From gopinath at cshl.edu Tue Sep 4 16:14:29 2007 From: gopinath at cshl.edu (Gopinathrao, Gopal) Date: Tue, 4 Sep 2007 19:14:29 -0400 Subject: [gofriends] [Reactome-announce] Ver 22 released! Message-ID: Version 22 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 and Ewan Birney's group at European Bioinformatics Institute). 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). New topics released in Version 22 include Botulinum neurotoxicity, Membrane trafficking and Metabolism of vitamins, pathways for HIV Nef protein interactions (HIV infection pathway), Immunoregulatory interactions (Immune signaling pathway) and AMPK regulation of fatty acid oxidation (Integration of energy metabolism pathways). A new tool, Reactome Mart, is available for comprehensive datamining. Reactome Wiki is available for editing documentation by the user community. As before, Reactome data can be exported in SMBL, Prot?g?, and BioPAX level 2 formats. Protein-protein interaction datasets derived from curated human and predicted non-human events are available. A SOAP based Web Services API is also available along with other resources to access the Reactome data. Links to these are on the Download page. The standard display feature allows the user to choose the focus species annotations - curated (for human) and electronically inferred (for 22 other species). Updated release statistics and the Editorial Calendar are available. Like everything in Reactome, these downloaded and exported materials can be reused and redistributed freely. For questions and comments please reply to this message or write to help at reactome.org _______________________________________________ Reactome-announce mailing list Reactome-announce at reactome.org http://mail.reactome.org/mailman/listinfo/reactome-announce -- 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 phornbeck at cellsignal.com Fri Sep 7 03:32:26 2007 From: phornbeck at cellsignal.com (Peter Hornbeck) Date: Fri, 7 Sep 2007 06:32:26 -0400 Subject: [gofriends] positions available: biocurator/cell biology scientist Message-ID: Cell Signaling Technology (CST) is seeking highly motivated cell biologists to curate and annotate information from the literature and other sources into PhosphoSite (http://www.phosphosite.org), a public proteomics resource focusing on mammalian protein modifications, especially phosphorylation. PhosphoSite , developed by scientists at CST with ongoing NIH funding, is in the process of a significant expansion. Qualifications include a PhD in cell biology, protein biochemistry, or related discipline; post-doctoral research and a successful publication record; and experience working with databases, spreadsheets, literature searches, biological sequence searches and analyses, and related bioinformatics technology. Successful candidates must be detail-oriented, yet be able to quickly and accurately interpret scientific literature; and must be able to work independently within a team and possess excellent communication skills. Experience with PERL, SQL and related querying tools a plus. The positions are contractual for two years with the possibility of conversion to full-time positions after that. Please submit an application package consisting of a letter of interest containing contact information and citizenship status, a curriculum vitae and a one-page statement of research interests. Include the contact information for three referees. Submit the application package electronically as a PDF file to phornbeck at cellsignal.com. Peter Hornbeck, Ph.D. Senior Scientist, Director of PhosphoSite? http://www.phosphosite.org Cell Signaling Technology 3 Trask Lane Danvers, MA 01923 (978) 867-2368 phornbeck at cellsignal.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20070907/4b753966/attachment.html From markov at mpiz-koeln.mpg.de Wed Sep 12 08:16:38 2007 From: markov at mpiz-koeln.mpg.de (markov at mpiz-koeln.mpg.de) Date: Wed, 12 Sep 2007 17:16:38 +0200 (CEST) Subject: [gofriends] GO ontology in OWL format Message-ID: <30431.195.37.46.17.1189610198.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi list, I'm new here and hope this is the appropriate list for this question. If you know of a better list for it, please tell me. I am trying to load the GO ontology, including annotations (synonyms, etc.) as well as is_a and part_of relationships, into a Sesame 2.0 repository. Seems that it should be a common enough task to have an easy solution -- perhaps somebody has done this successfully? Anyway, here's what I've tried. To get the data into the Sesame repository, I am using the (RDFFormat.)RDF-XML format choice, since the other options are N3, Turtle, TRIG, TRIX, N Triples (which I'm not too familiar with myself but assume GO comes in none of these). If I use the GO .rdf-xml files from their download page, ironically, I get errors that disappear when using the .owl files. Namely, I get " is not allowed as a property element", and