From val at sanger.ac.uk Mon Apr 2 06:21:02 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Mon, 02 Apr 2007 14:21:02 +0100 Subject: Ku70-binding protein/assembly of the F0 sector of the F1F0 ATP synthase complex?/annot query Message-ID: <4611033E.3030207@sanger.ac.uk> Some proteins in Uniprot and the MODs appear to be annotated as Ku70-binding protein, (possibly from the KOGs annotation?). However, this appears to be involved in assembly of the F0 sector of the F1F0 ATP synthase complex (see details in Pfam submission below) You can see some of the affected gene products here: http://www.sanger.ac.uk/cgi-bin/PostGenomics/S_pombe/YOGY/yogy-search.pl?gene=SPCC320.12&species=S._pombe&wild=No&go_term=No&go_final=No or here: http://www.sanger.ac.uk/cgi-bin/Pfam/getallproteins.pl?name=Pfam-B_10086&acc=PB010086&type=full&verbose=true&zoom_factor=0.5&list=View+Graphic If anybody has any experimantal basis for Ku binding, can they let me know and I'll update the Pfam submission. Thanks ------------------------------ ATP23 >From SGD annotation: Putative metalloprotease of the mitochondrial inner membrane, required for processing of Atp6p; has an additional role in assembly of the F0 sector of the F1F0 ATP synthase complex. The peptidase activity is also supported Interpro hit to IPR006025 This protein is sometimes annotated as a Ku-binding protein DNA-dependent protein kinase or double-strand break repair via nonhomologous end joining in metazoans (in human, drosophila mouse), but usually these appear to be inferred from sequence similarity or traceable author statements. I haven't been able to trace any experimental evidence for any of these annotations. The peptidase activity is also supported Interpro hit to IPR006025 I suppose the other reported annotations could be correct but as this is conserved one copy per organism this would be unusual. PMID: 17135290 Val -- -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From cyamasak at jbirc.aist.go.jp Fri Apr 6 05:44:52 2007 From: cyamasak at jbirc.aist.go.jp (Chisato Yamasaki) Date: Fri, 6 Apr 2007 21:44:52 +0900 Subject: Question: how to find a list of deleted GO ? References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> Message-ID: <0d4201c77849$5f380100$2bd95296@1704019> I have one basic question about GO database. I am looking for the list of deleted GO IDs to check our annotation. Could anyone tell me where to find the information ? Thank you very much for your help in advance. Regards, Chisato Yamasaki H-InvDB: http://www.h-invitational.jp/ Japan Biological Information Research Center, JBIRC Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. Tel: +81-3-3599-8800, Fax: +81-3-3599-8801, E-mail: cyamasak at jbirc.aist.go.jp --- From rama at genome.Stanford.EDU Fri Apr 6 11:55:41 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Fri, 6 Apr 2007 11:55:41 -0700 Subject: Question: how to find a list of deleted GO ? In-Reply-To: <0d4201c77849$5f380100$2bd95296@1704019> References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> <0d4201c77849$5f380100$2bd95296@1704019> Message-ID: <7585D6CF-D702-43F2-9099-45B0CBCEFFF5@genome.stanford.edu> GOIDs are never deleted, they are obsoleted. All the Obsolete IDs should be in the gene_ontology_edit.obo file. Regarding how to retrieve these IDs from the GO database, I am not familiar with the database schema. I have copied the GO database group on this email. You will hear from them. You can download the gene_ontology_edit file from the CVS and search for the IDs you are interested in. http://www.geneontology.org/GO.downloads.ontology.shtml You will see a table on this web page, and you can click on the OBO v1.2 file to download. Obsolete terms can be identified by looking at the 'def' line and 'is_obsolete:true' tag (see example below). [Term] id: GO:0000008 name: thioredoxin namespace: molecular_function alt_id: GO:0000013 def: "OBSOLETE. A small disulfide-containing redox protein that serves as a general protein disulfide oxidoreductase. Interacts with a broad range of proteins by a redox mechanism, based on the reversible oxidation of 2 cysteine thiol groups to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulfide and a dithiol." [GOC:kd] comment: This term was made obsolete because it represents gene products. To update annotations, consider the molecular function term 'thiol-disulfide exchange intermediate activity ; GO:0030508'. is_obsolete: true Hope this helps. Please let us know if you have any questions. Best, Rama On Apr 6, 2007, at 5:44 AM, Chisato Yamasaki wrote: > I have one basic question about GO database. > > I am looking for the list of deleted GO IDs to check our annotation. > Could anyone tell me where to find the information ? > > Thank you very much for your help in advance. > > Regards, > Chisato Yamasaki > > H-InvDB: http://www.h-invitational.jp/ > Japan Biological Information Research Center, JBIRC > > Waterfront Bio-IT Research Building, 2-42 Aomi, > Koto-ku, Tokyo 135-0064, Japan. > Tel: +81-3-3599-8800, Fax: +81-3-3599-8801, > E-mail: cyamasak at jbirc.aist.go.jp > --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070406/339fc186/attachment.html From hitz at genome.Stanford.EDU Fri Apr 6 11:58:37 2007 From: hitz at genome.Stanford.EDU (Benjamin Hitz) Date: Fri, 6 Apr 2007 11:58:37 -0700 Subject: Question: how to find a list of deleted GO ? In-Reply-To: <7585D6CF-D702-43F2-9099-45B0CBCEFFF5@genome.stanford.edu> References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> <0d4201c77849$5f380100$2bd95296@1704019> <7585D6CF-D702-43F2-9099-45B0CBCEFFF5@genome.stanford.edu> Message-ID: in sql: select * from term where is_obsolete = 1; Ben > > GOIDs are never deleted, they are obsoleted. All the Obsolete IDs > should be in the gene_ontology_edit.obo file. > > Regarding how to retrieve these IDs from the GO database, I am not > familiar with the database schema. I have copied the GO database > group on this email. You will hear from them. > > You can download the gene_ontology_edit file from the CVS and > search for the IDs you are interested in. > http://www.geneontology.org/GO.downloads.ontology.shtml > You will see a table on this web page, and you can click on the OBO > v1.2 file to download. > > Obsolete terms can be identified by looking at the 'def' line and > 'is_obsolete:true' tag (see example below). > > [Term] > id: GO:0000008 > name: thioredoxin > namespace: molecular_function > alt_id: GO:0000013 > def: "OBSOLETE. A small disulfide-containing redox protein that > serves as a general protein disulfide oxidoreductase. Interacts > with a broad range of proteins by a redox mechanism, based on the > reversible oxidation of 2 cysteine thiol groups to a disulfide, > accompanied by the transfer of 2 electrons and 2 protons. The net > result is the covalent interconversion of a disulfide and a > dithiol." [GOC:kd] > comment: This term was made obsolete because it represents gene > products. To update annotations, consider the molecular function > term 'thiol-disulfide exchange intermediate activity ; GO:0030508'. > is_obsolete: true > > Hope this helps. Please let us know if you have any questions. > > Best, > > Rama > > > On Apr 6, 2007, at 5:44 AM, Chisato Yamasaki wrote: > >> I have one basic question about GO database. >> >> I am looking for the list of deleted GO IDs to check our annotation. >> Could anyone tell me where to find the information ? >> >> Thank you very much for your help in advance. >> >> Regards, >> Chisato Yamasaki >> >> H-InvDB: http://www.h-invitational.jp/ >> Japan Biological Information Research Center, JBIRC >> >> Waterfront Bio-IT Research Building, 2-42 Aomi, >> Koto-ku, Tokyo 