From midori at ebi.ac.uk Tue Jul 1 05:36:15 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 1 Jul 2008 13:36:15 +0100 (BST) Subject: [Go] Ontology development - June highlights Message-ID: Dear GO, The most recent monthly report on ontology content, for June 2008, is now available at: http://wiki.geneontology.org/index.php/Jun2008_report Ontology development highlights from June: * Work has begun to overhaul the peptidase/protease activity terms in the function ontology. We hope to be able to retire many of the gene product terms in this branch (http://wiki.geneontology.org/index.php/Proteases). * An overhaul of transcription and transcription factors has begun (http://wiki.geneontology.org/index.php/Transcription). * As before, function-process links are still being gathered for electron transport and metabolic pathways. Function-process main page: http://wiki.geneontology.org/index.php/Function-Process_Links. * Last month we announced that 'regulates' F-P links will be made; we're now working on a more detailed announcement aimed especially at tool developers (first announcement in May newsletter: http://www.geneontology.org/newsletter/archive/200805.shtml) * The overhaul of signal transduction process terms continues (http://wiki.geneontology.org/index.php/Signaling). * Drug tranpsorters have come into focus, as part of the ongoing work on transport and transporters (http://wiki.geneontology.org/index.php/Transporters). As noted in recent months, the function-process work will continue, as will the signaling overhaul, taxon links, and quality control work connected with the regulation terms. In July, we plan to work on thee terms and relationships in the metabolism branch of the process ontology. Our plans for implementing cross-products based on Chris' new suggestion are unchanged (see http://wiki.geneontology.org/index.php/Cross_Product_Guide and files in the go/scratch/xps/ directory), as are plans to improve the metabolism branch with respect to structure and consistency with ChEBI. As usual, details of small- and medium-scale changes are available in the SourceForge Curator Requests tracker. Please contact us if you want to help out with ontology work in a particular area, or if you have any comments or questions about what's going on. Ontology Development wiki: http://wiki.geneontology.org/index.php/Ontology_Development SourceForge Curator Requests tracker: https://sourceforge.net/tracker/?group_id=36855&atid=440764 Midori & David on behalf of GO's ontology developers From midori at ebi.ac.uk Tue Jul 1 09:00:11 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 1 Jul 2008 16:00:11 UT Subject: [Go] SourceForge Update Message-ID: <200807011600.m61G0Br1252008@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Jul 2 09:00:11 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 2 Jul 2008 16:00:11 UT Subject: [Go] SourceForge Update Message-ID: <200807021600.m62G0Bt1258905@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From jdeegan at ebi.ac.uk Thu Jul 3 08:46:56 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Thu, 03 Jul 2008 16:46:56 +0100 Subject: [Go] Ontology-editors@geneontology.org Message-ID: <486CF470.2080400@ebi.ac.uk> Hi, The GO Ontology Editors have started a new mailing list called Ontology-editors at geneontology.org. This list is for those people who regularly check out, edit, and commit the gene_ontology_write.obo file. It is for technical discussions on issues to do with the integrity of the file, and for questions on current editing policy. For example, 'Which version of OBO-Edit am I meant to be committing from?', or 'Can anyone help me to revert the OBO file, as I have just committed a file with a cycle in it.' I think most people were signed up when the list was started, but just in case I missed anyone the sign-up page is here: http://fafner.stanford.edu/mailman/listinfo/ontology-editors Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From midori at ebi.ac.uk Thu Jul 3 09:00:11 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 3 Jul 2008 16:00:11 UT Subject: [Go] SourceForge Update Message-ID: <200807031600.m63G0BE1049432@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From suzi at berkeleybop.org Thu Jul 3 09:44:58 2008 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 3 Jul 2008 09:44:58 -0700 Subject: [Go] Ontology-editors@geneontology.org In-Reply-To: <486CF470.2080400@ebi.ac.uk> References: <486CF470.2080400@ebi.ac.uk> Message-ID: <43352BD0-95E9-4A8E-B4EE-4408981997C1@berkeleybop.org> Why is a new list needed? What distinguishes this from go-editors? I don't see a need for this. My sense is that if the purpose of different mailing lists gets too fine-grained then people don't know which one to use and are unable to consistently pick the appropriate list to send to. On Jul 3, 2008, at 8:46 AM, Jennifer Deegan (nee Clark) wrote: > Hi, > > The GO Ontology Editors have started a new mailing list called Ontology-editors at geneontology.org > . > > This list is for those people who regularly check out, edit, and > commit the gene_ontology_write.obo file. It is for technical > discussions on issues to do with the integrity of the file, and for > questions on current editing policy. For example, 'Which version of > OBO-Edit am I meant to be committing from?', or 'Can anyone help me > to revert the OBO file, as I have just committed a file with a cycle > in it.' > > I think most people were signed up when the list was started, but > just in case I missed anyone the sign-up page is here: > > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > > Thanks, > > Jen > > > > > -- > Jennifer Deegan (nee Clark) > EMBL-European Bioinformatics Institute > Gene Ontology Consortium > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From cjm at fruitfly.org Thu Jul 3 09:49:54 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 3 Jul 2008 09:49:54 -0700 Subject: [Go] Ontology-editors@geneontology.org In-Reply-To: <43352BD0-95E9-4A8E-B4EE-4408981997C1@berkeleybop.org> References: <486CF470.2080400@ebi.ac.uk> <43352BD0-95E9-4A8E-B4EE-4408981997C1@berkeleybop.org> Message-ID: <75450016-8A13-45C1-9659-B990D1853767@fruitfly.org> On Jul 3, 2008, at 9:44 AM, Suzanna Lewis wrote: > Why is a new list needed? What distinguishes this from go-editors? > I don't see a need for this. go-editors is not a list, it's an alias for the editors at cambridge. You can't subscribe to go-editors and it's not archived. > My sense is that if the purpose of different mailing lists gets too > fine-grained then people don't know which one to use and are unable > to consistently pick the appropriate list to send to. My understanding was that this was to be an ontology content/ development discussion and coordination list. It's seems fairly basic and obvious that we should have one list for each of the GO groups > On Jul 3, 2008, at 8:46 AM, Jennifer Deegan (nee Clark) wrote: > >> Hi, >> >> The GO Ontology Editors have started a new mailing list called >> Ontology-editors at geneontology.org. >> >> This list is for those people who