if I replace this tag in the data file with the OWL equivalent, or whatever, I get further problems. The .owl termdb file on the ftp download (ftp://ftp.geneontology.org/pub/go/godatabase/archive/) works (or rather worked; the archive put up on Sept 11 2007 gives unzip errors, something like "can't find end of file"). However, this file does not contain any is_a or part_of, just the annotations. There is no other relevant .owl file. The .obo termdb file, as well as the .rdf-xml termdb file, include the is_a and part_of. Therefore I tried to use the obo2owl perl thingy to conert the .obo into an owl file. However I get "format problem detected" about 62353 lines into the file, on some very long GO term name. Finally I downloaded OBO-Edit and tried to use the OWL plugin (mentioned here: http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page#OboEdit_OWL_plugin) to convert obo to owl. However, putting the plugin files into the extensions directory (as per the instructions) resulted in a series of NullPointerErrors that prevented OBO-Edit from starting up. Without the plugin, OBO-Edit works fine. Cheers, Maria Markov -- 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 cjm at fruitfly.org Wed Sep 12 10:20:21 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 12 Sep 2007 18:20:21 +0100 Subject: [gofriends] GO ontology in OWL format In-Reply-To: <30431.195.37.46.17.1189610198.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <30431.195.37.46.17.1189610198.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: On Sep 12, 2007, at 4:16 PM, markov at mpiz-koeln.mpg.de wrote: > Hi list, > > I'm new here and hope this is the appropriate list for this > question. If > you know of a better list for it, please tell me. Hi Maria We have a mail list, go-help at genome.stanford.edu, for questions about the GO and the resources it produces. However, I will keep this discussion on gofriends since others may be interested. > I am trying to load the GO ontology, including annotations (synonyms, > etc.) as well as is_a and part_of relationships, into a Sesame 2.0 > repository. Seems that it should be a common enough task to have an > easy > solution -- perhaps somebody has done this successfully? We have successfully loaded all of OBO into Sesame 1.2.6, but haven't tried with 2.0 yet > Anyway, here's > what I've tried. > > To get the data into the Sesame repository, I am using the > (RDFFormat.)RDF-XML format choice, since the other options are N3, > Turtle, > TRIG, TRIX, N Triples (which I'm not too familiar with myself but > assume > GO comes in none of these). > > If I use the GO .rdf-xml files from their download page, > ironically, I get > errors that disappear when using the .owl files. Namely, I get > " > is not allowed as a property element", and if I replace this tag in > the > data file with the OWL equivalent, or whatever, I get > further > problems. Note that owl:OWL isn't part of the OWL language. There are a few issues with the GO RDF-XML format due to its age (it predates OWL considerably). It's more of a pseudo-RDF format, you have to strip the surrounding XML tags; see http://wiki.geneontology.org/index.php/GO_FAQ#Why_won.27t_the_RDF- XML_file_parse_using_RDF_parsers.3F I would recommend you use OWL here, with caveats (see below) > The .owl termdb file on the ftp download > (ftp://ftp.geneontology.org/pub/go/godatabase/archive/) works (or > rather > worked; the archive put up on Sept 11 2007 gives unzip errors, > something > like "can't find end of file"). The Sept 12 file validates in Pellet. Perhaps this was a download error? > However, this file does not contain any > is_a or part_of, just the annotations. There is no other relevant .owl > file. is_a is mapped to owl:subClassOf part_of links are mapped to existential restrictions For example: > The .obo termdb file, as well as the .rdf-xml termdb file, include the > is_a and part_of. Therefore I tried to use the obo2owl perl thingy to > conert the .obo into an owl file. However I get "format problem > detected" > about 62353 lines into the file, on some very long GO term name. Send me the full .obo file and error report off-list and I'll investigate There is a new release of go-perl on CPAN with the latest version of the obo2owl xslt included > Finally I downloaded OBO-Edit and tried to use the OWL plugin > (mentioned > here: > http://www.bioontology.org/wiki/index.php/ > OboInOwl:Main_Page#OboEdit_OWL_plugin) > to convert obo to owl. However, putting the plugin files into the > extensions directory (as per the instructions) resulted in a series of > NullPointerErrors that prevented OBO-Edit from starting up. Without > the > plugin, OBO-Edit works fine. I'll investigate this off-list - email me the version of oboedit you're using. Let me also give you some information on the results of our experiments using OWL and Sesame, as part of a different project outside GO. Triplestores such as Sesame seem to work