From asidhu at biomap.org Mon Feb 4 00:50:45 2008 From: asidhu at biomap.org (Amandeep Sidhu) Date: Mon, 4 Feb 2008 17:50:45 +0900 Subject: [gofriends] Last CFP: 3rd Special Track on Ontologies for BiomedicalSystems for CBMS 2008 Message-ID: <2dbc82b00802040050m3605bf05w1ccf2cd7d57a0e56@mail.gmail.com> 3rd Special Track on Ontologies for Biomedical Systems for 21st IEEE International Symposium on Computer-Based Medical Systems Jyv?skyl?, Finland June 17-19 2008 http://cbms08.biomap.org/ Call for Papers Biomedical Ontologies have developed in an uncoordinated way, often reflecting mere relations of 'association' between what are called 'concepts', and serving primarily the purposes of information extraction from on-line biomedical literature and databases. In recent years, we have learned a great deal about the criteria which must be satisfied if ontology is to allow true information integration and automatic reasoning across data and information derived from different sources. The goal of this track is to survey existing biomedical ontologies and reform them in such a way as to allow true information integration in biomedical domain. Authors are invited to submit original papers exploring the theories, techniques, and applications of biomedical ontologies. Papers are invited (but not limited) to the following themes: * Biomedical Ontologies for Genetics, Proteomics, Diseases, Privacy etc. * Conceptual Models for Biological and Medical Data * Semantics in Biological Data Modeling * Use of semantics to manage Interoperation in Biomedical Databases * Semantic Web technologies and formalisms for Biomedical Data * Ontology representation and exchange languages for bioinformatics * Biomedical Ontologies and OWL * Biological Data Integration and Management using Ontologies * Biomedical Data Engineering using Ontologies * Application of Biomedical Ontologies for Heterogeneous Database Access * Query Optimization Techniques for Biomedical Database using Ontologies * Support of Ontologies for Biological Information Retrieval and Web Services * Change Management in Biomedical Ontologies * Tools for Development and Management of Biomedical Ontologies Important Dates 04 February 2008 Paper Submission Due 28 February 2008 Notification of acceptance 28 March 2008 Final camera-ready paper due 28 March 2008 Pre-registration deadline Paper Submission Procedures Submitted papers have to be original, containing new and original results. Use a maximum of 6 pages IEEE two-column format, including figures and references. All submissions will be done electronically via the CBMS 2008 web submission system (http://www.easychair.org/conferences/?conf=CBMS2008). Submission implies the willingness of at least one of the authors to register and present the paper at the CBMS 2008 Symposium. All papers will be peer reviewed by at least two independent referees. All accepted papers will be included in the conference proceedings. High Quality submissions will be published in a special issue of Biomedical Ontologies Journal by Oxford University Press. Track Organizers Amandeep S. Sidhu Curtin University of Technology, Perth http://www.amandeep.org/ Tharam S. Dillon Curtin University of Technology, Perth Jake Chen Indiana University, USA http://informatics.iupui.edu/people/profile.php?id=74 Elizabeth Chang Curtin University of Technology, Australia http://www.fit.cbs.curtin.edu.au/~chang/docs/index.php Program Committee Alexey Tsymbal (Siemens, Germany) David Hansen (e-Health Research Centre, CSIRO, Australia) David Taniar (Monash University, Australia) Ernesto Damiani (Computer Science Department, Milan University, Italy) Fabio Porto (Database Laboratory, EPFL, Switzerland) Farookh K. Hussain (Curtin University of Technology, Australia) Fedja Hadzic (University of Technology Sydney, Australia) Huiru Zheng (University of Ulster, UK) Jake Chen (Indiana University, USA) James Geller (New Jersey Institute of Technology, USA) Jason Wang (New Jersey Institute of Technology, USA) Li Liao (University of Delaware, USA) Ling Feng (Tsinghua University, China) Maja Hadzic (Curtin University of Technology, Australia) Midori Harris (GO Consortium, European Bioinformatics Institute) Mustafa Jarrar (Vrije Universiteit Brussel, Belgium) Robert Meersman (Vrije Universiteit Brussel, Belgium) Silke Eckstein (Technical University of Braunschweig, Germany) Sourav S Bhowmick (Nanyang Technological University, Singapore) Sun Kim (School of Informatics, Indiana University, USA) Wenny Rahayu (La Trobe University, Australia) Werner