regularly check out, edit, and >> commit the gene_ontology_write.obo file. It is for technical >> discussions on issues to do with the integrity of the file, and >> for questions on current editing policy. For example, 'Which >> version of OBO-Edit am I meant to be committing from?', or 'Can >> anyone help me to revert the OBO file, as I have just committed a >> file with a cycle in it.' >> >> I think most people were signed up when the list was started, but >> just in case I missed anyone the sign-up page is here: >> >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> >> Thanks, >> >> Jen >> >> >> >> >> -- >> Jennifer Deegan (nee Clark) >> EMBL-European Bioinformatics Institute >> Gene Ontology Consortium >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From suzi at berkeleybop.org Thu Jul 3 09:54:42 2008 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 3 Jul 2008 09:54:42 -0700 Subject: [Go] Ontology-editors@geneontology.org In-Reply-To: <75450016-8A13-45C1-9659-B990D1853767@fruitfly.org> References: <486CF470.2080400@ebi.ac.uk> <43352BD0-95E9-4A8E-B4EE-4408981997C1@berkeleybop.org> <75450016-8A13-45C1-9659-B990D1853767@fruitfly.org> Message-ID: Ah, okay then. A list for this group makes sense. On Jul 3, 2008, at 9:49 AM, Chris Mungall wrote: > > On Jul 3, 2008, at 9:44 AM, Suzanna Lewis wrote: > >> Why is a new list needed? What distinguishes this from go-editors? >> I don't see a need for this. > > go-editors is not a list, it's an alias for the editors at > cambridge. You can't subscribe to go-editors and it's not archived. > >> My sense is that if the purpose of different mailing lists gets too >> fine-grained then people don't know which one to use and are unable >> to consistently pick the appropriate list to send to. > > My understanding was that this was to be an ontology content/ > development discussion and coordination list. It's seems fairly > basic and obvious that we should have one list for each of the GO > groups > >> On Jul 3, 2008, at 8:46 AM, Jennifer Deegan (nee Clark) wrote: >> >>> Hi, >>> >>> The GO Ontology Editors have started a new mailing list called Ontology-editors at geneontology.org >>> . >>> >>> This list is for those people who regularly check out, edit, and >>> commit the gene_ontology_write.obo file. It is for technical >>> discussions on issues to do with the integrity of the file, and >>> for questions on current editing policy. For example, 'Which >>> version of OBO-Edit am I meant to be committing from?', or 'Can >>> anyone help me to revert the OBO file, as I have just committed a >>> file with a cycle in it.' >>> >>> I think most people were signed up when the list was started, but >>> just in case I missed anyone the sign-up page is here: >>> >>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>> >>> Thanks, >>> >>> Jen >>> >>> >>> >>> >>> -- >>> Jennifer Deegan (nee Clark) >>> EMBL-European Bioinformatics Institute >>> Gene Ontology Consortium >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > From cherry at stanford.edu Thu Jul 3 11:44:03 2008 From: cherry at stanford.edu (Mike Cherry) Date: Thu, 3 Jul 2008 11:44:03 -0700 Subject: [Go] Ontology-editors@geneontology.org In-Reply-To: <75450016-8A13-45C1-9659-B990D1853767@fruitfly.org> References: <486CF470.2080400@ebi.ac.uk> <43352BD0-95E9-4A8E-B4EE-4408981997C1@berkeleybop.org> <75450016-8A13-45C1-9659-B990D1853767@fruitfly.org> Message-ID: Just checking: When the list was created the description was "Editors of the Ontology". Also thus the name. I guess this could be changed to "Ontology Content/Development Discussions and Coordination". I'm not going to change the name of the list. I understand this is not a list for the basic OBO-edit technical discussions of how to make changes to the ontology files. -Mike On Jul 3, 2008, at 9:49 AM, Chris Mungall wrote: > > On Jul 3, 2008, at 9:44 AM, Suzanna Lewis wrote: > >> Why is a new list needed? What distinguishes this from go-editors? >> I don't see a need for this. > > go-editors is not a list, it's an alias for the editors at > cambridge. You can't subscribe to go-editors and it's not archived. > >> My sense is that if the purpose of different mailing lists gets too >> fine-grained then people don't know which one to use and are unable >> to consistently pick the appropriate list to send to. > > My understanding was that this was to be an ontology content/ > development discussion and coordination list. It's seems fairly > basic and obvious that we should have one list for each of the GO > groups > >> On Jul 3, 2008, at 8:46 AM, Jennifer Deegan (nee Clark) wrote: >> >>> Hi, >>> >>> The GO Ontology Editors have started a new mailing list called Ontology-editors at geneontology.org >>> . >>> >>> This list is for those people who regularly check out, edit, and >>> commit the gene_ontology_write.obo file. It is for technical >>> discussions on issues to do with the integrity of the file, and >>> for questions on current editing policy. For example, 'Which >>> version of OBO-Edit am I meant to be committing from?', or 'Can >>> anyone help me to revert the OBO file, as I have just committed a >>> file with a cycle in it.' >>> >>> I think most people were signed up when the list was started, but >>> just in case I missed anyone the sign-up page is here: >>> >>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>> >>> Thanks, >>> >>> Jen >>> >>> >>> >>> >>> -- >>> Jennifer Deegan (nee Clark) >>> EMBL-European Bioinformatics Institute >>> Gene Ontology Consortium >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From midori at ebi.ac.uk Sat Jul 5 09:00:11 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 5 Jul 2008 16:00:11 UT Subject: [Go] SourceForge Update Message-ID: <200807051600.m65G0Bx1063259@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Mon Jul 7 09:00:14 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 7 Jul 2008 16:00:14 UT Subject: [Go] SourceForge Update Message-ID: <200807071600.m67G0En1076137@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Jul 9 09:00:12 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 9 Jul 2008 16:00:12 UT Subject: [Go] SourceForge Update Message-ID: <200807091600.m69G0D21110801@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Thu Jul 10 09:00:14 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 10 Jul 2008 16:00:14 UT Subject: [Go] SourceForge Update Message-ID: <200807101600.m6AG0EZ1373101@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Fri Jul 11 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 11 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807111600.m6BG0Du1129379@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Fri Jul 11 09:53:52 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 11 Jul 2008 17:53:52 +0100 (BST) Subject: [Go] Alert: proposal to obsolete GO:0006512 that impacts existing annotation Message-ID: Hello, The proposal has been made to obsolete ubiquitin cycle ; GO:0006512 The reason for making this term obsolete is that it implies that every protein that s ubiquitinated is also subsequently