From Peter.D'Eustachio at nyumc.org Tue Jul 1 10:26:12 2008 From: Peter.D'Eustachio at nyumc.org (D'Eustachio, Peter) Date: Tue, 1 Jul 2008 13:26:12 -0400 Subject: [Gofriends] [Reactome-announce] Reactome version 25 released Message-ID: <31A1FDA7388B374585A811D2487E8F8107B06A@MSGWSDCPMB03.nyumc.org> Version 25 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: An expanded and reorganized pathway module for biological oxidations along with the pathway topics: glutamate neurotransmitter release cycle, beta cell development, and integrin cell surface interactions. The pathway topics updated with new curated events include: apoptosis - regulatory reactions, metabolism of amino acids - ODC regulation, metabolism of vitamins, NGF signaling, and lipid metabolism - HDL synthesis. A new project annotating cellular transport events has been initiated. 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 expand the scope of pathway annotations in the Reactome model to more organisms can write to help at reactome.org. The pathway visualization tool (beta version) is available on the website from the Tools menu. A new look Search tool with features of popular search engines has been implemented. Please try these tools and let us know your comments Pathway annotations from Reactome are now incorporated into the Pathway Interaction Database (PID), a collaborative project betwen 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 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= _______________________________________________ Reactome-announce mailing list Reactome-announce at reactome.org http://mail.reactome.org/mailman/listinfo/reactome-announce From dbarrell at ebi.ac.uk Fri Jul 4 03:50:40 2008 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Fri, 04 Jul 2008 11:50:40 +0100 Subject: [Gofriends] July 2008 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <486E0080.4050904@ebi.ac.uk> GOA releases: July 2008 ============================ [Please see below for important proposed form at change] 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. **Proposed GOA gene association file format change** The GOA group is intending to change the contents of columns 3, 10 and 11 in all GOA gene association files except gene_association.goa_pdb.gz. The changes being proposed are outlined below and will ensure that the format of the affected columns is in line with GO Consortium requirements. While the ordering of identifiers in these columns will change, no identifiers will be removed. These changes will come into effect at the end of July (Release 65 of GOA UniProt, i.e. the next release of GOA). *Column 3 (DB_Object_Symbol)* Current content: UniProt identifier (e.g. PRG4_HUMAN) Future content: Primary gene symbol when available (e.g. PRG4), otherwise will contain locus name or will repeat the value present in column 2 (either a UniProtKB accession, IPI, Ensembl, VEGA, HINV, TAIR or RefSeq peptide identifier). *Column 10 (DB_Object_Name)* Current content: A list of gene symbols and protein name. (e.g. PRG4, MSF, SZP: Proteoglycan-4 precursor) Future content: protein name only when available (e.g. Proteoglycan-4 precursor). Otherwise will be left blank. Column 11 (Synonym) Current content: IPI identifiers when available (e.g. IPI00024825) Future content: A pipe-delimited list of alternative gene symbol synonyms, IPI and UniProtKB identifiers (e.g. MSF|SZP|IPI00024825|PRG4_HUMAN). Please contact us if you have any concerns about these proposed changes. Regards The UniProt GOA Team From cbaker at i2r.a-star.edu.sg Mon Jul 7 10:57:37 2008 From: cbaker at i2r.a-star.edu.sg (Christopher J. O. Baker) Date: Tue, 8 Jul 2008 01:57:37 +0800 Subject: [Gofriends] REVISED DEADLINE - ECCB 2008 Workshop: Annotation, interpretation and management of Mutations (AIMM)- call for papers References: <2dbc82b00801260159j7996fb52n663da78315d2d254@mail.gmail.com> <162B8AFBFBBB2148A9A1B8F9C57534280261960F@mailbe01.teak.local.net> <162B8AFBFBBB2148A9A1B8F9C5753428042B1422@mailbe01.teak.local.net> <162B8AFBFBBB2148A9A1B8F9C5753428042B162C@mailbe01.teak.local.net> <162B8AFBFBBB2148A9A1B8F9C5753428042B162F@mailbe01.teak.local.net> Message-ID: <162B8AFBFBBB2148A9A1B8F9C5753428042B1634@mailbe01.teak.local.net> Dear Researcher, Due to requests for an extension of the paper submission deadline for the AIMM2008, we decided revise it to July 18th (start of SIG meetings at the ISMB2008). Only minor extension can be granted thereafter. In addition, we encourage the submission of short position papers on topics that have not yet been published in research publications, including proposals outlining how to address the representation and integration of phenotypic information for the annotation of genotypic variability. We look forward to seeing you in Sardinia AIMM workshop @ ECCB 2008 =================================================================================================== ECCB 2008 Workshop: Annotation, interpretation and management of Mutations (AIMM) - call for papers =================================================================================================== Preamble: Genetic variability (SNPs, mutations) plays a key role in the analysis of genetic mechanisms and complex diseases. The effort in the gathering and understanding of the information regarding human variability is large, e.g. data collection from the 1000 genomes project. In step with such initiatives this workshop will focus