From tonys at ebi.ac.uk Tue Sep 1 07:42:33 2009 From: tonys at ebi.ac.uk (Tony Sawford) Date: Tue, 01 Sep 2009 15:42:33 +0100 Subject: [Gofriends] GOA release [2009-09-01] Message-ID: <4A9D32D9.4070605@ebi.ac.uk> GOA releases: 01 September 2009 =============================== GOA (GO Annotation at EBI) is a project run by the European Bioinformatics Institute that provides 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 For further information read: http://www.ebi.ac.uk/GOA or contact goa at ebi.ac.uk. Regards, GOA Production From jrsmith at mcw.edu Tue Sep 1 15:52:19 2009 From: jrsmith at mcw.edu (Smith, Jennifer) Date: Tue, 1 Sep 2009 17:52:19 -0500 Subject: [Gofriends] RGD releases the second video in the Introduction to Biomedical Ontologies series Message-ID: <1448A38A42714048B9C53E473E13CCF0027296E0@davis.hmgc.mcw.edu> The Rat Genome Database (RGD) has just released the newest video in our series of tutorials about biomedical ontologies. The previous video in this series gave a general overview of what an ontology is. This video looks at the ontology annotations themselves. For novice users, "Anatomy of an Ontology Annotation, part 1" is primarily designed as a companion to the first video of the series. However, for those who are already somewhat familiar with ontology terms and their use, it can also stand alone as an introduction to some of the components of ontology annotations. The video touches on how the use of ontology annotations can save researchers both time and effort, then discusses the distinction between annotations which were made by curators based on experimental data and those based solely on computational evidence. Finally, it introduces the evidence code as a way to tell the difference between these two categories of annotations. For users who want to know more about annotations, the upcoming video "Anatomy of an Ontology Annotation, part 2" will delve into more detail about specific evidence codes, qualifiers and the "WITH" field. Like the first video of the series, "Anatomy of an Ontology Annotation, part 1" has been posted on both SciVee (http://www.scivee.tv/node/12395) and Vimeo (http://www.vimeo.com/6300201). RGD is pleased to make this video available for the GO community to use. If you have any questions, comments or suggestions, including suggested content for future videos, please do not hesitate to send them to Jennifer Smith at jrsmith at mcw.edu. The RGD Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From coulet at stanford.edu Thu Sep 3 18:23:55 2009 From: coulet at stanford.edu (Adrien Coulet) Date: Thu, 03 Sep 2009 18:23:55 -0700 Subject: [Gofriends] Second CFA - PSB GPD-Rxn Workshop: Genotype-Phenotype-Drug Relationship Extraction from Text Message-ID: <4AA06C2B.4030008@stanford.edu> ======================================================================= CALL FOR ABSTRACTS - PSB Workshop: GPD-Rxn Workshop ======================================================================= GPD-Rxn WORKSHOP: Genotype-Phenotype-Drug Relationship Extraction from Text Co-located with the Pacific Symposium on Biocomputing, January 4-8 2010, The Big Island of Hawaii The aim of this workshop is to bring together researchers working on the automatic or semi-automatic extraction of relationships between biomedical entities from research literature. The workshop will focus particularly on methods for the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships and the use of the relationships for advancing pharmacogenomic research. CALL FOR PARTICIPATION Advances in concept recognition have led to the development of various tools that enable the identification of biomedical entities and relationships between them in text. The aim of the GPD-Rxn workshop is to examine the current state of art and discuss the next steps for making the extraction of relationships between biomedical entities integral to the curation and knowledge management workflow in Pharmacogenomics. The workshop will focus particularly on the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships that are of interest to Pharmacogenomics. Extracting and structuring such text-mined relationships is a key to support the evaluation and the validation of multiple hypotheses