deubiquinitated, which is not true. Also, the process ontology does not include analogous terms for other small modifiers. Terms suggested for annotation updates: protein deubiquitination ; GO:0016597 protein ubiquitination ; GO:0016567 Annotations to GO:0006512 exist as follows: gene_association.cgd.gz IEA non-IEA Total 2 0 2 gene_association.dictyBase.gz IEA non-IEA Total 97 0 97 gene_association.fb.gz IEA non-IEA Total 25 33 58 gene_association.GeneDB_Lmajor.gz IEA non-IEA Total 34 0 34 gene_association.GeneDB_Pfalciparum.gz IEA non-IEA Total 25 0 25 gene_association.GeneDB_Spombe.gz IEA non-IEA Total 7 0 7 gene_association.GeneDB_Tbrucei.gz IEA non-IEA Total 31 24 55 gene_association.goa_chicken.gz IEA non-IEA Total 126 0 126 gene_association.goa_cow.gz IEA non-IEA Total 210 0 210 gene_association.goa_human.gz IEA non-IEA Total 502 8 510 gene_association.goa_uniprot.gz IEA non-IEA Total 7372 2 7374 gene_association.gramene_oryza.gz IEA non-IEA Total 0 16 16 gene_association.mgi.gz IEA non-IEA Total 423 34 457 gene_association.rgd.gz IEA non-IEA Total 201 9 210 gene_association.sgd.gz IEA non-IEA Total 137 9 146 gene_association.tair.gz IEA non-IEA Total 7 53 60 gene_association.tigr_Tbrucei_chr2.gz IEA non-IEA Total 0 3 3 gene_association.wb.gz IEA non-IEA Total 28 0 28 gene_association.zfin.gz IEA non-IEA Total 29 0 29 The term is used in the following external mappings: interpro2go:InterPro:IPR000011 Ubiquitin-activating enzyme, E1 > GO:ubiquitin cycle ; GO:0006512 interpro2go:InterPro:IPR000127 Ubiquitin-activating enzyme repeat > GO:ubiquitin cycle ; GO:0006512 interpro2go:InterPro:IPR000569 HECT > GO:ubiquitin cycle ; GO:0006512 interpro2go:InterPro:IPR003126 Zinc finger, N-recognin > GO:ubiquitin cycle ; GO:0006512 interpro2go:InterPro:IPR003977 Parkin > GO:ubiquitin cycle ; GO:0006512 interpro2go:InterPro:IPR006615 Ubiquitin carboxyl-terminal hydrolase, N-terminal region 1 > GO:ubiquitin cycle ; GO:0006512 interpro2go:InterPro:IPR008883 Tumour susceptibility gene 101 > GO:ubiquitin cycle ; GO:0006512 interpro2go:InterPro:IPR010309 E3 ubiquitin ligase, region of unknown function DUF908 > GO:ubiquitin cycle ; GO:0006512 interpro2go:InterPro:IPR010314 E3 ubiquitin ligase, region of unknown function DUF913 > GO:ubiquitin cycle ; GO:0006512 pfam2go:Pfam:PF00632 HECT > GO:ubiquitin cycle ; GO:0006512 pfam2go:Pfam:PF02134 UBACT > GO:ubiquitin cycle ; GO:0006512 pfam2go:Pfam:PF02207 zf-UBR > GO:ubiquitin cycle ; GO:0006512 pfam2go:Pfam:PF05743 UEV > GO:ubiquitin cycle ; GO:0006512 pfam2go:Pfam:PF06012 DUF908 > GO:ubiquitin cycle ; GO:0006512 pfam2go:Pfam:PF06025 DUF913 > GO:ubiquitin cycle ; GO:0006512 pirsf2go:PIRSF:PIRSF037880 Parkin > GO:ubiquitin cycle ; GO:0006512 prints2go:PRINTS:PR01475 PARKIN > GO:ubiquitin cycle ; GO:0006512 prints2go:PRINTS:PR01849 UBIQUITINACT > GO:ubiquitin cycle ; GO:0006512 prosite2go:PROSITE:PS00536 UBIQUITIN_ACTIVAT_1 > GO:ubiquitin cycle ; GO:0006512 prosite2go:PROSITE:PS00865 UBIQUITIN_ACTIVAT_2 > GO:ubiquitin cycle ; GO:0006512 prosite2go:PROSITE:PS50237 HECT > GO:ubiquitin cycle ; GO:0006512 prosite2go:PROSITE:PS51157 ZF_UBR > GO:ubiquitin cycle ; GO:0006512 smart2go:SMART:SM00119 HECTc > GO:ubiquitin cycle ; GO:0006512 smart2go:SMART:SM00695 DUSP > GO:ubiquitin cycle ; GO:0006512 spkw2go:SP_KW:KW-0833 Ubl conjugation pathway > GO:ubiquitin cycle ; GO:0006512 This term is not in any GO slim or subset maintained in the GO .obo files. SourceForge link: https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1729553&group_id=36855 The comment period ends Friday, July 25, 2008. *** Unless objections are received by July 25, we will assume that you agree to this change. *** From cherry at stanford.edu Fri Jul 11 12:37:55 2008 From: cherry at stanford.edu (Mike Cherry) Date: Fri, 11 Jul 2008 12:37:55 -0700 Subject: [Go] Abbreviations used in gene association files Message-ID: <66C5F785-F664-41F8-93A0-EFBA21481E3A@stanford.edu> There is interest in the GOC using standard abbr in our GAFs. To help you identify issues in your GAF I have created an abbreviation checker. Its in CVS at: go/software/utilities/check-abbr-ga-file.pl This script reports when the abbreviation is one of the defined synonyms, and thus should be changed to the standard abbr. For example the use of UniProt include of the defined standard UniProtKB. The script will also report when the case of your abbr does not match the stanford. For example, INTERPRO instead of InterPro. The GOC using the same abbreviations is good for the community, they will see that we too can make a standard and use it. It also helps those that process our files, they can easily find common IDs without processing all the abbreviations themselves. Use of a standard also helps AmiGO work better, hyperlinking code can be simplified, thus be more reliable. Please use the above script to fix your project's GAF file. The following filtered GAFs have abbreviation issues. The majority of the mismatches are in the WITH column, but there are problems with ASSIGNED_BY, DB and DB:REF. goa_pdb mgi fb gramene_oryza wb sgd tair GeneDB_Lmajor GeneDB_Tbrucei rgd GeneDB_Pfalciparum goa_human reactome goa_uniprot goa_cow goa_chicken dictyBase zfin GeneDB_Spombe tigr_Tbrucei_chr2 PAMGO_Mgrisea -Mike From midori at ebi.ac.uk Sat Jul 12 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 12 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807121600.m6CG0Dv1396340@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Mon Jul 14 09:00:09 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 14 Jul 2008 16:00:09 UT Subject: [Go] SourceForge Update Message-ID: <200807141600.m6EG0991407742@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Tue Jul 15 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 15 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807151600.m6FG0DT1163938@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Jul 16 09:00:12 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 16 Jul 2008 16:00:12 UT Subject: [Go] SourceForge Update Message-ID: <200807161600.m6GG0C21433985@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From pgaudet at northwestern.edu Wed Jul 16 09:47:41 2008 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Wed, 16 Jul 2008 12:47:41 -0400 Subject: [Go] GOC meeting: October 21-22, 2008 Message-ID: <487E262D.5080100@northwestern.edu> An HTML attachment was scrubbed... URL: From midori at ebi.ac.uk Thu Jul 17 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 17 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807171600.m6HG0D31173054@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From jdeegan at ebi.ac.uk Fri Jul 18 01:51:52 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Fri, 18 Jul 2008 09:51:52 +0100 Subject: [Go] GO Managers' Meeting July 16th Message-ID: <488059A8.6080501@ebi.ac.uk> Hi, The minutes for the July 16th managers' meeting are now available on the wiki: http://wiki.geneontology.org/index.php/Managers_16July08 If you would like a particular issue to be discussed at the next managers meeting, please contact the relevant manager(s): Reference Genomes/Annotation: Pascale User Advocacy: Jane Content Development: Midori and David Annotation Outreach: Jennifer Software: Chris Or the GO PIs (go-top at genome.stanford.edu) for general management and budget issues. Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From midori at ebi.ac.uk Fri Jul 18 09:00:14 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 18 Jul 2008 16:00:14 UT Subject: [Go] SourceForge Update Message-ID: <200807181600.m6IG0E81434255@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Sat Jul 19 09:00:11 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 19 Jul 2008 16:00:11 UT Subject: [Go] SourceForge Update Message-ID: <200807191600.m6JG0B41173180@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From ma11 at gen.cam.ac.uk Sat Jul 19 10:05:27 2008 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Sat, 19 Jul 2008 13:05:27 -0400 Subject: [Go] GO Managers' Meeting July 16th In-Reply-To: <488059A8.6080501@ebi.ac.uk> References: <488059A8.6080501@ebi.ac.uk> Message-ID: wrt: It seems like maybe one of the PIs needs to be the rep since it would take their kind of authority to be able to make the decisions that are needed. and OBO Foundry, yes Suzi or I will do this Michael On 18 Jul 2008, at 04:51, Jennifer Deegan (nee Clark) wrote: > Hi, > > The minutes for the July 16th managers' meeting are now available > on the > wiki: > > http://wiki.geneontology.org/index.php/Managers_16July08 > > If you would like a particular issue to be discussed at the next > managers meeting, please contact the relevant manager(s): > > Reference Genomes/Annotation: Pascale > User Advocacy: Jane > Content Development: Midori and David > Annotation Outreach: Jennifer > Software: Chris > > Or the GO PIs (go-top at genome.stanford.edu) for general management and > budget issues. > > Thanks, > > Jen > > -- > Jennifer Deegan (nee Clark) > EMBL-European Bioinformatics Institute > Gene Ontology Consortium > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From midori at ebi.ac.uk Mon Jul 21 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 21 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807211600.m6LG0D11170075@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Tue Jul 22 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 22 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807221600.m6MG0DD1436253@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Jul 23 09:00:12 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 23 Jul 2008 16:00:12 UT Subject: [Go] SourceForge Update Message-ID: <200807231600.m6NG0Cr1183429@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From aji at ebi.ac.uk Wed Jul 23 11:07:16 2008 From: aji at ebi.ac.uk (Amelia Ireland) Date: Wed, 23 Jul 2008 19:07:16 +0100 (BST) Subject: [Go] FAO: Users/editors of GO.references, GO.xrf_abbs and the bibliography data file Message-ID: Hello all, I'd like to propose some alterations to the format of these files to make them more uniform. There's a wiki page here: http://wiki.geneontology.org/index.php/File_format_proposals I'd be grateful if those involved with these files could comment and/or give a suggested time frame for making and deploying changes. I am not sure how many people use these files and how large a difference the changes would make to them. Thanks! -- Amelia Ireland GO Editorial Office http://www.ebi.ac.uk || http://www.berkeleybop.org BBOP Plant Project: http://bbopgarden.blogspot.com From midori at ebi.ac.uk Thu Jul 24 04:41:51 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 24 Jul 2008 12:41:51 +0100 (BST) Subject: [Go] FAO: Users/editors of GO.references, GO.xrf_abbs and the bibliography data file In-Reply-To: References: Message-ID: On Wed, 23 Jul 2008, Amelia Ireland wrote: > Hello all, > > I'd like to propose some alterations to the format of these files to make > them more uniform. There's a wiki page here: > > http://wiki.geneontology.org/index.php/File_format_proposals > > I'd be grateful if those involved with these files could comment and/or > give a suggested time frame for making and deploying changes. I am not > sure how many people use these files and how large a difference the > changes would make to them. I've put some comments on the wiki. m From midori at ebi.ac.uk Thu Jul 24 08:40:04 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 24 Jul 2008 16:40:04 +0100 (BST) Subject: [Go] secretion merge - SF 2024385 Message-ID: Hello, In SF 2024385, there's a proposal to merge 'secretion by cell' (GO:0032940) into 'exocytosis' (GO:0006887). Any comments or objections? If not, we'll go ahead in a few days. https://sourceforge.net/tracker/index.php?func=detail&aid=2024385&group_id=36855&atid=440764 cheers, midori From midori at ebi.ac.uk Thu Jul 24 08:54:01 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 24 Jul 2008 16:54:01 +0100 (BST) Subject: [Go] Alert: proposal to obsolete GO:0000051 (no annotations affected) Message-ID: Hello, The proposal has been made to obsolete urea cycle intermediate metabolic process ; GO:0000051 This term is not used in any annotations; it is used in the following external2go mappings, and is in the prokaryote GO subset maintained within the OBO flat file. mips2go:MIPS_funcat:01.01.05 metabolism of urea cycle, creatine and polyamines > GO:urea cycle intermediate metabolism ; GO:0000051 mips2go:MIPS_funcat:01.01.05.03 metabolism of urea (urea cycle) > GO:urea cycle intermediate metabolism ; GO:0000051 The reason for making these terms obsolete is that it is a grouping term that is not useful, but causes true path violations. Suggested terms for annotations: urea cycle ; GO:0000050 arginine metabolic process ; GO:0006525 argininosuccinate metabolic process ; GO:0000053 citrulline metabolic process ; GO:0000052 ornithine metabolic process; GO:0006591 SourceForge link: https://sourceforge.net/tracker/index.php?func=detail&aid=2023928&group_id=36855&atid=440764 *** Unless objections are received by August 1, we will assume that you agree to this change. *** Midori _______________________________________________ Go mailing list Go at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go From midori at ebi.ac.uk Thu Jul 24 08:58:40 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 24 Jul 2008 16:58:40 +0100 (BST) Subject: [Go] secretion merge - SF 2024385 In-Reply-To: References: Message-ID: Sorry, ignore this -- we forgot about the non-exocytotic bacterial secretion mechanisms, so we won't merge these two after all. feeling foolish, m On Thu, 24 Jul 2008, Midori Harris wrote: > Hello, > > In SF 2024385, there's a proposal to merge 'secretion by cell' (GO:0032940) > into 'exocytosis' (GO:0006887). Any comments or objections? If not, we'll go > ahead in a few days. > > https://sourceforge.net/tracker/index.php?func=detail&aid=2024385&group_id=36855&atid=440764 > > cheers, > midori > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From midori at ebi.ac.uk Thu Jul 24 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 24 