135-0064, Japan. >> Tel: +81-3-3599-8800, Fax: +81-3-3599-8801, >> E-mail: cyamasak at jbirc.aist.go.jp >> --- > -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070406/18c42110/attachment.html From cjm at fruitfly.org Fri Apr 6 12:01:06 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Fri, 6 Apr 2007 12:01:06 -0700 Subject: Question: how to find a list of deleted GO ? In-Reply-To: <7585D6CF-D702-43F2-9099-45B0CBCEFFF5@genome.stanford.edu> References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> <0d4201c77849$5f380100$2bd95296@1704019> <7585D6CF-D702-43F2-9099-45B0CBCEFFF5@genome.stanford.edu> Message-ID: Common queries on the GO Database can be found here: http://wiki.geneontology.org/index.php/Example_Queries Querying by obsolete IDs: http://wiki.geneontology.org/index.php/Example_Queries#Obsolete_terms If your question isn't answered here let us know On Apr 6, 2007, at 11:55 AM, Rama Balakrishnan wrote: > > GOIDs are never deleted, they are obsoleted. All the Obsolete IDs > should be in the gene_ontology_edit.obo file. > > Regarding how to retrieve these IDs from the GO database, I am not > familiar with the database schema. I have copied the GO database > group on this email. You will hear from them. > > You can download the gene_ontology_edit file from the CVS and > search for the IDs you are interested in. > http://www.geneontology.org/GO.downloads.ontology.shtml > You will see a table on this web page, and you can click on the OBO > v1.2 file to download. > > Obsolete terms can be identified by looking at the 'def' line and > 'is_obsolete:true' tag (see example below). > > [Term] > id: GO:0000008 > name: thioredoxin > namespace: molecular_function > alt_id: GO:0000013 > def: "OBSOLETE. A small disulfide-containing redox protein that > serves as a general protein disulfide oxidoreductase. Interacts > with a broad range of proteins by a redox mechanism, based on the > reversible oxidation of 2 cysteine thiol groups to a disulfide, > accompanied by the transfer of 2 electrons and 2 protons. The net > result is the covalent interconversion of a disulfide and a > dithiol." [GOC:kd] > comment: This term was made obsolete because it represents gene > products. To update annotations, consider the molecular function > term 'thiol-disulfide exchange intermediate activity ; GO:0030508'. > is_obsolete: true > > Hope this helps. Please let us know if you have any questions. > > Best, > > Rama > > > On Apr 6, 2007, at 5:44 AM, Chisato Yamasaki wrote: > >> I have one basic question about GO database. >> >> I am looking for the list of deleted GO IDs to check our annotation. >> Could anyone tell me where to find the information ? >> >> Thank you very much for your help in advance. >> >> Regards, >> Chisato Yamasaki >> >> H-InvDB: http://www.h-invitational.jp/ >> Japan Biological Information Research Center, JBIRC >> >> Waterfront Bio-IT Research Building, 2-42 Aomi, >> Koto-ku, Tokyo 135-0064, Japan. >> Tel: +81-3-3599-8800, Fax: +81-3-3599-8801, >> E-mail: cyamasak at jbirc.aist.go.jp >> --- > From suzi at berkeleybop.org Sun Apr 8 15:27:54 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 8 Apr 2007 15:27:54 -0700 Subject: Question: how to find a list of deleted GO ? In-Reply-To: References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> <0d4201c77849$5f380100$2bd95296@1704019> <7585D6CF-D702-43F2-9099-45B0CBCEFFF5@genome.stanford.edu> Message-ID: <63937AAE-C9BB-413F-B4B1-FC53489EA26B@berkeleybop.org> ah, so nice to have documentation to point at (and build upon) On Apr 6, 2007, at 12:01 PM, Chris Mungall wrote: > > Common queries on the GO Database can be found here: > http://wiki.geneontology.org/index.php/Example_Queries > > Querying by obsolete IDs: > http://wiki.geneontology.org/index.php/Example_Queries#Obsolete_terms > > If your question isn't