that emerge form high throughput translational studies spanning multiple measurement modalities. In order to advance this agenda, it is essential that existing relationship extraction methods be compared to one another and that a community wide benchmark corpus emerges; against which future methods can be compared. The workshop aims to bring together researchers working on the automatic or semi-automatic extraction of relationships between biomedical entities from research literature in order to identify the key groups interested in creating such a benchmark. IMPORTANT TOPICS RELEVANT TO THIS WORKSHOP * Natural Language Processing methods for the extraction of relationships * Machine learning methods for the characterization of biomedical relationships * Use of prior knowledge to improve relationship extraction * Ontologies for relationships * Applications and uses of text-extracted relationships Approaches that combine text-mining and knowledge-based systems are of special interest. ABSTRACTS We are soliciting both research and position abstracts (up to 500 words) related to the topics mentioned above. The GPD-Rxn workshop will combine invited talks, talks selected from abstract submissions to this call, and a panel discussion. Submitted abstracts that will be reviewed by the co-chairs for selecting submitted talks. In addition, other relevant submissions will have the possibility to be presented a poster-session at the end of the workshop. Workshop participants must register for PSB; abstracts may be submitted prior to registering. Authors of accepted abstracts must register for PSB as soon as they are notified of paper acceptance. Abstracts should be emailed to Adrien Coulet (coulet at stanford dot edu). CO-CHAIRS *Adrien Coulet *Nigam Shah *Larry Hunter *Chitta Baral *Russ B. Altman IMPORTANT DATES *Abstract deadline: September 15, 2009 *Speaker notification: October 15, 2009 *Deadline for early registration: October 31, 2009 *Workshop: Date to be announced; will be scheduled during the main conference (January 5-8, 2010) LINKS PSB 2010: http://psb.stanford.edu/ GPD-Rxn Workshop: http://psb.stanford.edu/gdprxn-workshop.html CONTACT Adrien Coulet, coulet at stanford dot edu From adrian.paschke at gmx.de Sat Sep 19 14:53:47 2009 From: adrian.paschke at gmx.de (Adrian Paschke) Date: Sat, 19 Sep 2009 23:53:47 +0200 Subject: [Gofriends] CFP SWAT4LS - Semantic Web Applications and Tools for Life Sciences Workshop Message-ID: <200909192153.n8JLrs4b024332@fafner.Stanford.EDU> SWAT4LS Semantic Web Applications and Tools for Life Sciences *** apologies for multiple postings *** --- updates --- We are glad to announce that there will be a special issue of the BMC Journal of Biomedical Semantics dedicated to the SWAT4LS workshop. This is a new open access journal published by BMC and we are confident that the supplement will benefit from the additional exposure and promotion associated with its launch (more information on this journal can be found at http://www.jbiomedsem.com/). The call for this special issue will be open to all the contributors to the SWAT4LS workshop (accepted papers, posters and demos). Authors will be invited to submit an extended version of their work, elaborated in the light of the discussion held at the workshop. Workshop proceedings will be published on CEUR. In order to facilitate submissions, we have extended submission deadlines as follows: intention to submit (abstract only): October 5th submission of papers: October 12 submission of posters and demos: October 15 communication of acceptance: October 28 camera ready: November 13 Due to the limited time for reviews, we would ask you to submit an abstract of your paper by October 5th, in order to facilitate assignment of reviews. The lenght of contributions to the workshop as been revised to offer more flexibility: * Submissions for Oral communications should be between 8 and 15 pages. * Posters submissions should be between 2 and 4 pages. * Software demo proposals should also be between 2 and 4 pages. Finally, we would like to announce that the special issue BMC Bioinformatics dedicated to SWAT4LS-2008 will be published on October 1st (BMC Bioinformatics, Vol 10, Supp 10) --- call for papers --- ***Location and date Amsterdam, Science Park, November 20th 2009 (http://swat4ls.org/2009/) ***Rationale The adoption of semantic-enabled applications and collaborative social environments is ever more common in the Life Sciences. The Semantic Web provides a set of technologies and standards that are key to support semantic markup, ontology development, distributed information resources and collaborative social environments. Altogether the adoption of the Semantic Web in the Life Sciences has potential impact on the future of publishing, biological research and medecine. This workshop will provide a venue to present and discuss benefits and limits of the adoption of these technologies and tools in biomedical informatics and computational biology. It will showcase experiences, information resources, tools development and applications. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences. ***Topics Topics of interest include, but are not limited to: * Standards, Technologies, Tools for the Semantic Web o Semantic Web standards and new proposals (RDF, OWL, SKOS,... ) o Biomedical Ontologies and related tools o Formal approaches to large biomedical knowledge bases * Systems for a Semantic Web for Bioinformatics o RDF stores, Reasoners, query and visualization systems for life sciences o Semantic biomedical Web Services o Semantics aware Biological Data Integration Systems * Existing and prospective applications of the Semantic Web for Bioinformatics o Semantics aware application tools o Semantic collaborative research environments o Case studies, use cases, and scenarios ***Scientific Program The workshop will be interactive and include keynotes, oral presentations, panel discussion and a poster and demo session. The keynote speakers of this edition will be: * Barend Mons (http://www.biosemantics.org/index.php?page=barend-mons ) * Michael Schroeder (http://www.biotec.tu-dresden.de/schroeder) * Alan Ruttenberg (http://sciencecommons.org/about/whoweare/ruttenberg/ ) ***Scientific Committee (committed so far:) * Christopher J. O. Baker, Department of Computer Science and Applied Statistics, University of Brunswick, Canada * Pedro Barahona, Department of Informatics, New University of Lisboa, Lisboa, Portugal * Liliana Barrio-Alvers, Transinsight GmbH, Dresden, Germany * Olivier Bodenreider, National Library of Medicine, Bethesda, MD, United States of America * Matt-Mouley Bouamrane, School of Computer Science, University of Machester, manchester, United Kingdom * Werner Ceusters, NY CoE in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, United States of America * Kei Cheung, Center for Medical Informatics, Yale University School of Medicine, New Haven, United States of America * Tim Clark, Massachusetts General Hospital and Harvard Medical School, Boston MA, United States of America * Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France * Olivier Dameron, INSERM U936, University of Rennes 1, France * Michel Dumontier, Carleton University, Ottawa, Ontario, Canada * Huajun Chen, Zhejiang University, China * Duncan Hull, School of Chemistry, University of Manchester, UK * C. Maria Keet, Faculty of Computer Science, Free University of Bozen-Bolzano, Bolzano, Italy * Graham Kemp, Chalmers University of Technology, Sweden * Jacob Tilman Koehler, Department of Molecular Biotechnology, Institute of Medical Biology, University of Troms?, Troms?, Norway * Michael Krauthammer, Department of Pathology, Yale University School of Medicine, United States of America * Martin Kuiper, Department of Pathology, Systems Biology group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway * Patrick Lambrix, Department of Computer and Information Science, Link?ping University, Link?ping, Sweden * Phillip Lord, School of Computing Science, Newcastle University, Newcastle-upon-Tyne, United Kingdom * M. Scott Marshall, Leiden University Medical Center / University of Amsterdam, The Netherlands * Chris Mungall, Lawrence Berkeley National Laboratories, United States of America * Stephan Philippi, Institute for Software Technology, University of Koblenz-Landau, Koblenz, Germany * Marco Roos, Instituut voor Informatica, University of Amsterdam, Netherlands * Alan Ruttenberg, Science Commons, Cambridge, MA, United States of America * Matthias Samwald, DERI, Galway, Ireland, and Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria * Nigam Shah, Center for Biomedical Informatics Research, Stanford, United States of America * Michael Schr?der, Biotechnology Centre, TU Dresden, Dresden, Germany * Robert Stevens, School of Computer Science, University of Manchester, Manchester, United Kingdom * Tetsuro Toyoda, Genomic Sciences Center, RIKEN, Yokohama, Japan * Mark D. Wilkinson, iCAPTURE Center, St. Paul Hospital, Vancouver, Canada and the organizers ***Type of contributions The following possible contributions are sought: * Oral communications (regular papers) * Posters * Software demos ***Proceedings All accepted oral communications and posters will be published with the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). We are finalizing the agreement to have a dedicated special issue on the 2009 edition of swat4ls in an international scientific journal of the BMC group (open access, pubmed indexed). To this end, a special Call will be launched shortly after the workshop, for extended and revised versions of contributions submitted to the workshop and accepted either as oral communication or poster. ***New Deadlines * Intention to submit (abstract only): October 5th * Submission of papers: October 12 * Submission of posters and demos: October 15 * Communication of acceptance: October 28 * Camera ready: November 13 ***Instructions All papers and posters must be in English and must be submitted through the EasyChair review system at http://www.easychair.org/conferences/?conf=swat4ls-09 . Please upload all submissions as PDF files in LNCS format (http://www.springer.de/comp/lncs/authors.html ). To ensure high quality, submitted papers will be carefully peer- reviewed by at least three members of the Scientific Committee. * Submissions for Oral communications should be between 8 and 15 pages. * Posters submissions should be between 2 and 4 pages. * Software demo proposals should also be between 2 and 4 pages. ***Organization * M. Scott Marshall, Leiden University Medical Center / University of Amsterdam, The Netherlands * Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, Scotland, United Kingdom * Adrian Paschke, Corporate Semantic Web, Freie Universitaet Berlin, Germany * Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova, Italy * Andrea Splendiani, Biomathematics and Bioinformatics dept., Rothamsted Research, UK ***More information * http://www.swat4ls.org/2009/ * http://swat4ls.blogspot.com * info at swat4ls.org From Robin.Haw at oicr.on.ca Tue Sep 22 13:37:45 2009 From: Robin.Haw at oicr.on.ca (Robin Haw) Date: Tue, 22 Sep 2009 16:37:45 -0400 Subject: [Gofriends] Reactome Pathway Database User Survey Message-ID: Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools. You can access the survey at: http://tinyurl.com/l48zzq Thank you for taking part. Robin Haw Manager of Reactome Outreach Outreach [at] reactome.org http://www.reactome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From erika.feltrin at cribi.unipd.it Mon Sep 28 01:46:57 2009 From: erika.feltrin at cribi.unipd.it (Erika Feltrin) Date: Mon, 28 Sep 2009 10:46:57 +0200 Subject: [Gofriends] Need a software to map GO annotation Message-ID: <1254127617.3715.18.camel@sophie.cribi.unipd.it> Dear all, I am working on the grape annotation project and in particular on the GO annotation of grape genes/proteins. Currently I have a list of genes annotated to GO vocabularies and I would like to visualize these genes on the DAG GO structure like AmiGO does. The file has a column with the grape gene ID and a column with the GO ID. I do not find any tool with this function. Does anybody know if there is a software that allows to map custom GO annotation of a non-consortium organism to the GO DAG graph? Thanks Erika -- ******************************** Erika Feltrin, PhD Bioinformatics Lab CRIBI-Padua University Viale G. Colombo, 3 35121 Padova-Italy http://genomics.cribi.unipd.it Phone. +39. 049 827-6165 Fax. +39. 049 827-6159 ******************************** From jimhu at tamu.edu Mon Sep 28 07:37:38 2009 From: jimhu at tamu.edu (Jim Hu) Date: Mon, 28 Sep 2009 09:37:38 -0500 Subject: [Gofriends] Need a software to map GO annotation In-Reply-To: <1254127617.3715.18.camel@sophie.cribi.unipd.it> References: <1254127617.3715.18.camel@sophie.cribi.unipd.it> Message-ID: <97DA7EA1-FDA1-41F9-A14A-49F5B614B023@tamu.edu> Hi Erika, Are you looking for something like these? http://gowiki.tamu.edu/wiki/index.php/Category:Complement_comparison http://gowiki.tamu.edu/wiki/index.php/Category:apolipoproteins_involved_in_RCT At GONUTS, we have a wiki based system for people who don't have a MOD to do and visualize GO annotations. We've used this for electronic annotation jamborees within the GO consortium, and any registered user can create gene pages and summary pages. Current limitations are that it requires that the genes be in UniProt and that the figures, which come from a web service at MGI, filter out IEA annotations. Of course, anything you put in will be publicly viewable immediately. We're working on a web-based bulk loader for users from a GAF file. In the meantime, we can bulk load for you. Let me know if I should set up an account for you. Hope this helps! Jim Hu On Sep 28, 2009, at 3:46 AM, Erika Feltrin wrote: > Dear all, > > I am working on the grape annotation project and in particular on > the GO > annotation of grape genes/proteins. > Currently I have a list of genes annotated to GO vocabularies and I > would like to visualize these genes on the DAG GO structure like AmiGO > does. > The file has a column with the grape gene ID and a column with the GO > ID. > I do not find any tool with this function. Does anybody know if > there is > a software that allows to map custom GO annotation of a non-consortium > organism to the GO DAG graph? > > Thanks > Erika > > > -- > ******************************** > Erika Feltrin, PhD > Bioinformatics Lab > CRIBI-Padua University > Viale G. Colombo, 3 > 35121 Padova-Italy > > http://genomics.cribi.unipd.it > Phone. +39. 049 827-6165 > Fax. +39. 049 827-6159 > ******************************** > > _______________________________________________ > Gofriends mailing list > Gofriends at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/gofriends ===================================== 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: From Mary_Dolan at umit.maine.edu Mon Sep 28 11:02:30 2009 From: Mary_Dolan at umit.maine.edu (Mary Dolan) Date: Mon, 28 Sep 2009 14:02:30 -0400 Subject: [Gofriends] Need a software to map GO annotation In-Reply-To: <1254127617.3715.18.camel@sophie.cribi.unipd.it> References: <1254127617.3715.18.camel@sophie.cribi.unipd.it> Message-ID: Erika Feltrin writes: >Currently I have a list of genes annotated to GO vocabularies and I >would like to visualize these genes on the DAG GO structure like AmiGO >does. >The file has a column with the grape gene ID and a column with the GO >ID. >I do not find any tool with this function. Does anybody know if there is >a software that allows to map custom GO annotation of a non-consortium >organism to the GO DAG graph? > Hi, Erika. I have a simple prototype tool that does this: http://proto.informatics.jax.org/prototypes/GOTools/web-docs/graph_any_organism.html I think it is self-explanatory (upload file, click "Search") but you will have to click the "Link to show select GO ids on DAG" link to get to the graph. I hope this helps -- please let me know if you have any problem with it. Thanks. Mary Mary E. Dolan, Ph.D. ************************************ Mouse Genome Informatics Consortium, The Jackson Laboratory mdolan at informatics.jax.org (207)288-6439 Research Faculty, NCGIA Department of Spatial Information Science and Engineering, University of Maine Boardman Hall 329 University of Maine Orono, Maine 04469 fax: 207.581.2206 mary_dolan at umit.maine.edu ************************************ From sherlock at genome.stanford.edu Mon Sep 28 10:59:37 2009 From: sherlock at genome.stanford.edu (Gavin Sherlock) Date: Mon, 28 Sep 2009 10:59:37 -0700 Subject: [Gofriends] Need a software to map GO annotation In-Reply-To: <1254127617.3715.18.camel@sophie.cribi.unipd.it> References: <1254127617.3715.18.camel@sophie.cribi.unipd.it> Message-ID: <51EA5E26-763E-447A-A88D-C4DA8D5B1B17@genome.stanford.edu> Hi Erika, GO::TermFinder (http://search.cpan.org/dist/GO-TermFinder/) has a module, called GO::View that allows creation of images (postscript or png) of subparts of the DAG annotated with genes. Not sure if that's what you're looking for, but thought I'd mention it. Cheers, Gavin ________________________________________________________ Gavin Sherlock Assistant Professor, Research Dept. of Genetics S201A, Grant Building, Stanford University Medical School, Stanford, CA 94305-5120 Tel: 650 498 6012 Fax: 650 724 3701 http://genome-www.stanford.edu/~sherlock On Sep 28, 2009, at 1:46 AM, Erika Feltrin wrote: > Dear all, > > I am working on the grape annotation project and in particular on > the GO > annotation of grape genes/proteins. > Currently I have a list of genes annotated to GO vocabularies and I > would like to visualize these genes on the DAG GO structure like AmiGO > does. > The file has a column with the grape gene ID and a column with the GO > ID. > I do not find any tool with this function. Does anybody know if > there is > a software that allows to map custom GO annotation of a non-consortium > organism to the GO DAG graph? > > Thanks > Erika > > > -- > ******************************** > Erika Feltrin, PhD > Bioinformatics Lab > CRIBI-Padua University > Viale G. Colombo, 3 > 35121 Padova-Italy > > http://genomics.cribi.unipd.it > Phone. +39. 049 827-6165 > Fax. +39. 049 827-6159 > ******************************** > > _______________________________________________ > Gofriends mailing list > Gofriends at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/gofriends From d.m.a.martin at dundee.ac.uk Mon Sep 28 12:33:02 2009 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Mon, 28 Sep 2009 20:33:02 +0100 Subject: [Gofriends] Need a software to map GO annotation In-Reply-To: <51EA5E26-763E-447A-A88D-C4DA8D5B1B17@genome.stanford.edu> References: <1254127617.3715.18.camel@sophie.cribi.unipd.it> <51EA5E26-763E-447A-A88D-C4DA8D5B1B17@genome.stanford.edu> Message-ID: <4AC10F6E.6050506@dundee.ac.uk> There is plenty of code in the GOtcha app that can be turned to such a task. I'm just catching up with updating the code to take into account the regulates relationships, and it should be fairly straightforward to add a composite map for gene lists to the set of applications. ..d From cherry at stanford.edu Tue Sep 29 12:55:58 2009 From: cherry at stanford.edu (cherry at stanford.edu) Date: Tue, 29 Sep 2009 12:55:58 -0700 (PDT) Subject: [Gofriends] Gene Ontology Email lists unavailable Oct 2nd Message-ID: <200909291955.n8TJtww0025472@fafner.Stanford.EDU> The mailserver that provides the Gene Ontology mailing lists will be down this weekend. All lists and the web site for the mailing lists will be unavailable from noon (Pacific) October 2nd and back before noon (Pacific) October 4rd. You are subscribed to the one of the GOC lists. I apologize for the trouble if you receive this message more than once. All subscriptions to all lists are being sent this message. If you happen to send an email during the down time you do not need to send the message again. It is normal for mailservers to keep trying for five days. Your message will simply be delayed. The main GO web sites and tools are not affected and will be available. Cheers, Mike Cherry From sjupe at ebi.ac.uk Wed Sep 30 04:38:00 2009 From: sjupe at ebi.ac.uk (Steven Jupe) Date: Wed, 30 Sep 2009 12:38:00 +0100 Subject: [Gofriends] [Reactome-announce] Version 30 of the Reactome Knowledgebase has been released Message-ID: <4AC34318.2070405@ebi.ac.uk> Version 30 of the Reactome Knowledgebase has been released and is accessible at http://www.reactome.org. * New and Updated Topics* Version 30 includes the new topic_ _Cell-cell adhesion systems with annotations of adherens junctions interactions and tight junction interactions. Pathway topics revised and updated to incorporate new events include the GPCR signaling pathway (Downstream events in GPCR signaling and the Olfactory signaling pathway), Signaling in immune system (Costimulation by the CD28 family) , Transmembrane transport of small molecules (SLC-mediated transmembrane transport) , Membrane Trafficking (Clathrin derived vesicle budding) , Axon Guidance (Signaling by Robo receptor) and Gene Expression (Nuclear receptor pathway). New metabolism