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807241600.m6OG0DL1444404@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From jimhu at tamu.edu Thu Jul 24 10:18:22 2008 From: jimhu at tamu.edu (Jim Hu) Date: Thu, 24 Jul 2008 12:18:22 -0500 Subject: [Go] secretion merge - SF 2024385 In-Reply-To: References: Message-ID: <7E37A1E1-93E3-4E16-8207-DDB7CB634FCD@tamu.edu> whew! Jim On Jul 24, 2008, at 10:58 AM, Midori Harris wrote: > Sorry, ignore this -- we forgot about the non-exocytotic bacterial > secretion mechanisms, so we won't merge these two after all. > > feeling foolish, > m > > On Thu, 24 Jul 2008, Midori Harris wrote: > >> Hello, >> >> In SF 2024385, there's a proposal to merge 'secretion by cell' (GO: >> 0032940) into 'exocytosis' (GO:0006887). Any comments or >> objections? If not, we'll go ahead in a few days. >> >> https://sourceforge.net/tracker/index.php?func=detail&aid=2024385&group_id=36855&atid=440764 >> >> cheers, >> midori >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go ===================================== 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 ccollmer at wells.edu Thu Jul 24 13:04:56 2008 From: ccollmer at wells.edu (Candace Collmer) Date: Thu, 24 Jul 2008 16:04:56 -0400 Subject: [Go] secretion merge - SF 2024385 Message-ID: <48775FC6@webmail> yep -- I agree -- whew! Candace >===== Original Message From Jim Hu ===== >whew! > >Jim > >On Jul 24, 2008, at 10:58 AM, Midori Harris wrote: > >> Sorry, ignore this -- we forgot about the non-exocytotic bacterial >> secretion mechanisms, so we won't merge these two after all. >> >> feeling foolish, >> m >> >> On Thu, 24 Jul 2008, Midori Harris wrote: >> >>> Hello, >>> >>> In SF 2024385, there's a proposal to merge 'secretion by cell' (GO: >>> 0032940) into 'exocytosis' (GO:0006887). Any comments or >>> objections? If not, we'll go ahead in a few days. >>> >>> https://sourceforge.net/tracker/index.php?func=detail&aid=2024385&group_id=368 55&atid=440764 >>> >>> cheers, >>> midori >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > >===================================== >Jim Hu >Associate Professor >Dept. of Biochemistry and Biophysics >2128 TAMU >Texas A&M Univ. >College Station, TX 77843-2128 >979-862-4054 > > > > >_______________________________________________ >Go mailing list >Go at geneontology.org >http://fafner.stanford.edu/mailman/listinfo/go ---------------------------- Candace W. Collmer, Ph.D. Professor of Biology Chair, Division of Natural and Mathematical Sciences Wells College Aurora, NY 13026 phone at Wells: 315-364-3271 phone at Cornell: 607-254-7297 fax: 315-364-3464 email: ccollmer at wells.edu From midori at ebi.ac.uk Fri Jul 25 04:09:55 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 25 Jul 2008 12:09:55 +0100 (BST) Subject: [Go] Alert: proposal to obsolete many peptidase activity terms from the molecular function ontology Message-ID: Dear GO, For a few weeks now, a small group of curators from GO, MEROPS, and PRO have been working on a substantial reorganization of the peptidase activity terms in the molecular function ontology. Background and notes from this effort are on the wiki: http://wiki.geneontology.org/index.php/Proteases One important outcome of this work is that many of the existing peptidase activity terms will be made obsolete, in most cases because they represent gene products. This course of action was readily agreed upon by all of the working group, and actively encouraged by the peptidase experts at MEROPS. These terms will be made obsolete on August 15, 2008. The IDs and names of the terms to become obsolete are: GO:0001509 legumain activity GO:0003802 coagulation factor VIIa activity GO:0003803 coagulation factor IXa activity GO:0003804 coagulation factor Xa activity GO:0003805 coagulation factor XIa activity GO:0003806 coagulation factor XIIa activity GO:0003807 plasma kallikrein activity GO:0003808 protein C (activated) activity GO:0003809 thrombin activity GO:0003812 alternative-complement-pathway C3/C5 convertase activity GO:0003813 classical-complement-pathway C3/C5 convertase activity GO:0003815 complement component C1r activity GO:0003816 complement component C1s activity GO:0003817 complement factor D activity GO:0003818 complement factor I activity GO:0004178 leucyl aminopeptidase activity GO:0004179 membrane alanyl aminopeptidase activity GO:0004182 carboxypeptidase A activity GO:0004183 carboxypeptidase E activity GO:0004184 lysine carboxypeptidase activity GO:0004186 carboxypeptidase C activity GO:0004187 carboxypeptidase D activity GO:0004188 serine-type Pro-X carboxypeptidase activity GO:0004189 tubulinyl-Tyr carboxypeptidase activity GO:0004191 barrierpepsin activity GO:0004192 cathepsin D activity GO:0004193 cathepsin E activity GO:0004194 pepsin A activity GO:0004195 renin activity GO:0004196 saccharopepsin activity GO:0004213 cathepsin B activity GO:0004214 dipeptidyl-peptidase I activity GO:0004215 cathepsin H activity GO:0004216 cathepsin K activity GO:0004217 cathepsin L activity GO:0004218 cathepsin S activity GO:0004219 pyroglutamyl-peptidase I activity GO:0004226 Gly-X carboxypeptidase activity GO:0004228 gelatinase A activity GO:0004229 gelatinase B activity GO:0004230 glutamyl aminopeptidase activity GO:0004231 insulysin activity GO:0004232 interstitial collagenase activity GO:0004234 macrophage elastase activity GO:0004235 matrilysin activity GO:0004237 membrane dipeptidase activity GO:0004238 meprin A activity GO:0004239 methionyl aminopeptidase activity GO:0004240 mitochondrial processing peptidase activity GO:0004243 mitochondrial intermediate peptidase activity GO:0004244 mitochondrial inner membrane peptidase activity GO:0004245 neprilysin activity GO:0004246 peptidyl-dipeptidase A activity GO:0004247 saccharolysin activity GO:0004248 stromelysin 1 activity GO:0004249 stromelysin 3 activity GO:0004250 aminopeptidase I activity GO:0004251 X-Pro dipeptidase activity GO:0004253 gamma-renin activity GO:0004254 acylaminoacyl-peptidase activity GO:0004261 cathepsin G activity GO:0004262 cerevisin activity GO:0004263 chymotrypsin activity GO:0004274 dipeptidyl-peptidase IV activity GO:0004275 enteropeptidase activity GO:0004276 furin activity GO:0004277 granzyme A activity GO:0004278 granzyme B activity GO:0004281 pancreatic elastase II activity GO:0004283 plasmin activity GO:0004284 acrosin activity GO:0004285 proprotein convertase 1 activity GO:0004286 proprotein convertase 2 activity GO:0004287 prolyl oligopeptidase activity GO:0004289 subtilase activity GO:0004290 kexin activity GO:0004291 subtilisin activity GO:0004293 tissue kallikrein activity GO:0004294 tripeptidyl-peptidase II activity GO:0004295 trypsin activity GO:0008125 pancreatic elastase I activity GO:0008129 actinidain activity GO:0008130 neutrophil collagenase activity GO:0008132 pancreatic elastase activity GO:0008133 collagenase activity GO:0008243 plasminogen activator activity GO:0008319 prenyl protein specific endopeptidase activity GO:0008322 Pro-X carboxypeptidase activity GO:0008423 bleomycin hydrolase activity GO:0008439 monophenol monooxygenase activator