answered here let us know > > On Apr 6, 2007, at 11:55 AM, Rama Balakrishnan wrote: > >> >> GOIDs are never deleted, they are obsoleted. All the Obsolete IDs >> should be in the gene_ontology_edit.obo file. >> >> Regarding how to retrieve these IDs from the GO database, I am not >> familiar with the database schema. I have copied the GO database >> group on this email. You will hear from them. >> >> You can download the gene_ontology_edit file from the CVS and >> search for the IDs you are interested in. >> http://www.geneontology.org/GO.downloads.ontology.shtml >> You will see a table on this web page, and you can click on the >> OBO v1.2 file to download. >> >> Obsolete terms can be identified by looking at the 'def' line and >> 'is_obsolete:true' tag (see example below). >> >> [Term] >> id: GO:0000008 >> name: thioredoxin >> namespace: molecular_function >> alt_id: GO:0000013 >> def: "OBSOLETE. A small disulfide-containing redox protein that >> serves as a general protein disulfide oxidoreductase. Interacts >> with a broad range of proteins by a redox mechanism, based on the >> reversible oxidation of 2 cysteine thiol groups to a disulfide, >> accompanied by the transfer of 2 electrons and 2 protons. The net >> result is the covalent interconversion of a disulfide and a >> dithiol." [GOC:kd] >> comment: This term was made obsolete because it represents gene >> products. To update annotations, consider the molecular function >> term 'thiol-disulfide exchange intermediate activity ; GO:0030508'. >> is_obsolete: true >> >> Hope this helps. Please let us know if you have any questions. >> >> Best, >> >> Rama >> >> >> On Apr 6, 2007, at 5:44 AM, Chisato Yamasaki wrote: >> >>> I have one basic question about GO database. >>> >>> I am looking for the list of deleted GO IDs to check our annotation. >>> Could anyone tell me where to find the information ? >>> >>> Thank you very much for your help in advance. >>> >>> Regards, >>> Chisato Yamasaki >>> >>> H-InvDB: http://www.h-invitational.jp/ >>> Japan Biological Information Research Center, JBIRC >>> >>> Waterfront Bio-IT Research Building, 2-42 Aomi, >>> Koto-ku, Tokyo 135-0064, Japan. >>> Tel: +81-3-3599-8800, Fax: +81-3-3599-8801, >>> E-mail: cyamasak at jbirc.aist.go.jp >>> --- >> > > From cyamasak at jbirc.aist.go.jp Mon Apr 9 02:46:37 2007 From: cyamasak at jbirc.aist.go.jp (Chisato Yamasaki) Date: Mon, 9 Apr 2007 18:46:37 +0900 Subject: Question: how to find a list of deleted GO ? References: <1175174799.19114.39.camel@paul.gen.cam.ac.uk> <0d4201c77849$5f380100$2bd95296@1704019> <7585D6CF-D702-43F2-9099-45B0CBCEFFF5@genome.stanford.edu> <63937AAE-C9BB-413F-B4B1-FC53489EA26B@berkeleybop.org> Message-ID: <032601c77a8b$f8750590$2bd95296@1704019> Dear Rama, Chris, Erick and Suzanna, Thank you very much for your replies. Now I am sure that GOIDs are never deleted, they are obsoleted. In fact GO ID I was checking at AmiGO was below; GO:0005554 molecular function unknown I found the GO ID as only alt_id so htat I misunderstood that it was deleted. Accession: GO:0003674 Ontology: molecular_function Synonyms: narrow: molecular function unknown alt_id: GO:0005554 Thank you very much for all of your help again. Best regards, Chisato Yamasaki Japan Biological Information Research Center, JBIRC Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. Tel: +81-3-3599-8800, Fax: +81-3-3599-8801, E-mail: cyamasak at jbirc.aist.go.jp --- ----- Original Message ----- From: "Suzanna Lewis" To: "Chris Mungall" Cc: "Rama Balakrishnan" ; "GO Annotation list" ; "Benjamin Hitz" ; "Seth Carbon" ; "Stan Dong" Sent: Monday, April 09, 2007 7:27 AM Subject: Re: Question: how to find a list of deleted GO ? > ah, so nice to have documentation to point at (and build upon) > > On Apr 6, 2007, at 12:01 PM, Chris Mungall wrote: > >> >> Common queries on the GO Database can be found here: >> http://wiki.geneontology.org/index.php/Example_Queries >> >> Querying by obsolete IDs: >> http://wiki.geneontology.org/index.php/Example_Queries#Obsolete_terms >> >> If your question isn't answered here let us know >> >> On Apr 6, 2007, at 11:55 AM, Rama Balakrishnan wrote: >> >>> >>> GOIDs are never deleted, they are obsoleted. All the Obsolete IDs >>> should be in the gene_ontology_edit.obo file. >>> >>> Regarding how to retrieve these IDs from the GO database, I am not >>> familiar with the database schema. I have copied the GO database group >>> on this email. You will hear from them. >>> >>> You can download the gene_ontology_edit file from the CVS and search >>> for the IDs you are interested in. >>> http://www.geneontology.org/GO.downloads.ontology.shtml >>> You will see a table on this web page, and you can click on the OBO >>> v1.2 file to download. >>> >>> Obsolete terms can be identified by looking at the 'def' line and >>> 'is_obsolete:true' tag (see example below). >>> >>> [Term] >>> id: GO:0000008 >>> name: thioredoxin >>> namespace: molecular_function >>> alt_id: GO:0000013 >>> def: "OBSOLETE. A small disulfide-containing redox protein that serves >>> as a general protein disulfide oxidoreductase. Interacts with a broad >>> range of proteins by a redox mechanism, based on the reversible >>> oxidation of 2 cysteine thiol groups to a disulfide, accompanied by the >>> transfer of 2 electrons and 2 protons. The net result is the covalent >>> interconversion of a disulfide and a dithiol." [GOC:kd] >>> comment: This term was made obsolete because it represents gene >>> products. To update annotations, consider the molecular function term >>> 'thiol-disulfide exchange intermediate activity ; GO:0030508'. >>> is_obsolete: true >>> >>> Hope this helps. Please let us know if you have any questions. >>> >>> Best, >>> >>> Rama >>> >>> >>> On Apr 6, 2007, at 5:44 AM, Chisato Yamasaki wrote: >>> >>>> I have one basic question about GO database. >>>> >>>> I am looking for the list of deleted GO IDs to check our annotation. >>>> Could anyone tell me where to find the information ? >>>> >>>> Thank you very much for your help in advance. >>>> >>>> Regards, >>>> Chisato Yamasaki >>>> >>>> H-InvDB: http://www.h-invitational.jp/ >>>> Japan Biological Information Research Center, JBIRC >>>> >>>> Waterfront Bio-IT Research Building, 2-42 Aomi, >>>> Koto-ku, Tokyo 135-0064, Japan. >>>> Tel: +81-3-3599-8800, Fax: +81-3-3599-8801, >>>> E-mail: cyamasak at jbirc.aist.go.jp >>>> --- >>> >> >> > > > From midori at ebi.ac.uk Mon Apr 9 22:00:04 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 10 Apr 2007 05:00:04 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200704100500.l3A504j1554790@mozart.ebi.ac.uk> An HTML attachment was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070415/e86a0272/attachment.pl From val at sanger.ac.uk Mon Apr 23 10:49:34 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Mon, 23 Apr 2007 18:49:34 +0100 Subject: question about phase terms Message-ID: <462CF1AE.2000309@sanger.ac.uk> I was wondering how people used the "phase" terms like "S phase of mitotic cell cycle" (specifically whether they are only used for 'regulation' of progression?, it seems they could be but this isn't explicit in the defs or the graph) There is a SF item if anybody has any ideas, comments Cheers Val https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1701499&group_id=36855 -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From midori at ebi.ac.uk Tue Apr 24 22:00:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 25 Apr 2007 05:00:06 UT Subject: SourceForge Annotation Tracker Update Message-ID: <200704250500.l3P506e1465402@mozart.ebi.ac.uk> An HTML attachment was scrubbed... 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