annotations? If so, how can I do this? > My goal is to produce the often seen pie chart representations of > protein categorization from a broad protein analysis (biol. process, > function or compartment). Thank you for your help. - Mark -- 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 Thu Nov 22 02:54:18 2007 From: aconesa at cipf.es (Ana Conesa) Date: Thu, 22 Nov 2007 11:54:18 +0100 Subject: [gofriends] GO tool required to create GO pie chart from set of GI numbers In-Reply-To: <47455805.3050007@ebi.ac.uk> References: <47455805.3050007@ebi.ac.uk> Message-ID: <47455FDA.7080206@cipf.es> Hi Mark You can use Blast2GO for this (www.blast2go.org) . Simply create a file with your identifiers, import in Blast2GO. You should create then a Combined Graph and subsequently a Pie chart of your GO term assignments. Note that you can create Pies both per GO level or a "multilevel pie", which takes the lowest term in each branch that fulfills given number of annotated proteins. Best wishes Ana Conesa E Dimmer wrote: > Hi, > > Does anyone know of a tool that could help Mark's query (below)? > If so, we would be grateful if you could send any details. > > Thanks, > Emily > > contactName: Mark Ross > contactEmail: mross7 at gmu.edu > contactText: Can I enter protein database GI numbers, such as from the > NCBI database, and retrieve GO annotations? If so, how can I do this? > My goal is to produce the often seen pie chart representations of > protein categorization from a broad protein analysis (biol. process, > function or compartment). Thank you for your help. - Mark > -- 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/