Ceusters (New York State Center of Excellence in Bioinformatics & Life Sciences, USA) Yi Pan (Georgia State University, USA) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080204/44a92552/attachment.html From eurie at genome.Stanford.EDU Wed Feb 13 14:07:26 2008 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Wed, 13 Feb 2008 14:07:26 -0800 Subject: [gofriends] GO annotations with IEAs to be added to SGD's gene_association file on March 8th Message-ID: Hello, On March 8, 2008, the Saccharomyces Genome Database (SGD) will change the contents of our file that contains GO annotations. This is a major change as we will add annotations that are associated with computationally predicted methods. The SGD file currently does not include annotations that are made using the IEA evidence code. These annotations will include computationally predicted annotations to the Gene Ontology created by the Gene Ontology Annotation (GOA) project at EBI, Hinxton UK. The file available from the GO Consortium is called 'gene_association.sgd' and is available from the following locations: GO Consortium web page: http://www.geneontology.org/GO.current.annotations.shtml FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/ CVS: http://www.geneontology.org/GO.downloads.ftp.cvs.shtml#cvs Subscribe to our RSS feed for current information regarding this change: http://www.yeastgenome.org/xml/SGD_RSS.shtml Please do not hesitate to contact us at yeast-curator at genome.stanford.edu if you have any questions regarding this change. Cheers, Eurie ******************************************* Eurie L. Hong, Ph.D. Saccharomyces Genome Database Stanford University School of Medicine Department of Genetics Stanford, CA 94305-5120 http://www.yeastgenome.org/ ******************************************* -- 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 Mon Feb 18 03:44:56 2008 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Mon, 18 Feb 2008 11:44:56 +0000 Subject: [gofriends] February 2008 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <47B96FB8.4080509@ebi.ac.uk> GOA releases: February 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 tberardi at acoma.Stanford.EDU Tue Feb 26 14:04:24 2008 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Tue, 26 Feb 2008 14:04:24 -0800 Subject: [gofriends] SECOND ANNOUNCEMENT: Introduction of New Relationship Types in GO (March 25, 2008) Message-ID: <8e22ab960802261404r517f7f27hdba941e10c432ee4@mail.gmail.com> Please note that the name of the file to be used for testing has been updated. GO Consortium members: Please let us know when you have successfully tested loading the new files. ------------- We are pleased to announce that The Gene Ontology Consortium will introduce three new relationship types -- regulates, negatively_regulates and positively_regulates -- into the Biological Process ontology. For some time now, the GO content developers have been aware that regulatory processes are not necessarily integral to the processes (as previously indicated by the use of the 'part_of' relation) that they regulate. Nevertheless, regulatory processes have been represented as part_of the processes they regulate. We have long intended to replace these part_of relationships with a new relationship type called 'regulates'. We are now in a position to make this replacement. Ontology developers have thoroughly reviewed the relationships involving regulatory processes and their targets to ensure internal consistency. If a term 'regulation of process X' exists in the ontology, it must be a valid subtype of 'regulation of biological process', and must have a part_of relationship (which will be transformed into one of the 'regulates' relationships) with 'process X' or be a valid subtype of another regulatory process. We have also introduced two new high-level regulation terms, 'regulation of molecular function' (for example, 'regulation of cyclase activity') and 'regulation of biological quality' (for example, 'regulation of blood pressure'), to represent processes that regulate the activity of gene products and processes that regulate measurable biological attributes, respectively. Regulation of molecular function terms have been aligned with the corresponding terms in the molecular function ontology. WE PLAN TO REPLACE THE CURRENT 'part_of' RELATIONSHIPS IN THE ONTOLOGY WITH THE NEW 'regulates' RELATIONSHIP ON MARCH 25,2008. Software developers should ensure that their procedures for loading the ontologies into their resources are compatible with