From FMcCarthy at cvm.msstate.edu Thu Mar 6 14:09:00 2008 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Thu, 06 Mar 2008 16:09:00 -0600 Subject: [gofriends] 2nd Announcement: Delivering Value from Avian Genomics Message-ID: This is a further 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. Information about the conference venue (including travel & accommodation details) and a preliminary schedule for both conference & workshop is now available at the Conference & Workshop website: http://www.idb.msstate.edu/events.html Abstracts are due Tuesday 1 April. Student travel awards are available and students wishing to be considered for an award should submit an abstract to be considered. 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 deustp01 at med.nyu.edu Wed Mar 12 08:37:54 2008 From: deustp01 at med.nyu.edu (Peter D'Eustachio) Date: Wed, 12 Mar 2008 11:37:54 -0400 Subject: [gofriends] [Reactome-announce] Reactome version 24 release today Message-ID: <001301c88457$1bc9a480$4b14a10a@DFWFS881> Version 24 of the Reactome Knowledgebase has been released and is accessible at http://www.reactome.org. Reactome is a curated knowledgebase developed and maintained by the Reactome Knowledgebase team (Lincoln Stein's group at CSHL, Ewan Birney's group at the European Bioinformatics Institute, and Peter D'Eustachio's group at NYU). Reactome covers human biological processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI, Entrez Gene, RefSeq, OMIM, Ensembl genome annotations, HapMap, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). The web interface allows users to view the curated annotations of human biological processes and orthology-based electronic inferences from these annotations for 22 other species. New additions to curated content include the pathway topics: Signaling by VEGF, Metabolism of nitric oxide, and MicroRNA biogenesis, and new modules added to existing pathways: Cleavage reactions (Apoptosis), Generic transcription pathway (Gene expression), Tie2 and PECAM events (Hemostasis), TCR cascade (Immune signaling), Pyruvate Decarboxylase regulation (Energy metabolism), COP II mediated events (Membrane Trafficking), Hypusine synthesis (Post translational modifications), PLC-gamma and Grb2 mediated downstream events (EGFR signaling). This material was generated in collaboration with K Schulze-Osthoff, and L Castognoli (authors), and S Ranganathan, LP Freedman, J Trowsdale, J Lippincott-Schwartz, G Enikolopov, F Karginov, GJ Hannon, CH Heldin, and L Claesson-Welsh (reviewers). A new pathway visualization tool (beta version) is available with this release. Please try it, and send us feedback. Pathway annotations from Reactome are now incorporated into the Pathway Interaction Database (PID), a collaborative project between the US National Cancer Institute and Nature Publishing Group. Access to 703 Reactome curated pathways and a primer for using Reactome data are available from PID's website at http://pid.nci.nih.gov/ Updated release statistics and the Editorial Calendar are available. Data download including database dumps and protein-protein interaction datasets are available from the download page on the website. Reactome data can be exported in SMBL, Prot?g?, and BioPAX level 2 formats. Like everything in Reactome, these downloaded and exported materials can be reused. Users can subscribe to Reactome announcement list from the webpage at http://mail.reactome.org/mailman/listinfo/reactome-announce. Reactome is seeking expert help for the curation of new modules. The Reactome knowledgebase relies on collaborations with research biologists to construct expert consensus views of key biological processes, and to integrate these with other processes already in Reactome. We are seeking new author-collaborators. If you're interested, or would like more information about our data acquisition process, please contact us at editorial at reactome.org. For questions and comments please reply to this message or write to help at reactome.org. -The Reactome team -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080312/9df08ef0/attachment.html -------------- next part -------------- _______________________________________________ Reactome-announce mailing list Reactome-announce at reactome.org http://mail.reactome.org/mailman/listinfo/reactome-announce From dbarrell at ebi.ac.uk Thu Mar 13 04:28:26 2008 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Thu, 13 Mar 2008 11:28:26 +0000 Subject: [gofriends] March 2008 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <47D90FDA.8010804@ebi.ac.uk> GOA releases: March 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 rama at genome.Stanford.EDU Mon Mar 17 21:51:19 2008 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Mon, 17 Mar 2008 21:51:19 -0700 Subject: [gofriends] Downtime for GO pages Message-ID: <91F56F17-37FE-480B-A141-2BADEA7B9792@genome.stanford.edu> Hi All, The following services will be unavailable Wednesday, March 19th, 2008 starting at 6.00 AM PST (9:00 PM EST, 1:00 PM GMT, and 10:00 PM March 19, JST) due to work on the air conditioner in the server room. *GO web pages (http://www.geneontology.org/) *Write access to the CVS repository During this time, the AmiGO database (http://amigo.geneontology.org), the anonymous access to the GO FTP (ftp://ftp.geneontology.org/pub/ go/), web access to the CVS repository (http:// cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/) will