on solutions in text mining, data warehousing and machine learning that allow better integration of mutation relevant information into a bioinformatics infrastructure. Altogether, the meeting participants will discuss the methods for the prediction of phenotypic effects induced by mutations, support to clinical decision processes involving mutations and the means that allow access and management of mutations with annotations from different data resources. Synergistic use of these technologies should facilitate inference of knowledge from sequence to structure to function and to phenotypes. The workshop brings together members of different disciplines to improve know-how and technology transfer as well as better hypothesis generation for yet un-annotated mutations. Keynote Speakers: Catherine Worth Leibniz-Institut f. Molekulare Pharmakologie, Berlin, DE In Collaboration with Tom Blundell, Cambridge, UK Kevin B. Cohen, The Hunter Lab, Center for Computational Pharmacology University of Colorado Health Sciences Center, Colorado, US Intended audience: This workshop reaches out to the following participants: data architects working on data modeling and knowledge representation, data warehouse curators seeking to address a backlog of un-curated mutations from the literature, designers of mining solutions and services for unstructured text, machine learning specialists developing classifiers for predictive analyses, structural biologists involved in protein engineering and physicians involved in genome scale population studies. The workshop includes keynote talks reporting on the management of SNP data and giving better insights on the importance of non-synonymous SNPs on diseases. Submissions: We invite both long (4000 words / 12 pages) and short papers (2000 words / 6 pages) on the topics listed below. Manuscript preparation and formatting instructions are available at the following website http://www.ebi.ac.uk/Rebholz-srv/aimm-instructions.html > We encourage proposals for workshop presentations that describe: * Infrastructures and metadata to support archival and study of perturbations (mutations) and variations (SNPs) within biological systems. * Integration of mutation-related data into systems level analysis of a biological sciences (disease, biomarkers, clinical, metabolomics). * Novel techniques (information extraction, machine learning and others solutions) for the extraction of mutations and generation of annotations from the scientific literature. * Tools and analyses predicting the impacts of mutations * Hypothesis generation and reuse: building the derived insights of mutational studies into biological models Submissions can be made through the EasyChair submission page: http://www.easychair.org/conferences?conf=aimm2008 > All papers will be published in an online workshop proceedings with CEUR http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/ > Long papers may be invited to submit extended versions to a journal special issue. Organizers Christopher J. O. Baker , PhD Principal Investigator Data Mining Department Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613 Tel: +65 6874 3495 Email: cbaker at i2r.a-star.edu.sg Dietrich Rebholz-Schuhmann, MD, PhD Research Group Leader European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, CB101SD, United Kingdom Tel: +44 (0)1223 492 594 Email: Rebholz at ebi.ac.uk Important Deadlines: Paper Submission: July 7th Acceptance: August 4th Final Manuscripts: August 18th Workshop: Monday, September 22, 2008 Venue: ECCB2008 @ Cagliari, Sardinia - Italy Session Topics: Mutation Databases and Metadata: Design, Content, Accuracy. =========================================================== Over 400 mutation databases can be found with a 'google' search. Many are no longer maintained and cover very specific data sets. These repositories have been designed to support a wide range of features from SNPs, point mutations, insertions, deletions, and observed phenotypes. Furthermore they incorporate a wide range of modified protein features and metrics in the accompanying annotations to the mutation descriptions. In the main these databases are manually curated however mutation annotations are frequently inaccurate e.g. in the PDB, inaccurate to the degree of 40 % of all PDB records. Extraction of mutations and annotations from literature: ======================================================== AI techniques such as text mining and natural language processing have been used to enable . A number of systems have been developed generally showing that extraction mutations from texts can be achieved with high levels of precision and recall. These systems remain prototype scale their adoption to measure the accuracy, recreation and update of existing mutation databases as we as their incorporation into semi manual annotation pipelines is the next milestone. In addition there is continuing discussion over the appropriate metrics for individual tasks within these systems which requires community involvement. This emergent technology now needs standardization. Predicting the impacts of Mutations: ==================================== The ability to predict the impact of a mutation or the consequence of a sequence variant is central to the diagnosis of genetic diseases. Non-synonymous mutations may impact translational regulation, mRNA stability, mRNA splicing and rates of translation. Proteins affected by nsSNPs may have altered; catalytic sites, stability, ability to aggregate, and or posttranslational modifications. Moving from SNP to sequence to structure and function has been addressed with varying degrees of accuracy with sequence and structure based (molecular mechanism, empirical energy function or machine learning) methods. The need to apply such techniques at a genome scale requires that robust approaches are identified, benchmarked with standard metrics in order to assign valid significance to ns mutations. Reuse of existing mutation databases for checking quality of predictions is pivotal. Mutation Data Integration and Reuse: Panel Discussion ===================================================== http://www.ebi.ac.uk/Rebholz-srv/aimm.html ------------ Institute For Infocomm Research - Disclaimer -------------This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.-------------------------------------------------------- From shameer at ncbs.res.in Tue Jul 8 01:39:11 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Tue, 8 Jul 2008 14:09:11 +0530 (IST) Subject: [Gofriends] GO term enrichment analysis Message-ID: <42684.192.168.1.1.1215506351.squirrel@mail.ncbs.res.in> Dear Go Friends, I am a member of this list for last six months. This is my first post to the list. I am working with experimental group in the computational annotation of genes from a high throughput RNAi experiment. We have screened 5000 genes and we have got almost 500 genes as hits. Now we need to know the GO term enrichment of this set of 500 genes. I could see various programs (standalone, webserver) are available that are available to perform GO Term enrichment analysis . I would like to know while performing such an analysis what are all the statistical parameters I should take care of (Some tools have statistics based on FDR, other are mostly P-Value based). Is there any reliable command line program that can also be integrated to the database we are developing ? Which program(s) are generally used by GO Friends for such large scale analysis ? Thanks in advance, K. Shameer NCBS - TIFR From sherlock at genome.stanford.edu Mon Jul 28 23:00:09 2008 From: sherlock at genome.stanford.edu (Gavin Sherlock) Date: Mon, 28 Jul 2008 23:00:09 -0700 Subject: [Gofriends] MGED 11 Meeting, Trentino, Italy : Final abstract submission deadline is August 5th Message-ID: Dear Colleagues, Apologies if you receive this more than once. The MGED 11 final abstract submission deadline is next Tuesday, August 5th. Further information on MGED 11 is available at http://www.mgedmeeting.org/ Registration will stay open up until the meeting begins. The scientific focus of the meeting will be high throughput technologies - in particular microarrays and ultra high throughput sequencing - and associated data handling issues, analysis techniques and standards. We have lined up some outstanding speakers who will be giving talks on these topics. 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 ---------------------------------------------------------------------------------- MGED 11 Program Sunday 31st Aug. 15:00 - Registration and Exhibit Area are open Monday 1st Sept. 07:30- Registration opens 08:30- 09:00 Welcome, Introduction and organization details: Chris Stoeckert, Catherine Ball, Cesare Furlanello ENCODE Session 09:00-10:00 Keynote Lecture: Piero Carninci 10:00-10:45 Plenary Lecture: Barbara Wold 10:45-11:15 Break 11:15-12:00 Plenary Lecture: Shirley Liu 12:00-12:30 Talks from Submitted abstracts (2) 12:30-14:00 Lunch Wine Genomics Session 14:00-14:45 Plenary Talk: Claudio Moser 14:45-15:30 Talks from Submitted abstracts (2) 15:30-16:00 Break 16:00-16:45 Plenary Talk: Duccio Cavalieri 16:45-17:45 Keynote Talk: Grant Cramer 18:00-20:00 Welcome cocktail 21.00 Public Science Conference I Tuesday 2nd Sept. Human Disease Session 09:00-10:00 Keynote Lecture: Joe Gray 10:00-10:45 Plenary Lecture: Mike Bittner 10:45-11:00 Break 11:00-11:45 Plenary Lecture: Nigel Carter 11:45-12:30 Talks from Submitted abstracts (3) 12:30-14:00 Lunch Quality and Standards in Action 14:00-14:15 Introduction and update on MGED Standards: Chris Stoeckert 14:15-14:30 MAGE-TAB Tools: Helen Parkinson/Tim Rayner 14:30-14:45 ISA-TAB and integrative standards: Susanna-Assunta Sansone 14:45-15:30 Title TBA (Semantic Web and Gene Expression): Alan Ruttenberg 15:30-16:00 Break 16:00-18:00 Poster Session I 19:00-21:00 Conference Dinner Wednesday 3rd Sept. Learning from Microarray Data 09:00-10:00 Keynote Lecture: Naama Barkai 09:45-10:30 Plenary Talk: Rainer Spang 10:30-11:00 Break 11:00-11:45 Plenary Talk: Atul Butte 11:45-12:30 Talks from Submitted Abstracts (3) 12:30-14:00 Lunch Functional Genomics and Systems Biology 14:00-15:00 Keynote Lecture : Stephen Oliver 15:00-15:30 Break 15:30-16:15 Talks from Submitted Abstracts (3) 16:15-17:00 Keynote Lecture: Ewan Birney 17:00-19:00 Poster Session II Close of Meeting, Final Announcements, Award of Poster Prizes 20.15 Public Science Conference 2 Thursday 4th Sept. Workshops 8:00 - 11:00 Morning Parallel Sessions ? Data Analysis Tutorial: John Quackenbush and Roger Bumgarner ? Tutorial on using Bioconductor for Array Quality Assessment: Audrey Kauffmann and Wolfgang Huber 11:00 - 14:30 Gene Pattern tutorial: Ted Liefeld 15:00 - 18:00 Afternoon Parallel Sessions ? Using ArrayExpress Tutorial: Gabriella Rustici andMisha Kapushesky ? EMERALD Workshop on Array Quality Assessment Methods: Marc Salit and Wolfgang Huber