these changes by this date. Below is an example of a current OBO 1.2 stanza for a regulates term and a new stanza with the regulates relationship in place. EXAMPLES OF CURRENT STANZAS [Term] id: GO:0000019 name: regulation of mitotic recombination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA recombination during mitosis." [GOC:go_curators] narrow_synonym: "regulation of recombination within rDNA repeats" [] is_a: GO:0000018 ! regulation of DNA recombination relationship: part_of GO:0006312 ! mitotic recombination [Term] id: GO:0045596 name: negative regulation of cell differentiation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cell differentiation." [GOC:go_curators] subset: gosubset_prok synonym: "down regulation of cell differentiation" EXACT [] synonym: "down-regulation of cell differentiation" EXACT [] synonym: "downregulation of cell differentiation" EXACT [] synonym: "inhibition of cell differentiation" NARROW [] is_a: GO:0045595 ! regulation of cell differentiation is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051093 ! negative regulation of developmental process EXAMPLES OF NEW STANZAS [Term] id: GO:0000019 name: regulation of mitotic recombination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA recombination during mitosis." [GOC:go_curators] synonym: "regulation of recombination within rDNA repeats" NARROW [] is_a: GO:0000018 ! regulation of DNA recombination relationship: regulates GO:0006312 ! mitotic recombination [Term] id: GO:0045596 name: negative regulation of cell differentiation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cell differentiation." [GOC:go_curators] subset: gosubset_prok synonym: "down regulation of cell differentiation" EXACT [] synonym: "down-regulation of cell differentiation" EXACT [] synonym: "downregulation of cell differentiation" EXACT [] synonym: "inhibition of cell differentiation" NARROW [] is_a: GO:0045595 ! regulation of cell differentiation is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051093 ! negative regulation of developmental process relationship: negatively_regulates GO:0030154 ! cell differentiation The regulates relationship is transitive over both the is_a and part_of relationships. is_a transitivity: If process B exists in the GO biological process ontology and it is an is_a child of process A then any process that regulates process B also regulates process A. part_of transitivity: If process Y exists in the GO biological process ontology and it is a part_of child of process X then any process that regulates process Y also regulates process X. We strongly suggest that you test your loading scripts to ensure that your database loads execute correctly. There is a test OBO 1.2 file available at: /go/scratch/regulates_relations_examples/go_regtest_withPosNeg_noPF_noXP.obo Please feel free to contact us with any questions or concerns about this change. 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/20080226/75c928b8/attachment.html From vpetri at mcw.edu Wed Feb 27 12:09:20 2008 From: vpetri at mcw.edu (Petri, Victoria) Date: Wed, 27 Feb 2008 14:09:20 -0600 Subject: [gofriends] Gene Ontology Newsletter - February 2008 issue Message-ID: <1448A38A42714048B9C53E473E13CCF0010A62C2@davis.hmgc.mcw.edu> Gene Ontology Newsletter February 2008, Issue No. 8 In this issue: 1. New relationship types in Biological Process Ontology 2. SGD gene_association file with IEA 3. Genes of the quarter: Peroxins 4. New subcodes for the ISS evidence code 5. Upcoming events 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080227/27aa9efd/attachment.html From tberardi at acoma.Stanford.EDU Fri Feb 29 12:37:49 2008 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Fri, 29 Feb 2008 12:37:49 -0800 Subject: [gofriends] Cut and paste error in newsletter: regulates test file Message-ID: <8e22ab960802291237m7e22961do6dd9f98bc4d417f5@mail.gmail.com> Dear GO friends, We've noticed that we made a cut and paste error for the test regulates file in the February 2008 GO newsletter. The correct filename has been posted online in both the HTML and PDF versions of the newsletter. The file for testing should be: ftp://ftp.geneontology.org/pub/go/scratch/regulates_relations_examples/go_regtest_withPosNeg_noPF_noXP.obo instead of ftp://ftp.geneontology.org/pub/go/scratch/regulates_relations_examples/go_regtest_noPosNeg_noPF_noXP.obo (withPosNeg instead of noPosNeg) We're sorry for the error. Tanya Berardini David Hill -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080229/541a66fc/attachment.html