be available. We expect the work to take approximately 12 hours (should finish by 6.00PM PST, 9.00PM EST, 1.00AM GMT March 20th, 10.00AM JST March 20th) but we will make every attempt to keep it as short as possible. We apologize for the short notice and for any inconvenience this may cause. Rama ****************************** Rama Balakrishnan PhD Saccharomyces Genome Database Stanford University, CA ****************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080317/28627fd0/attachment.html From rama at genome.Stanford.EDU Wed Mar 19 17:10:29 2008 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Wed, 19 Mar 2008 17:10:29 -0700 Subject: [gofriends] GO web pages are back up In-Reply-To: <91F56F17-37FE-480B-A141-2BADEA7B9792@genome.stanford.edu> References: <91F56F17-37FE-480B-A141-2BADEA7B9792@genome.stanford.edu> Message-ID: <10940485-E265-401E-8F03-71E2F0256304@genome.stanford.edu> Hi All, All GO services are now back up and running. Please let us know if you notice any odd behavior. Best, Rama On Mar 17, 2008, at 9:51 PM, Rama Balakrishnan wrote: > Hi All, > > The following services will be unavailable Wednesday, March 19th, > 2008 starting at 6.00 AM PST (9:00 PM EST, 1:00 PM GMT, and 10:00 PM > March 19, JST) due to work on the air conditioner in the server room. > > *GO web pages (http://www.geneontology.org/) > *Write access to the CVS repository > > During this time, the AmiGO database (http:// > amigo.geneontology.org), the anonymous access to the GO FTP (ftp://ftp.geneontology.org/pub/go/ > ), web access to the CVS repository (http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/ > ) will be available. > > We expect the work to take approximately 12 hours (should finish by > 6.00PM PST, 9.00PM EST, 1.00AM GMT March 20th, 10.00AM JST March > 20th) but we will make every attempt to keep it as short as possible. > > We apologize for the short notice and for any inconvenience this may > cause. > > Rama > > > > ****************************** > Rama Balakrishnan PhD > Saccharomyces Genome Database > Stanford University, CA > ****************************** > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080319/b3a5a474/attachment.html From cjm at fruitfly.org Wed Mar 26 09:23:29 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 26 Mar 2008 09:23:29 -0700 Subject: [gofriends] Forthcoming changes to URLs for downloading GO Message-ID: <052D6E69-31F0-482A-92A9-D00B7E44025D@fruitfly.org> This is to announce forthcoming changes to the location at which the gene ontology obo file can be downloaded from. These changes are entirely backwards compatible, no action is required on anyone's part. The current URLs are: http://www.geneontology.org/ontology/gene_ontology_edit.obo -- obo format 1.2 http://www.geneontology.org/ontology/gene_ontology.obo -- obo format 1.0 These URLs will continue to be supported. However, the same content will be available from URLs which more accurately reflect their content, specifically: http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology. 1_2.obo http://www.geneontology.org/ontology/obo_format_1_0/gene_ontology. 1_0.obo (these URLs will be dead links until this change comes into effect) Once they change comes into effect, you are encouraged to change the URLs you use for the purpose of linking, automatic downloading of the ontology, at a time of your convenience. The current URLs *will* continue to be supported, and will continue to contain the up-to-date (updated daily) content of GO. However, the new URLs indicate the contents of the file more clearly. Note that the version used by the ontology editors has moved to: http://www.geneontology.org/ontology/editors/gene_ontology_write.obo However, you are strongly recommended not to link to, download or use the editors URL. You can get the same content in a timely fashion from one of the recommended URLs above. As a reminder, the cvs revision number in these files should never be used as a version number. These numbers are specific to the file- path, not the contents of these file. For more download options, please see: http://www.geneontology.org/GO.downloads.ontology.shtml This change will go into effect within the next few weeks, and will be announced on this list. -- 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 Thu Mar 27 09:20:08 2008 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Thu, 27 Mar 2008 09:20:08 -0700 Subject: [gofriends] New relationship types have been integrated into GO Message-ID: <8e22ab960803270920h2e9a9b11hbed1c14a6c2cbb9b@mail.gmail.com> As previously announced, The Gene Ontology Consortium has now introduced three new relationship types -- regulates,negatively_regulates and positively_regulates -- into the Biological Process ontology. These relationship types improve the representation of regulatory processes in the GO. Please see the following pages on the GO website for more information: http://geneontology.org/GO.process.guidelines.shtml#reg http://geneontology.org/GO.doc.shtml#ontology-structure http://geneontology.org/GO.usage.shtml#relationships The new relationship types will be visible through the AmiGO browser by the end of this month and at the various model organism databases that display GO as they update their ontology files. Sincerely, Tanya Berardini David Hill Chris Mungall on behalf of the GO Consortium -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080327/40ea323a/attachment.html