activity GO:0008450 O-sialoglycoprotein endopeptidase activity GO:0008451 X-Pro aminopeptidase activity GO:0008462 endopeptidase Clp activity GO:0008464 gamma-glutamyl hydrolase activity GO:0008472 metallocarboxypeptidase D activity GO:0008487 prenyl-dependent CAAX protease activity GO:0008533 astacin activity GO:0008581 ubiquitin-specific protease 5 activity GO:0008717 D-alanyl-D-alanine endopeptidase activity GO:0008769 X-His dipeptidase activity GO:0008846 endopeptidase La activity GO:0008931 murein DD-endopeptidase activity GO:0008944 oligopeptidase A activity GO:0008945 oligopeptidase B activity GO:0008947 omptin activity GO:0008956 peptidyl-dipeptidase Dcp activity GO:0008975 pitrilysin activity GO:0008978 prepilin peptidase activity GO:0008981 protease IV activity GO:0008991 serine-type signal peptidase activity GO:0008992 repressor LexA activity GO:0009003 signal peptidase activity GO:0009004 signal peptidase I activity GO:0009005 signal peptidase II activity GO:0009049 aspartic-type signal peptidase activity GO:0009377 HslUV protease activity GO:0009980 glutamate carboxypeptidase activity GO:0009983 tyrosine aminopeptidase activity GO:0010320 arginine/lysine endopeptidase activity GO:0016284 alanine aminopeptidase activity GO:0016285 cytosol alanyl aminopeptidase activity GO:0016511 endothelin-converting enzyme activity GO:0016512 endothelin-converting enzyme 1 activity GO:0016804 prolyl aminopeptidase activity GO:0016808 proprotein convertase activity GO:0016919 nardilysin activity GO:0016921 pyroglutamyl-peptidase II activity GO:0016946 cathepsin F activity GO:0017026 procollagen C-endopeptidase activity GO:0017039 dipeptidyl-peptidase III activity GO:0017074 procollagen N-endopeptidase activity GO:0017088 X-Pro dipeptidyl-peptidase activity GO:0017092 sterol regulatory element-binding protein site 2 protease activity GO:0017093 sterol regulatory element-binding protein protease activity GO:0017094 sterol regulatory element-binding protein site 1 protease activity GO:0017165 dipeptidase E activity GO:0019131 tripeptidyl-peptidase I activity GO:0019132 C-terminal processing peptidase activity GO:0019783 small conjugating protein-specific protease activity GO:0019784 NEDD8-specific protease activity GO:0019785 ISG15-specific protease activity GO:0019786 APG8-specific protease activity GO:0030019 tryptase activity GO:0030271 chymase activity GO:0030303 stromelysin 2 activity GO:0030402 matrilysin-2 activity GO:0030403 collagenase 4 activity GO:0030404 collagenase 3 activity GO:0030405 matrix metalloproteinase 19 activity GO:0030406 matrix metalloproteinase 25 activity GO:0030601 aminopeptidase B activity GO:0030602 chymosin activity GO:0030693 caspase activity GO:0031079 picornain 3C activity GO:0031368 Pro-X metallocarboxypeptidase activity GO:0033264 bontoxilysin activity GO:0042029 fibrolase activity GO:0042315 cytosol nonspecific dipeptidase activity GO:0042499 signal peptide peptidase activity GO:0042576 aspartyl aminopeptidase activity GO:0042708 elastase activity GO:0043275 glutamate carboxypeptidase II activity GO:0043859 cyanophycinase activity GO:0045024 peptidyl-glutamyl peptide hydrolyzing enzyme activity GO:0046560 scytalidopepsin B activity GO:0046561 penicillopepsin activity GO:0050424 alanine carboxypeptidase activity GO:0050425 carboxypeptidase B activity GO:0050426 peptidyl-glycinamidase activity GO:0051397 N-terminal basic amino acid aminopeptidase activity GO:0051398 N-terminal lysine aminopeptidase activity GO:0051399 N-terminal arginine aminopeptidase activity GO:0051404 clostripain activity GO:0051405 microbial collagenase activity Because there are so many terms affected (174), I have not included all of the usual details -- specific reasons, annotation counts, and substitute terms -- in this email. For a complete list of terms slated to become obsolete, in OBO format, with the specific reasons for obsoletion filled in, see (this file is also linked to the wiki page): http://www.geneontology.org/scratch/peptidase_terms_with_obs_tags.obo Details of existing annotations to these terms are also on the wiki: http://wiki.geneontology.org/index.php/Peptidase_annotations Every peptidase term that we make obsolete will have at least one 'replaced_by' tag pointing to a peptidase activity term; these are also shown in the .obo file cited above. A longer term goal is to add new terms to the protein ontology (PRO) representing the gene products that have peptidase activity. When the PRO terms become available, many of the obsolete GO peptidase activity terms will point to PRO terms via 'consider' tags. Please let us know if you have any questions about this plan, or about the files noted above. The comment period ends Friday, August 15, 2008. *** Unless objections are received by August 15, we will assume that you agree to this change. *** Regards, Midori (on behalf of the peptidase activity working group) From val at sanger.ac.uk Fri Jul 25 04:28:08 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 25 Jul 2008 11:28:08 UT Subject: [Go] Alert: proposal to obsolete many peptidase activity terms from the molecular function ontology Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Fri Jul 25 04:36:39 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 25 Jul 2008 12:36:39 +0100 (BST) Subject: [Go] Alert: proposal to obsolete many peptidase activity terms from the molecular function ontology In-Reply-To: References: Message-ID: Hi Val, In the vast majority of cases the reason not to merge is that the term represents a gene product, and if we did merges we'd end up with a few terms, each with a ton of narrow synonyms and alt_ids. People already often get confused by the alt_ids even when a term has just one or two. Gene products are clearly outside the scope of GO, so for those terms obsoleting is more appropriate. The small-conjugating-etc. terms are a bit different, in that they're not just obviously gene product names with 'activity' slapped on the end. But we're leaning towards making them obsolete as well, mainly because one of the conclusions the working group reached is that trying to use substrate specificity to sub-divide peptidases wouldn't work, except for the endo- vs. exo- and dipeptidase/tripeptidase cases. m On Fri, 25 Jul 2008, Valerie Wood wrote: > Midori, > > Its looks great, a lot of work. > > Only one question, a number seem to have single parents (like the small > conjugating protein specific protease terms and children), so I'm > assuming the pointer will just be to the parent. Any reason why these > can't be merges? Or are the resolutions always more complicated? > > I did look in the obo file for 'conjugating' and I couldn't see the > replace by tages for this term (or for any terms close by in the file) > just is_obsolete: true > > Val > > Midori Harris wrote: >> Dear GO, >> >> For a few weeks now, a small group of curators from GO, MEROPS, and PRO >> have been working on a substantial reorganization of the peptidase >> activity terms in the molecular function ontology. Background and notes >> from this