best when you are storing instances rather than classes and class level relations. Sesame has no knowledge of OWL entailment rules (there is an addon called OWLIM that provides this). This means you are out of luck if you want to make queries over the GO such as "what is the nuclear chromosome part of?". You may be tempted to treat GO classes as instances and query these using normal RDFS semantics (for example, by loading the semi- deprecated GO RDF-XML file). This will give you better results in the short term, as you will be able to ask queries such as the part_of one above. However, this approach may turn out to be a dead end in the long run. In my opinion SQL (with entailments pre-computed) still turns out to be a far superior choice to existing semantic web technology - I'd be interested to see the SPARQL equivalents of the following queries: http://wiki.geneontology.org/index.php/Example_Queries I'd like to continue this discussion with you, but right now we are outside the realm of anything that is specifically to do with GO and into the realm of semantic web technology. I would encourage you to subscribe to this list and post details of what you are doing there: http://lists.w3.org/Archives/Public/public-semweb-lifesci/ There are many people on this list engaged in this kind of discussion Cheers Chris > Cheers, > > Maria Markov > > > > -- > 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/ > -- 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 erant at psb.ugent.be Tue Sep 18 09:36:17 2007 From: erant at psb.ugent.be (Erick Antezana) Date: Tue, 18 Sep 2007 18:36:17 +0200 Subject: [gofriends] parsing error Message-ID: <46EFFE81.9030608@psb.ugent.be> Hi, I just got the latest GO OBO file. And, while parsing it with the OBO parser from onto-perl (http://search.cpan.org/~easr/onto-perl-0.32/) we came across the following line (61699): ATP: protein-L-histidine N-pros-phosphotransferase from term: [Term] id: GO:0008256 name: protein histidine pros-kinase activity ... it is a typo, isn't it? cheers, Erick -- ================================================================== Erick Antezana http://www.cellcycleontology.org PhD student Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM erant at psb.ugent.be http://www.psb.ugent.be/~erant ================================================================== -- 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 erant at psb.ugent.be Tue Sep 18 09:44:31 2007 From: erant at psb.ugent.be (Erick Antezana) Date: Tue, 18 Sep 2007 18:44:31 +0200 Subject: [gofriends] One more parsing problem... Message-ID: <46F0006F.1010706@psb.ugent.be> Hi again, I have just spotted another problem with a 'dbxref ' in the term: id: GO:0009703 name: nitrate reductase (NADH) activity ... The following exact synonym has an invalid DBXREF: exact_synonym: "NADH-nitrate reductase activity" [:e] cheers, Erick -- ================================================================== Erick Antezana http://www.cellcycleontology.org PhD student Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM erant at psb.ugent.be http://www.psb.ugent.be/~erant ================================================================== -- 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 midori at ebi.ac.uk Tue Sep 18 10:40:37 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 18 Sep 2007 18:40:37 +0100 (BST) Subject: [gofriends] One more parsing problem... In-Reply-To: <46F0006F.1010706@psb.ugent.be> References: <46F0006F.1010706@psb.ugent.be> Message-ID: Hello, I have fixed this and the previous error; apologies, and thanks for bringing them to our attention. Midori ============================ Midori A. Harris, Ph.D. GO Editor EMBL - EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 (0) 1223 494667 Fax: +44 (0) 1223 494468 Email: midori at ebi.ac.uk On Tue, 18 Sep 2007, Erick Antezana wrote: > Hi again, > > I have just spotted another problem with a 'dbxref ' in the term: > > id: GO:0009703 > name: nitrate reductase (NADH) activity > ... > > > The following exact synonym has an invalid DBXREF: > > exact_synonym: "NADH-nitrate reductase activity" [:e] > > cheers, > Erick > > -- 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 Fri Sep 21 07:03:13 2007 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Fri, 21 Sep 2007 15:03:13 +0100 Subject: [gofriends] September 2007 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <46F3CF21.3010500@ebi.ac.uk> GOA releases: September 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/ ` (updated over the weekend) 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. GOA News Update: ***************** New for this release are mapping files of UniProt accessions to GeneID and RefSeq identifiers: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/gp2protein/gp2protein.geneid.gz ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/gp2protein/gp2protein.refseq.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/