From dbarrell at ebi.ac.uk Wed Dec 5 06:55:21 2007 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Wed, 05 Dec 2007 14:55:21 +0000 Subject: [gofriends] December 2007 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <4756BBD9.2020408@ebi.ac.uk> GOA releases: December 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. 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 sherlock at genome.Stanford.EDU Thu Dec 6 18:26:04 2007 From: sherlock at genome.Stanford.EDU (Gavin Sherlock) Date: Thu, 6 Dec 2007 18:26:04 -0800 Subject: [gofriends] First Announcement for MGED 11 Meeting, Trentino, Italy Message-ID: <5BEC55B8-026D-408B-B6FE-EACD0A36F0A2@genome.stanford.edu> Dear Colleagues, Apologies if you receive this more than once. It is the pleasure of the Microarray Gene Expression and Data (MGED) society to announce the MGED11 meeting in Trentino, Italy, Monday September 1st -> Wednesday September 3rd, 2008. In addition, there will be two days of optional tutorials and workshops following the meeting on September 4th and 5th. Further information is available at http://mgedmeeting.org/ and key dates are: Registration and Abstract Submission Opens: March 1st Deadline for Abstract submission for consideration as an oral presentation : June 10th Notice of acceptance: June 25th Early registration ends: June 30th Abstract submission closes: August 5th The scientific focus of the meeting will be high throughput technologies - in particular microarrays and ultra high throughput sequencing - and associated data handling issues and analysis techniques. With the continued maturation of microarray annotation standards and tools, this year's meeting will offer more 'hands-on' tutorials and workshops to tackle specific practical applications of these concepts. Tutorials are expected to cover in depth data analysis and how to use Bioconductor. We have already lined up the following outstanding international keynote speakers: Naama Barkai - Weizmann Institute of Science Ewan Birney - EMBL-EBI Joe Gray - UCSF/ Lawrence Berkeley Nat'l Laboratory Steve Oliver - Cambridge University and will announce invited plenary speakers in the near future. In addition, this year we will again be selecting half of the plenary speakers from submitted abstracts, to encourage greater participation in the MGED community. Continuing from last year, we will again be running a poster competition, with prizes for the best posters presented by graduate and postdoctoral students. We look forward to seeing you all in Trentino, Sincerely, The Microarray and Gene Expression Data (MGED) Society -- 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 gopinath at cshl.edu Wed Dec 12 11:59:27 2007 From: gopinath at cshl.edu (Gopal Gopinathrao) Date: Wed, 12 Dec 2007 14:59:27 -0500 Subject: [gofriends] [Reactome-announce] Version 23 released Message-ID: Version 23 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. Additions to curated content include a new pathway, Signaling in BMP, and new modules within existing pathways: Apoptotic Execution Phase (Apoptosis), Cell Surface Interactions (Hemostasis), and TRKA Signaling (NGF signaling). 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/20071212/73accea2/attachment.html -------------- next part -------------- _______________________________________________ Reactome-announce mailing list Reactome-announce at reactome.org http://mail.reactome.org/mailman/listinfo/reactome-announce From vanauken at caltech.edu Wed Dec 12 13:23:42 2007 From: vanauken at caltech.edu (Kimberly Van Auken) Date: Wed, 12 Dec 2007 13:23:42 -0800 Subject: [gofriends] Re: Fwd: Web tool to replace GOFigure? In-Reply-To: References: <200712121322.lBCDMw02029631@fafner.Stanford.EDU> Message-ID: <4760515E.9010501@caltech.edu> Dear Alexander, Thanks for writing to the GO. I'm forwarding your query on to the gofriends mailing list to see if anyone is aware of a tool like GOFigure where you can choose the GO category you want returned prior to running a batch search with FASTA files. This may be a feature we could consider adding to the BLAST search on the AmiGO site. Regards, Kimberly Van Auken Database Curator, WormBase www.wormbase.org www.geneontology.org > Date: Wed, 12 Dec 2007 05:22:57 -0800 (PST) > Message-Id: <200712121322.FAA19483 at bread.Stanford.EDU > > > To: witeka at uni-mainz.de > Subject: GO Help query (from website) > From: noreply at genome.stanford.edu > > contactName: Alexander Witek > contactEmail: witeka at uni-mainz.de > contactText: Dear colleagues, > > i?m searching for a web-based gene ontology annotation toll like > GOfigure (wich is not available any more), where i can put in batch > jobs with fasta format sequences and where i can choose before > starting the job wich GO category i would like to prefer. > > Can you help me with that? > > Best wishes > > Alexander Witek > -- 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 pfey at northwestern.edu Fri Dec 14 08:07:38 2007 From: pfey at northwestern.edu (Petra Fey) Date: Fri, 14 Dec 2007 10:07:38 -0600 Subject: [gofriends] New Reference Genome Project Web Page Message-ID: <888B5821-66AF-4F13-AA54-F2843678B9B6@northwestern.edu> Dear All, there is a new web page that describes the Reference Genome Annotation Project: http://www.geneontology.org/GO.refgenome.shtml Have a look at the page and feel free to make comments and suggestions by writing to the GO Help Desk (gohelp at geneontology.org). Best wishes, Petra and the Ref Genome group --------------------------------------- Petra Fey dictyBase Scientific Curator Northwestern University Chicago, IL 60611 Tel. 312-695-2317 FAX. 312-695-1223 pfey at northwestern.edu http://dictybase.org/ --------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20071214/774975c6/attachment.html From sgoetz at cipf.es Mon Dec 17 06:33:22 2007 From: sgoetz at cipf.es (Stefan Goetz) Date: Mon, 17 Dec 2007 15:33:22 +0100 Subject: [gofriends] Re: Fwd: Web tool to replace GOFigure? In-Reply-To: <4760515E.9010501@caltech.edu> References: <200712121322.lBCDMw02029631@fafner.Stanford.EDU> <4760515E.9010501@caltech.edu> Message-ID: <476688B2.1090109@cipf.es> Dear Alexander, Kimberly and GO-Community, Go-Figure is a tool for Gene Ontology annotation based on BLAST. GoFigure maps GO terms to BLAST hits by minimum covering graph construction. Blast2GO generates/predicts GO annotations based on BLAST results considering the of the GO DAG structure plus GO Evidence Codes and all BLAST Hit similarities. (FASTA files as Input) Blast2GO is high-throughput capable and the Web-Start version, free available at www.blast2go.org, runs fine for 40.000 sequences (or more -> memory dependent ). Alexander, you are most welcome to write us for more details. We are right now implementing a full configurable, high-throughput, web version of Blast2GO which will be available in 2 to 3 weeks at http://babelomics.bioinfo.cipf.es. We will announce the release of Blast2GO-WEB on this list. Kimberly, I think it would be of great value to a lot of users who are working with novel or uncharacterised sequences/proteins to add a functional annotation feature based on BLAST directly to the Amigo website and Blast2GO would definitely be a solid option. In case you are considering this we would be very pleased to hear from you. Best regards, Stefan Goetz Kimberly Van Auken wrote: > Dear Alexander, > > Thanks for writing toDear Alexander, > > Thanks for writing to the GO. > > I'm forwarding your query on to the gofriends mailing list to see if > anyone > is aware of a tool like GOFigure where you can choose the GO category you > want returned prior to running a batch search with FASTA files. > > This may be a feature we could consider adding to the BLAST search on > the AmiGO site. > > Regards, > Kimberly Van the GO. > > I'm forwarding your query on to the gofriends mailing list to see if > anyone > is aware of a tool like GOFigure where you can choose the GO category you > want returned prior to running a batch search with FASTA files. > > This may be a feature we could consider adding to the BLAST search on > the AmiGO site. > > Regards, > Kimberly Van Auken > > Database Curator, WormBase > www.wormbase.org > www.geneontology.org > > > >> Date: Wed, 12 Dec 2007 05:22:57 -0800 (PST) >> Message-Id: <200712121322.FAA19483 at bread.Stanford.EDU >> > >> To: witeka at uni-mainz.de >> Subject: GO Help query (from website) >> From: noreply at genome.stanford.edu >> >> contactName: Alexander Witek >> contactEmail: witeka at uni-mainz.de >> contactText: Dear colleagues, >> >> i?m searching for a web-based gene ontology annotation toll like >> GOfigure (wich is not available any more), where i can put in batch >> jobs with fasta format sequences and where i can choose before >> starting the job wich GO category i would like to prefer. >> >> Can you help me with that? >> >> Best wishes >> >> Alexander Witek >> > > > -- > 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/ > -- -------------------------------------------- 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 dbarrell at ebi.ac.uk Tue Dec 18 08:00:15 2007 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Tue, 18 Dec 2007 16:00:15 +0000 Subject: [gofriends] December 18th 2007 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <4767EE8F.6080901@ebi.ac.uk> GOA releases: December 18th 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. ** NEWS ** Please note that in this release we use the abbreviation 'UniProtKB' instead of 'UniProt'. This follows the naming conventions set by the UniProt Consortium. We have added 2 new gp2protein files in this release containing all UniProt and RefSeq accessions for human and chicken in the followings files: gp2protein.human.gz gp2protein.chicken.gz 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/