effort are on the wiki: >> >> http://wiki.geneontology.org/index.php/Proteases >> >> One important outcome of this work is that many of the existing peptidase >> activity terms will be made obsolete, in most cases because they represent >> gene products. This course of action was readily agreed upon by all of the >> working group, and actively encouraged by the peptidase experts at MEROPS. >> These terms will be made obsolete on August 15, 2008. >> >> The IDs and names of the terms to become obsolete are: >> >> GO:0001509 legumain activity >> GO:0003802 coagulation factor VIIa activity >> GO:0003803 coagulation factor IXa activity >> GO:0003804 coagulation factor Xa activity >> GO:0003805 coagulation factor XIa activity >> GO:0003806 coagulation factor XIIa activity >> GO:0003807 plasma kallikrein activity >> GO:0003808 protein C (activated) activity >> GO:0003809 thrombin activity >> GO:0003812 alternative-complement-pathway C3/C5 convertase activity >> GO:0003813 classical-complement-pathway C3/C5 convertase activity >> GO:0003815 complement component C1r activity >> GO:0003816 complement component C1s activity >> GO:0003817 complement factor D activity >> GO:0003818 complement factor I activity >> GO:0004178 leucyl aminopeptidase activity >> GO:0004179 membrane alanyl aminopeptidase activity >> GO:0004182 carboxypeptidase A activity >> GO:0004183 carboxypeptidase E activity >> GO:0004184 lysine carboxypeptidase activity >> GO:0004186 carboxypeptidase C activity >> GO:0004187 carboxypeptidase D activity >> GO:0004188 serine-type Pro-X carboxypeptidase activity >> GO:0004189 tubulinyl-Tyr carboxypeptidase activity >> GO:0004191 barrierpepsin activity >> GO:0004192 cathepsin D activity >> GO:0004193 cathepsin E activity >> GO:0004194 pepsin A activity >> GO:0004195 renin activity >> GO:0004196 saccharopepsin activity >> GO:0004213 cathepsin B activity >> GO:0004214 dipeptidyl-peptidase I activity >> GO:0004215 cathepsin H activity >> GO:0004216 cathepsin K activity >> GO:0004217 cathepsin L activity >> GO:0004218 cathepsin S activity >> GO:0004219 pyroglutamyl-peptidase I activity >> GO:0004226 Gly-X carboxypeptidase activity >> GO:0004228 gelatinase A activity >> GO:0004229 gelatinase B activity >> GO:0004230 glutamyl aminopeptidase activity >> GO:0004231 insulysin activity >> GO:0004232 interstitial collagenase activity >> GO:0004234 macrophage elastase activity >> GO:0004235 matrilysin activity >> GO:0004237 membrane dipeptidase activity >> GO:0004238 meprin A activity >> GO:0004239 methionyl aminopeptidase activity >> GO:0004240 mitochondrial processing peptidase activity >> GO:0004243 mitochondrial intermediate peptidase activity >> GO:0004244 mitochondrial inner membrane peptidase activity >> GO:0004245 neprilysin activity >> GO:0004246 peptidyl-dipeptidase A activity >> GO:0004247 saccharolysin activity >> GO:0004248 stromelysin 1 activity >> GO:0004249 stromelysin 3 activity >> GO:0004250 aminopeptidase I activity >> GO:0004251 X-Pro dipeptidase activity >> GO:0004253 gamma-renin activity >> GO:0004254 acylaminoacyl-peptidase activity >> GO:0004261 cathepsin G activity >> GO:0004262 cerevisin activity >> GO:0004263 chymotrypsin activity >> GO:0004274 dipeptidyl-peptidase IV activity >> GO:0004275 enteropeptidase activity >> GO:0004276 furin activity >> GO:0004277 granzyme A activity >> GO:0004278 granzyme B activity >> GO:0004281 pancreatic elastase II activity >> GO:0004283 plasmin activity >> GO:0004284 acrosin activity >> GO:0004285 proprotein convertase 1 activity >> GO:0004286 proprotein convertase 2 activity >> GO:0004287 prolyl oligopeptidase activity >> GO:0004289 subtilase activity >> GO:0004290 kexin activity >> GO:0004291 subtilisin activity >> GO:0004293 tissue kallikrein activity >> GO:0004294 tripeptidyl-peptidase II activity >> GO:0004295 trypsin activity >> GO:0008125 pancreatic elastase I activity >> GO:0008129 actinidain activity >> GO:0008130 neutrophil collagenase activity >> GO:0008132 pancreatic elastase activity >> GO:0008133 collagenase activity >> GO:0008243 plasminogen activator activity >> GO:0008319 prenyl protein specific endopeptidase activity >> GO:0008322 Pro-X carboxypeptidase activity >> GO:0008423 bleomycin hydrolase activity >> GO:0008439 monophenol monooxygenase activator activity >> GO:0008450 O-sialoglycoprotein endopeptidase activity >> GO:0008451 X-Pro aminopeptidase activity >> GO:0008462 endopeptidase Clp activity >> GO:0008464 gamma-glutamyl hydrolase activity >> GO:0008472 metallocarboxypeptidase D activity >> GO:0008487 prenyl-dependent CAAX protease activity >> GO:0008533 astacin activity >> GO:0008581 ubiquitin-specific protease 5 activity >> GO:0008717 D-alanyl-D-alanine endopeptidase activity >> GO:0008769 X-His dipeptidase activity >> GO:0008846 endopeptidase La activity >> GO:0008931 murein DD-endopeptidase activity >> GO:0008944 oligopeptidase A activity >> GO:0008945 oligopeptidase B activity >> GO:0008947 omptin activity >> GO:0008956 peptidyl-dipeptidase Dcp activity >> GO:0008975 pitrilysin activity >> GO:0008978 prepilin peptidase activity >> GO:0008981 protease IV activity >> GO:0008991 serine-type signal peptidase activity >> GO:0008992 repressor LexA activity >> GO:0009003 signal peptidase activity >> GO:0009004 signal peptidase I activity >> GO:0009005 signal peptidase II activity >> GO:0009049 aspartic-type signal peptidase activity >> GO:0009377 HslUV protease activity >> GO:0009980 glutamate carboxypeptidase activity >> GO:0009983 tyrosine aminopeptidase activity >> GO:0010320 arginine/lysine endopeptidase activity >> GO:0016284 alanine aminopeptidase activity >> GO:0016285 cytosol alanyl aminopeptidase activity >> GO:0016511 endothelin-converting enzyme activity >> GO:0016512 endothelin-converting enzyme 1 activity >> GO:0016804 prolyl aminopeptidase activity >> GO:0016808 proprotein convertase activity >> GO:0016919 nardilysin activity >> GO:0016921 pyroglutamyl-peptidase II activity >> GO:0016946 cathepsin F activity >> GO:0017026 procollagen C-endopeptidase activity >> GO:0017039 dipeptidyl-peptidase III activity >> GO:0017074 procollagen N-endopeptidase activity >> GO:0017088 X-Pro dipeptidyl-peptidase activity >> GO:0017092 sterol regulatory element-binding protein site 2 protease >> activity >> GO:0017093 sterol regulatory element-binding protein protease >> activity >> GO:0017094 sterol regulatory element-binding protein site 1 protease >> activity >> GO:0017165 dipeptidase E activity >> GO:0019131 tripeptidyl-peptidase I activity >> GO:0019132 C-terminal processing peptidase activity >> GO:0019783 small conjugating protein-specific protease activity >> GO:0019784 NEDD8-specific protease activity >> GO:0019785 ISG15-specific protease activity >> GO:0019786 APG8-specific protease activity >> GO:0030019 tryptase activity >> GO:0030271 chymase activity >> GO:0030303 stromelysin 2 activity >> GO:0030402 matrilysin-2 activity >> GO:0030403 collagenase 4 activity >> GO:0030404 collagenase 3 activity >> GO:0030405 matrix metalloproteinase 19 activity >> GO:0030406 matrix metalloproteinase 