topics include Sphingolipid metabolism and Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) . Diabetes pathways now cover Synthesis, Secretion, and Deacylation of Ghrelin and Regulation of Insulin Secretion by Free Fatty Acids . Pathway annotations from Reactome are now available through NCBI BioSystems . *Reactome User Survey* Reactome is committed to providing access to high-quality pathway information and useful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know about your background and research interests so that we can continue to improve the Reactome site and tools. Please help us by completing this short survey at: http://tinyurl.com/l48zzq *About Reactome* 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. A preliminary list of Reactome spin-offs specific to non-human model organisms with contact information is available from http://www.reactome.org/other_reactomes.html. Users interested in contributing to these endeavors or expanding the scope of pathway annotations in the Reactome model to more organisms can write to help at reactome.org. 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. -- Dr. Steven Jupe, Reactome Group, European Bioinformatics Institute, Hinxton, Cambridge. CB10 1SA UK (01223) 492673 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Reactome-announce mailing list Reactome-announce at reactome.org http://mail.reactome.org/mailman/listinfo/reactome-announce From sorin at wayne.edu Mon Sep 28 19:44:21 2009 From: sorin at wayne.edu (Sorin Draghici) Date: Mon, 28 Sep 2009 22:44:21 -0400 Subject: [Gofriends] Need a software to map GO annotation In-Reply-To: <97DA7EA1-FDA1-41F9-A14A-49F5B614B023@tamu.edu> References: <1254127617.3715.18.camel@sophie.cribi.unipd.it> <97DA7EA1-FDA1-41F9-A14A-49F5B614B023@tamu.edu> Message-ID: <4AC17485.8080705@wayne.edu> Erika, Onto-Express to go (OE2GO) allows you to upload any custom annotations. Once you have uploaded them you can do any GO enrichment/depletion analysis. The results are displayed as a list of GO terms that can be sorted by p-values, etc. but also as a graphical tree. The DAG links are not shown as in AmiGO but as in a tree. The nodes with more than one parent can be reached from any parent. A search for a node with more than one parent will automatically expand all parents necessary showing all the paths from the root to the searched term. OE2GO is described in the following paper: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1933142&blobtype=pdf You can try the visualization capabilities using, Onto-Express, the on-line tool that does the same things. http://vortex.cs.wayne.edu You can use some of the sample data sets we have on-line to see if the capabilities are what you need. All the best, Sorin > > On Sep 28, 2009, at 3:46 AM, Erika Feltrin wrote: > >> Dear all, >> >> I am working on the grape annotation project and in particular on the GO >> annotation of grape genes/proteins. >> Currently I have a list of genes annotated to GO vocabularies and I >> would like to visualize these genes on the DAG GO structure like AmiGO >> does. >> The file has a column with the grape gene ID and a column with the GO >> ID. >> I do not find any tool with this function. Does anybody know if there is >> a software that allows to map custom GO annotation of a non-consortium >> organism to the GO DAG graph? >> >> Thanks >> Erika >> >> >> -- >> ******************************** >> Erika Feltrin, PhDwould >> Bioinformatics Lab >> CRIBI-Padua University >> Viale G. Colombo, 3 >> 35121 Padova-Italy >> >> http://genomics.cribi.unipd.it >> Phone. +39. 049 827-6165 >> Fax. +39. 049 827-6159 >> ******************************** >> >> _______________________________________________ >> Gofriends mailing list >> Gofriends at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/gofriends > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Gofriends mailing list > Gofriends at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/gofriends -- Associate Professor Director of the Intelligent Systems and Bioinformatics Laboratory Department of Computer Science Wayne State University Room 431 State Hall, 5143 Cass Ave, Detroit, MI 48202 Tel: 313-577-5484 Fax: 313-577-6868 http://vortex.cs.wayne.edu