25 activity >> GO:0030601 aminopeptidase B activity >> GO:0030602 chymosin activity >> GO:0030693 caspase activity >> GO:0031079 picornain 3C activity >> GO:0031368 Pro-X metallocarboxypeptidase activity >> GO:0033264 bontoxilysin activity >> GO:0042029 fibrolase activity >> GO:0042315 cytosol nonspecific dipeptidase activity >> GO:0042499 signal peptide peptidase activity >> GO:0042576 aspartyl aminopeptidase activity >> GO:0042708 elastase activity >> GO:0043275 glutamate carboxypeptidase II activity >> GO:0043859 cyanophycinase activity >> GO:0045024 peptidyl-glutamyl peptide hydrolyzing enzyme activity >> GO:0046560 scytalidopepsin B activity >> GO:0046561 penicillopepsin activity >> GO:0050424 alanine carboxypeptidase activity >> GO:0050425 carboxypeptidase B activity >> GO:0050426 peptidyl-glycinamidase activity >> GO:0051397 N-terminal basic amino acid aminopeptidase activity >> GO:0051398 N-terminal lysine aminopeptidase activity >> GO:0051399 N-terminal arginine aminopeptidase activity >> GO:0051404 clostripain activity >> GO:0051405 microbial collagenase activity >> >> Because there are so many terms affected (174), I have not included all of >> the usual details -- specific reasons, annotation counts, and substitute >> terms -- in this email. For a complete list of terms slated to become >> obsolete, in OBO format, with the specific reasons for obsoletion filled >> in, see (this file is also linked to the wiki page): >> >> http://www.geneontology.org/scratch/peptidase_terms_with_obs_tags.obo >> >> Details of existing annotations to these terms are also on the wiki: >> >> http://wiki.geneontology.org/index.php/Peptidase_annotations >> >> Every peptidase term that we make obsolete will have at least one >> 'replaced_by' tag pointing to a peptidase activity term; these are also >> shown in the .obo file cited above. >> >> A longer term goal is to add new terms to the protein ontology (PRO) >> representing the gene products that have peptidase activity. When the PRO >> terms become available, many of the obsolete GO peptidase activity terms >> will point to PRO terms via 'consider' tags. >> >> Please let us know if you have any questions about this plan, or about the >> files noted above. The comment period ends Friday, August 15, 2008. >> >> *** Unless objections are received by August 15, >> we will assume that you agree to this change. *** >> >> Regards, >> Midori >> >> (on behalf of the peptidase activity working group) >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> >> > > From val at sanger.ac.uk Fri Jul 25 05:19:21 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 25 Jul 2008 12:19:21 UT Subject: [Go] Alert: proposal to obsolete many peptidase activity terms from the molecular function ontology Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Fri Jul 25 09:00:12 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 25 Jul 2008 16:00:12 UT Subject: [Go] SourceForge Update Message-ID: <200807251600.m6PG0CA1180344@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Sat Jul 26 09:00:15 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 26 Jul 2008 16:00:15 UT Subject: [Go] SourceForge Update Message-ID: <200807261600.m6QG0F71439373@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Sun Jul 27 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sun, 27 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807271600.m6RG0DQ1174614@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Mon Jul 28 09:00:12 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 28 Jul 2008 16:00:12 UT Subject: [Go] SourceForge Update Message-ID: <200807281600.m6SG0CZ1435846@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Tue Jul 29 04:04:34 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 29 Jul 2008 12:04:34 +0100 (BST) Subject: [Go] GO:0005634 name change Message-ID: Dear GO, To avoid confusion and maintain univocity between GO and ChEBI, we plan to rename 'nucleus' (GO:0005634) to 'cell nucleus'. We will also change a few other term names that now end in 'from nucleus' to use 'from cell nucleus'; most terms using 'nucleus' will be unaffected because they're already unambiguous. There's a SourceForge item open: https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2024731&group_id=36855 We'll change names at the end of this week (August 1). Midori From midori at ebi.ac.uk Tue Jul 29 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 29 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807291600.m6TG0Dg1184830@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Jul 30 08:53:10 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 30 Jul 2008 16:53:10 +0100 (BST) Subject: [Go] synonym instead - Re: GO:0005634 name change In-Reply-To: References: Message-ID: Hi, Following a discussion among the GO managers today, we have modified the plan for GO:0005634. We will add 'cell nucleus' as an exact synonym instead of renaming the term. Midori On Tue, 29 Jul 2008, Midori Harris wrote: > Dear GO, > > To avoid confusion and maintain univocity between GO and ChEBI, we plan to > rename 'nucleus' (GO:0005634) to 'cell nucleus'. We will also change a few > other term names that now end in 'from nucleus' to use 'from cell nucleus'; > most terms using 'nucleus' will be unaffected because they're already > unambiguous. > > There's a SourceForge item open: > https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2024731&group_id=36855 > > We'll change names at the end of this week (August 1). > > Midori > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From midori at ebi.ac.uk Wed Jul 30 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 30 Jul 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200807301600.m6UG0D71447541@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From jane at ebi.ac.uk Thu Jul 31 04:51:51 2008 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 31 Jul 2008 12:51:51 +0100 Subject: [Go] August newsletter Message-ID: <4891A757.2040907@ebi.ac.uk> Hi all - we're about to start putting together the August newsletter so please sent in ideas for items you'd like to see included. So far we have a 'gene of the quarter' item for Excision-repair proteins... thanks, Jane -- Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From jdeegan at ebi.ac.uk Thu Jul 31 06:45:43 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Thu, 31 Jul 2008 14:45:43 +0100 Subject: [Go] open source website Message-ID: <4891C207.1000305@ebi.ac.uk> Hi, A new open source website has provided a webpage to publicise GO. They asked if we would like to contribute any information. I have added a few screenshots, but if anybody else would like to add something then please do go ahead. http://ostatic.com/23015-software-opensource/gene-ontology Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From midori at ebi.ac.uk Thu Jul 31 09:00:12 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 31 Jul 2008 16:00:12 UT Subject: [Go] SourceForge Update Message-ID: <200807311600.m6VG0CH1186344@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: