From rama at genome.Stanford.EDU Mon Jan 7 14:17:02 2008 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Mon, 7 Jan 2008 14:17:02 -0800 Subject: [annotation] question about use of 'colocalizes with' In-Reply-To: References: Message-ID: <29D24CCD-61AE-437A-B2E5-3488CA7F35F6@genome.stanford.edu> reposting... rama On Dec 19, 2007, at 12:50 PM, Rama Balakrishnan wrote: > > Hi All, > > We have a question about the use of 'colocalizes with' qualifier. > > We are curating- > > PMID: 16713564 > > Downregulation of PP2A(Cdc55) phosphatase by separase initiates > mitotic exit in budding yeast. Queralt E, Lehane C, Novak B, Uhlmann > F. Cell. 2006 May 19;125(4):719-32. > > In the section titled " Separase-Dependent Downregulation of PP2ACdc55 > at Anaphase Onset" the authors say that 'Colocalization with Net1 > revealed nucleolar enrichment of Cdc55 in metaphase'.... > The figure legend for > Fig 5A says 'Cdc55 localization in the nucleolus'. > > Should Cdc55 be annotated to 'nucleolus' directly or to 'colocalizes > with nucleolus'? The documentation on how to use this qualifier should > be updated with more examples. > > http://www.geneontology.org/ > GO.annotation.conventions.shtml#colocalizes_with > > Thanks for your help, > > Rama From val at sanger.ac.uk Tue Jan 8 02:36:38 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Tue, 08 Jan 2008 10:36:38 +0000 Subject: [annotation] question about use of 'colocalizes with' In-Reply-To: <29D24CCD-61AE-437A-B2E5-3488CA7F35F6@genome.stanford.edu> References: <29D24CCD-61AE-437A-B2E5-3488CA7F35F6@genome.stanford.edu> Message-ID: <47835236.3070309@sanger.ac.uk> Hi Rama, I don't think a qualifier is required in this case. However, one of the current examples is a pombe example (clp1), and even in the example I don't know if it is really necessary. Do we need to use co-localizes to capture transient localization? I know I haven't done this consistently. I have used it in cases like karyopherins (like sal3) where authors report a nuclear pore localization to indicate that this is not a 'component of' the nuclear pore. I think this is an example of the "This qualifier may also be used in cases where the resolution of an assay is not accurate enough to say that the gene product is a bona fide component member" type ? I don't think that it was devised to capture the results of a 'colocalization' experiment, when the component term which is indicated by the experiment is unambiguous. My 2C, (By the way, without the link the documentation for this is quite hard to find, I couldn't see it via the 'documentation' or 'Annotation Guide' links I'm not sure why 'Annotation Conventions' is separate from 'GO Annotation guide') Val Rama Balakrishnan wrote: > reposting... > > rama > > On Dec 19, 2007, at 12:50 PM, Rama Balakrishnan wrote: > >> >> Hi All, >> >> We have a question about the use of 'colocalizes with' qualifier. >> >> We are curating- >> >> PMID: 16713564 >> >> Downregulation of PP2A(Cdc55) phosphatase by separase initiates >> mitotic exit in budding yeast. Queralt E, Lehane C, Novak B, Uhlmann >> F. Cell. 2006 May 19;125(4):719-32. >> >> In the section titled " Separase-Dependent Downregulation of PP2ACdc55 >> at Anaphase Onset" the authors say that 'Colocalization with Net1 >> revealed nucleolar enrichment of Cdc55 in metaphase'.... > > >> The figure legend for >> Fig 5A says 'Cdc55 localization in the nucleolus'. >> >> Should Cdc55 be annotated to 'nucleolus' directly or to 'colocalizes >> with nucleolus'? The documentation on how to use this qualifier should >> be updated with more examples. >> >> http://www.geneontology.org/ >> GO.annotation.conventions.shtml#colocalizes_with >> >> Thanks for your help, >> >> Rama > > > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From edimmer at ebi.ac.uk Tue Jan 8 03:49:25 2008 From: edimmer at ebi.ac.uk (E Dimmer) Date: Tue, 08 Jan 2008 11:49:25 +0000 Subject: [annotation] question about use of 'colocalizes with' In-Reply-To: <47835236.3070309@sanger.ac.uk> References: <29D24CCD-61AE-437A-B2E5-3488CA7F35F6@genome.stanford.edu> <47835236.3070309@sanger.ac.uk> Message-ID: <47836345.5000509@ebi.ac.uk> Hi, Like Val, I wouldn't use the colocalizes_with qualifier as a matter of course for results obtained from colocalization experiments, as results often provides a clear indication of the proteins location. However we do use colocalizes_with when a protein has been shown to be transiently associated with subcellular component (e.g. shuttling between nucleus and cytoplasm) or peripherally with a complex. I think that the page must have been removed from the GO web site's menus at some point, I agree with Val that (once rewritten) the page should included in or at the very least linked to from the Annotation Guide page. Emily Valerie Wood wrote: > Hi Rama, > > I don't think a qualifier is required in this case. > However, one of the current examples is a pombe example (clp1), and > even in the example I don't know if it is really necessary. Do we need > to use co-localizes to capture transient localization? I know I > haven't done this consistently. > > I have used it in cases like karyopherins (like sal3) > where authors report a nuclear pore localization to indicate that > this is not a 'component of' the nuclear pore. I think this is an > example of the > > "This qualifier may also be used in cases where the resolution of an > assay is not accurate enough to say that the gene product is a bona > fide component member" > type ? > > I don't think that it was devised to capture the results of a > 'colocalization' experiment, when the component term which is > indicated by the experiment is unambiguous. > > My 2C, > > (By the way, without the link the documentation for this is quite hard > to find, I couldn't see it via the 'documentation' or 'Annotation > Guide' links I'm not sure why 'Annotation Conventions' is separate > from 'GO Annotation guide') > > > > > > Val > > > > Rama Balakrishnan wrote: > >> reposting... >> >> rama >> >> On Dec 19, 2007, at 12:50 PM, Rama Balakrishnan wrote: >> >>> >>> Hi All, >>> >>> We have a question about the use of 'colocalizes with' qualifier. >>> >>> We are curating- >>> >>> PMID: 16713564 >>> >>> Downregulation of PP2A(Cdc55) phosphatase by separase initiates >>> mitotic exit in budding yeast. Queralt E, Lehane C, Novak B, Uhlmann >>> F. Cell. 2006 May 19;125(4):719-32. >>> >>> In the section titled " Separase-Dependent Downregulation of PP2ACdc55 >>> at Anaphase Onset" the authors say that 'Colocalization with Net1 >>> revealed nucleolar enrichment of Cdc55 in metaphase'.... >> >> >>> The figure legend for >>> Fig 5A says 'Cdc55 localization in the nucleolus'. >>> >>> Should Cdc55 be annotated to 'nucleolus' directly or to 'colocalizes >>> with nucleolus'? The documentation on how to use this qualifier should >>> be updated with more examples. >>> >>> http://www.geneontology.org/ >>> GO.annotation.conventions.shtml#colocalizes_with >>> >>> Thanks for your help, >>> >>> Rama >> >> >> >> >> > > > -- Do you need any additional GO annotation resources? Which proteins would you like annotated with GO? Let us know in the GOA User Survey, available at: http://www.ebi.ac.uk/GOA/contactus.html ------------------------------------------------------------------ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk URL: http://www.ebi.ac.uk/goa From cherry at stanford.edu Tue Jan 8 08:29:35 2008 From: cherry at stanford.edu (Mike Cherry) Date: Tue, 8 Jan 2008 08:29:35 -0800 Subject: [annotation] email archives Message-ID: All the archives, web pages and search indices for the many GO email lists have been updated for 2008. If you notice any trouble with these please let me know. -Mike From midori at ebi.ac.uk Thu Jan 10 22:00:07 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 11 Jan 2008 06:00:07 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200801110600.m0B60751184535@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080111/eb15fc02/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080111/eb15fc02/attachment.pl From val at sanger.ac.uk Wed Jan 16 08:52:01 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 16 Jan 2008 16:52:01 +0000 Subject: [annotation] RNA trimethylguanosine cap binding query Message-ID: <478E3631.2030208@sanger.ac.uk> I recently used the term RNA trimethylguanosine cap binding to annotate pombe telomerase RNA and represent the fact that this is trimethylguanosine capped, but on re-reading the definition I'm not sure if this is correct? Can I use this for the modification itself? or is it for gene products which interact with a capped product? There do not appear to be any other annotations to this term despite the fact that many RNAs are capped which is another reason which made me suspect my usage may be wrong. Should the binding terms should only be used for non-covalent modifications (although this is only in some of the binding defs?), and does not represent the use of some terms. For instance GPI anchor binding is used for a number of proteins which are GPI anchored, in addition to proteins which bins the GPI moiety during GPI anchor biosynthesis. Cheers Val Def: Interacting selectively with the trimethylguanosine (m(3)(2,2,7)-GTP) moiety located at the 5' end of some RNA molecules. Such trimethylated cap structures, generally produced by posttranscriptional modification of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by RNA polymerase II, but have also be found on snRNAs transcribed by RNA polymerase III. They have also been found on a subset of the mRNA population in some species, e.g. C. elegans. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From hjd at informatics.jax.org Wed Jan 16 09:48:14 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Wed, 16 Jan 2008 12:48:14 -0500 Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478E3631.2030208@sanger.ac.uk> References: <478E3631.2030208@sanger.ac.uk> Message-ID: <478E435E.30002@informatics.jax.org> Valerie Wood wrote: > I recently used the term RNA trimethylguanosine cap binding to > annotate pombe telomerase RNA and represent the fact that this is > trimethylguanosine capped, but on re-reading the definition I'm not > sure if this is correct? > Can I use this for the modification itself? or is it for gene > products which interact with a capped product? It represents some gene product that binds to the triMeG cap present on an mRNA. Not the gene product that makes the cap. A binding term should never be used for a covalent bond. Binding implies a reversible reaction at STP, with a Ka and Kd. GPI anchor binding it meant to be used for something that binds the the GPI anchor and not covalently linked to it. > > There do not appear to be any other annotations to this term despite > the fact that many RNAs are capped which is another reason which made > me suspect my usage may be wrong. > > Should the binding terms should only be used for non-covalent > modifications (although this is only in some of the binding defs?), > and does not represent the use of some terms. For instance GPI anchor > binding is used for a number of proteins which are GPI anchored, in > addition to proteins which bins the GPI moiety during GPI anchor > biosynthesis. > > Cheers > > Val > > Def: > Interacting selectively with the trimethylguanosine (m(3)(2,2,7)-GTP) > moiety located at the 5' end of some RNA molecules. Such trimethylated > cap structures, generally produced by posttranscriptional modification > of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs > transcribed by RNA polymerase II, but have also be found on snRNAs > transcribed by RNA polymerase III. They have also been found on a > subset of the mRNA population in some species, e.g. C. elegans. > > From kchris at genome.Stanford.EDU Wed Jan 16 14:11:05 2008 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Wed, 16 Jan 2008 14:11:05 -0800 (PST) Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478E435E.30002@informatics.jax.org> References: <478E3631.2030208@sanger.ac.uk> <478E435E.30002@informatics.jax.org> Message-ID: Hi Val, Yea, I agree with Harold that the term 'RNA trimethylguanosine cap binding' should only be used for things that bind to the cap, once it's been created. What you're talking about, annotating the modification that occurs on the RNA, is completely different, and I think perhaps, completely outside the scope of GO. -Karen On Wed, 16 Jan 2008, Harold Drabkin wrote: > Valerie Wood wrote: >> I recently used the term RNA trimethylguanosine cap binding to annotate >> pombe telomerase RNA and represent the fact that this is trimethylguanosine >> capped, but on re-reading the definition I'm not sure if this is correct? >> Can I use this for the modification itself? or is it for gene products >> which interact with a capped product? > It represents some gene product that binds to the triMeG cap present on an > mRNA. Not the gene product that makes the cap. A binding term should never be > used for a covalent bond. Binding implies a reversible reaction at STP, with > a Ka and Kd. > > GPI anchor binding it meant to be used for something that binds the the GPI > anchor and not covalently linked to it. > >> >> There do not appear to be any other annotations to this term despite the >> fact that many RNAs are capped which is another reason which made me >> suspect my usage may be wrong. >> >> Should the binding terms should only be used for non-covalent >> modifications (although this is only in some of the binding defs?), and >> does not represent the use of some terms. For instance GPI anchor binding >> is used for a number of proteins which are GPI anchored, in addition to >> proteins which bins the GPI moiety during GPI anchor biosynthesis. >> >> Cheers >> >> Val >> >> Def: >> Interacting selectively with the trimethylguanosine (m(3)(2,2,7)-GTP) >> moiety located at the 5' end of some RNA molecules. Such trimethylated cap >> structures, generally produced by posttranscriptional modification of a >> 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by >> RNA polymerase II, but have also be found on snRNAs transcribed by RNA >> polymerase III. They have also been found on a subset of the mRNA >> population in some species, e.g. C. elegans. >> >> > From val at sanger.ac.uk Wed Jan 16 14:27:32 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 16 Jan 2008 22:27:32 UT Subject: [annotation] RNA trimethylguanosine cap binding query Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080116/badeb99f/attachment.pl From hjd at informatics.jax.org Wed Jan 16 15:12:01 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Wed, 16 Jan 2008 18:12:01 -0500 Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: References: Message-ID: <478E8F41.60106@informatics.jax.org> I actually noticed that the core term, binding, with def of : The selective, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. is missing the non-covalent idea; fixing it in this term should suffice for it's children The Oxford bible: binding: the act or process by which one molecule attaches to another by noncovalent forces. Valerie Wood wrote: > yes thanks it seems obvious now, although I think I have some rogue annotations to fix for GPI binding to fix.! This might be obvious to everyone, but it might be worth adding 'non covalent' to all of the binding term defs just to emphasise. Its quite clear when you read the 'RNA trimethylguanosine cap > binding def, but I'm not sure that it is for some of the others. > > thanks > > val > > > Karen Christie wrote: > >> Hi Val, >> >> Yea, I agree with Harold that the term 'RNA trimethylguanosine cap >> binding' should only be used for things that bind to the cap, once it's >> been created. >> >> What you're talking about, annotating the modification that occurs on the >> RNA, is completely different, and I think perhaps, completely outside the >> scope of GO. >> >> -Karen >> >> >> On Wed, 16 Jan 2008, Harold Drabkin wrote: >> >> >>> Valerie Wood wrote: >>> >>>> I recently used the term RNA trimethylguanosine cap binding to annotate >>>> pombe telomerase RNA and represent the fact that this is trimethylguanosine >>>> capped, but on re-reading the definition I'm not sure if this is correct? >>>> Can I use this for the modification itself? or is it for gene products >>>> which interact with a capped product? >>>> >>> It represents some gene product that binds to the triMeG cap present on an >>> mRNA. Not the gene product that makes the cap. A binding term should never be >>> used for a covalent bond. Binding implies a reversible reaction at STP, with >>> a Ka and Kd. >>> >>> GPI anchor binding it meant to be used for something that binds the the GPI >>> anchor and not covalently linked to it. >>> >>> >>>> There do not appear to be any other annotations to this term despite the >>>> fact that many RNAs are capped which is another reason which made me >>>> suspect my usage may be wrong. >>>> >>>> Should the binding terms should only be used for non-covalent >>>> modifications (although this is only in some of the binding defs?), and >>>> does not represent the use of some terms. For instance GPI anchor binding >>>> is used for a number of proteins which are GPI anchored, in addition to >>>> proteins which bins the GPI moiety during GPI anchor biosynthesis. >>>> >>>> Cheers >>>> >>>> Val >>>> >>>> Def: >>>> Interacting selectively with the trimethylguanosine (m(3)(2,2,7)-GTP) >>>> moiety located at the 5' end of some RNA molecules. Such trimethylated cap >>>> structures, generally produced by posttranscriptional modification of a >>>> 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by >>>> RNA polymerase II, but have also be found on snRNAs transcribed by RNA >>>> polymerase III. They have also been found on a subset of the mRNA >>>> population in some species, e.g. C. elegans. >>>> >>>> >>>> >> > > From kchris at genome.Stanford.EDU Wed Jan 16 15:22:49 2008 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Wed, 16 Jan 2008 15:22:49 -0800 (PST) Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478E8F41.60106@informatics.jax.org> References: <478E8F41.60106@informatics.jax.org> Message-ID: while you're right that terms inherit from their parents, it's still probably better to fix it everywhere, so that people who only look at a specific term and not all its parents get the non-covalent idea clearly. -Karen On Wed, 16 Jan 2008, Harold Drabkin wrote: > I actually noticed that the core term, binding, with def of : The > selective, often stoichiometric, interaction of a molecule with one or more > specific sites on another molecule. > is missing the non-covalent idea; fixing it in this term should suffice for > it's children > > > The Oxford bible: binding: the act or process by which one molecule attaches > to another by noncovalent forces. > > > Valerie Wood wrote: >> yes thanks it seems obvious now, although I think I have some rogue >> annotations to fix for GPI binding to fix.! This might be obvious to >> everyone, but it might be worth adding 'non covalent' to all of the binding >> term defs just to emphasise. Its quite clear when you read the 'RNA >> trimethylguanosine cap binding def, but I'm not sure that it is for some of >> the others. >> thanks >> >> val >> >> >> Karen Christie wrote: >>> Hi Val, >>> >>> Yea, I agree with Harold that the term 'RNA trimethylguanosine cap >>> binding' should only be used for things that bind to the cap, once it's >>> been created. >>> >>> What you're talking about, annotating the modification that occurs on the >>> RNA, is completely different, and I think perhaps, completely outside the >>> scope of GO. >>> >>> -Karen >>> >>> >>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>> >>> >>>> Valerie Wood wrote: >>>> >>>>> I recently used the term RNA trimethylguanosine cap binding to annotate >>>>> pombe telomerase RNA and represent the fact that this is >>>>> trimethylguanosine capped, but on re-reading the definition I'm not >>>>> sure if this is correct? >>>>> Can I use this for the modification itself? or is it for gene products >>>>> which interact with a capped product? >>>>> >>>> It represents some gene product that binds to the triMeG cap present on >>>> an mRNA. Not the gene product that makes the cap. A binding term should >>>> never be used for a covalent bond. Binding implies a reversible reaction >>>> at STP, with a Ka and Kd. >>>> >>>> GPI anchor binding it meant to be used for something that binds the the >>>> GPI anchor and not covalently linked to it. >>>> >>>> >>>>> There do not appear to be any other annotations to this term despite >>>>> the fact that many RNAs are capped which is another reason which made me >>>>> suspect my usage may be wrong. >>>>> >>>>> Should the binding terms should only be used for non-covalent >>>>> modifications (although this is only in some of the binding defs?), and >>>>> does not represent the use of some terms. For instance GPI anchor >>>>> binding is used for a number of proteins which are GPI anchored, in >>>>> addition to proteins which bins the GPI moiety during GPI anchor >>>>> biosynthesis. >>>>> >>>>> Cheers >>>>> >>>>> Val >>>>> >>>>> Def: >>>>> Interacting selectively with the trimethylguanosine (m(3)(2,2,7)-GTP) >>>>> moiety located at the 5' end of some RNA molecules. Such trimethylated >>>>> cap structures, generally produced by posttranscriptional modification >>>>> of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs >>>>> transcribed by RNA polymerase II, but have also be found on snRNAs >>>>> transcribed by RNA polymerase III. They have also been found on a subset >>>>> of the mRNA population in some species, e.g. C. elegans. >>>>> >>>>> >>>>> >>> >> >> From hjd at informatics.jax.org Wed Jan 16 15:52:33 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Wed, 16 Jan 2008 18:52:33 -0500 Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: References: <478E8F41.60106@informatics.jax.org> Message-ID: <478E98C1.4030608@informatics.jax.org> Hopefully a script can be designed to add this as a sentence to the end of each definition! hjd Karen Christie wrote: > while you're right that terms inherit from their parents, it's still > probably better to fix it everywhere, so that people who only look at > a specific term and not all its parents get the non-covalent idea > clearly. > > -Karen > > > On Wed, 16 Jan 2008, Harold Drabkin wrote: > >> I actually noticed that the core term, binding, with def of : The >> selective, often stoichiometric, interaction of a molecule with one >> or more specific sites on another molecule. >> is missing the non-covalent idea; fixing it in this term should >> suffice for it's children >> >> >> The Oxford bible: binding: the act or process by which one molecule >> attaches to another by noncovalent forces. >> >> >> Valerie Wood wrote: >>> yes thanks it seems obvious now, although I think I have some rogue >>> annotations to fix for GPI binding to fix.! This might be obvious to >>> everyone, but it might be worth adding 'non covalent' to all of the >>> binding term defs just to emphasise. Its quite clear when you read >>> the 'RNA trimethylguanosine cap binding def, but I'm not sure that >>> it is for some of the others. thanks >>> >>> val >>> >>> >>> Karen Christie wrote: >>>> Hi Val, >>>> >>>> Yea, I agree with Harold that the term 'RNA trimethylguanosine cap >>>> binding' should only be used for things that bind to the cap, once >>>> it's been created. >>>> >>>> What you're talking about, annotating the modification that occurs >>>> on the RNA, is completely different, and I think perhaps, >>>> completely outside the scope of GO. >>>> >>>> -Karen >>>> >>>> >>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>> >>>> >>>>> Valerie Wood wrote: >>>>> >>>>>> I recently used the term RNA trimethylguanosine cap binding to >>>>>> annotate pombe telomerase RNA and represent the fact that this is >>>>>> trimethylguanosine capped, but on re-reading the definition I'm >>>>>> not sure if this is correct? >>>>>> Can I use this for the modification itself? or is it for gene >>>>>> products which interact with a capped product? >>>>>> >>>>> It represents some gene product that binds to the triMeG cap >>>>> present on an mRNA. Not the gene product that makes the cap. A >>>>> binding term should never be used for a covalent bond. Binding >>>>> implies a reversible reaction at STP, with a Ka and Kd. >>>>> >>>>> GPI anchor binding it meant to be used for something that binds >>>>> the the GPI anchor and not covalently linked to it. >>>>> >>>>> >>>>>> There do not appear to be any other annotations to this term >>>>>> despite the fact that many RNAs are capped which is another >>>>>> reason which made me suspect my usage may be wrong. >>>>>> >>>>>> Should the binding terms should only be used for non-covalent >>>>>> modifications (although this is only in some of the binding >>>>>> defs?), and does not represent the use of some terms. For >>>>>> instance GPI anchor binding is used for a number of proteins >>>>>> which are GPI anchored, in addition to proteins which bins the >>>>>> GPI moiety during GPI anchor biosynthesis. >>>>>> >>>>>> Cheers >>>>>> >>>>>> Val >>>>>> >>>>>> Def: >>>>>> Interacting selectively with the trimethylguanosine >>>>>> (m(3)(2,2,7)-GTP) moiety located at the 5' end of some RNA >>>>>> molecules. Such trimethylated cap structures, generally produced >>>>>> by posttranscriptional modification of a 7-methylguanosine cap, >>>>>> are often found on snRNAs and snoRNAs transcribed by RNA >>>>>> polymerase II, but have also be found on snRNAs transcribed by >>>>>> RNA polymerase III. They have also been found on a subset of the >>>>>> mRNA population in some species, e.g. C. elegans. >>>>>> >>>>>> >>>>>> >>>> >>> >>> From midori at ebi.ac.uk Thu Jan 17 02:03:02 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 17 Jan 2008 10:03:02 +0000 (GMT) Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478E98C1.4030608@informatics.jax.org> References: <478E8F41.60106@informatics.jax.org> <478E98C1.4030608@informatics.jax.org> Message-ID: Has this gone into SF? (hint, hint) should be easy to fix ... On Wed, 16 Jan 2008, Harold Drabkin wrote: > Hopefully a script can be designed to add this as a sentence to the end of > each definition! > > hjd > > Karen Christie wrote: >> while you're right that terms inherit from their parents, it's still >> probably better to fix it everywhere, so that people who only look at a >> specific term and not all its parents get the non-covalent idea clearly. >> >> -Karen >> >> >> On Wed, 16 Jan 2008, Harold Drabkin wrote: >> >>> I actually noticed that the core term, binding, with def of : The >>> selective, often stoichiometric, interaction of a molecule with one or >>> more specific sites on another molecule. >>> is missing the non-covalent idea; fixing it in this term should suffice >>> for it's children >>> >>> >>> The Oxford bible: binding: the act or process by which one molecule >>> attaches to another by noncovalent forces. >>> >>> >>> Valerie Wood wrote: >>>> yes thanks it seems obvious now, although I think I have some rogue >>>> annotations to fix for GPI binding to fix.! This might be obvious to >>>> everyone, but it might be worth adding 'non covalent' to all of the >>>> binding term defs just to emphasise. Its quite clear when you read the >>>> 'RNA trimethylguanosine cap binding def, but I'm not sure that it is for >>>> some of the others. thanks >>>> >>>> val >>>> From adiehl at informatics.jax.org Thu Jan 17 02:12:13 2008 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Thu, 17 Jan 2008 10:12:13 +0000 Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: References: <478E8F41.60106@informatics.jax.org> <478E98C1.4030608@informatics.jax.org> Message-ID: <478F29FD.8030501@informatics.jax.org> While I agree that common annotation practice has been to exclude covalent bonds between gene products and other entities (including other proteins), the fact that this has not be specifically excluded by the definition of 1135 MF binding terms suggests to me the there could be in fact be many annotations using these binding terms that include covalent bonds. Per standard GO practice, we should obsolete all 1135 binding terms, provide equivalent, but redefined new binding terms, to force people to reexamine their annotations. Clearly, we are not going to do this. So in fact, I recommend that we do not change the definitions at all, although perhaps we could add a comment like, "Note that binding terms are not intended for annotation of covalent bonds." -- Alex Midori Harris wrote: > Has this gone into SF? (hint, hint) > > should be easy to fix ... > > On Wed, 16 Jan 2008, Harold Drabkin wrote: > >> Hopefully a script can be designed to add this as a sentence to the >> end of each definition! >> >> hjd >> >> Karen Christie wrote: >>> while you're right that terms inherit from their parents, it's still >>> probably better to fix it everywhere, so that people who only look >>> at a specific term and not all its parents get the non-covalent idea >>> clearly. >>> >>> -Karen >>> >>> >>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>> >>>> I actually noticed that the core term, binding, with def of : >>>> The selective, often stoichiometric, interaction of a molecule with >>>> one or more specific sites on another molecule. >>>> is missing the non-covalent idea; fixing it in this term should >>>> suffice for it's children >>>> >>>> >>>> The Oxford bible: binding: the act or process by which one molecule >>>> attaches to another by noncovalent forces. >>>> >>>> >>>> Valerie Wood wrote: >>>>> yes thanks it seems obvious now, although I think I have some >>>>> rogue annotations to fix for GPI binding to fix.! This might be >>>>> obvious to everyone, but it might be worth adding 'non covalent' >>>>> to all of the binding term defs just to emphasise. Its quite clear >>>>> when you read the 'RNA trimethylguanosine cap binding def, but I'm >>>>> not sure that it is for some of the others. thanks >>>>> >>>>> val >>>>> -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From midori at ebi.ac.uk Thu Jan 17 02:16:54 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 17 Jan 2008 10:16:54 +0000 (GMT) Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478F29FD.8030501@informatics.jax.org> References: <478E8F41.60106@informatics.jax.org> <478E98C1.4030608@informatics.jax.org> <478F29FD.8030501@informatics.jax.org> Message-ID: I can implement either; when the annotation list has reaced consensus, please put it in SourceForge. I'll do whatever I find there. m On Thu, 17 Jan 2008, Alexander Diehl wrote: > While I agree that common annotation practice has been to exclude covalent > bonds between gene products and other entities (including other proteins), > the fact that this has not be specifically excluded by the definition of 1135 > MF binding terms suggests to me the there could be in fact be many > annotations using these binding terms that include covalent bonds. Per > standard GO practice, we should obsolete all 1135 binding terms, provide > equivalent, but redefined new binding terms, to force people to reexamine > their annotations. > > Clearly, we are not going to do this. So in fact, I recommend that we do not > change the definitions at all, although perhaps we could add a comment like, > "Note that binding terms are not intended for annotation of covalent bonds." > > -- Alex > > > Midori Harris wrote: >> Has this gone into SF? (hint, hint) >> >> should be easy to fix ... >> >> On Wed, 16 Jan 2008, Harold Drabkin wrote: >> >>> Hopefully a script can be designed to add this as a sentence to the end of >>> each definition! >>> >>> hjd >>> >>> Karen Christie wrote: >>>> while you're right that terms inherit from their parents, it's still >>>> probably better to fix it everywhere, so that people who only look at a >>>> specific term and not all its parents get the non-covalent idea clearly. >>>> >>>> -Karen >>>> >>>> >>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>> >>>>> I actually noticed that the core term, binding, with def of : The >>>>> selective, often stoichiometric, interaction of a molecule with one or >>>>> more specific sites on another molecule. >>>>> is missing the non-covalent idea; fixing it in this term should suffice >>>>> for it's children >>>>> >>>>> >>>>> The Oxford bible: binding: the act or process by which one molecule >>>>> attaches to another by noncovalent forces. >>>>> >>>>> >>>>> Valerie Wood wrote: >>>>>> yes thanks it seems obvious now, although I think I have some rogue >>>>>> annotations to fix for GPI binding to fix.! This might be obvious to >>>>>> everyone, but it might be worth adding 'non covalent' to all of the >>>>>> binding term defs just to emphasise. Its quite clear when you read the >>>>>> 'RNA trimethylguanosine cap binding def, but I'm not sure that it is >>>>>> for some of the others. thanks >>>>>> >>>>>> val >>>>>> > > > From adiehl at informatics.jax.org Thu Jan 17 02:56:16 2008 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Thu, 17 Jan 2008 10:56:16 +0000 Subject: [Fwd: Re: [annotation] RNA trimethylguanosine cap binding query] In-Reply-To: <478E4A28.8000202@informatics.jax.org> References: <478E4A28.8000202@informatics.jax.org> Message-ID: <478F3450.9060104@informatics.jax.org> Harold, It is true I have made a number of annotations to the term 'GPI anchor binding' for CD24a and Thy1. I was always a bit uncomfortable about these annotations as they violated the idea of binding terms being for non-covalent bonds only, but in fact I was only following the precedent set by others in the GO for GPI-anchored proteins. You see for as long as I have been in the GO, and perhaps for much longer, we have had the SwissProt Keyword mapping, SP_KW:KW-0336 GPI-anchor > GO:GPI anchor binding ; GO:0048503 which basically means any protein identified by SwissProt curators as having a GPI-anchor has been mapped to 'GPI-anchor binding'. Apart from CD24a and Thy1, all the other genes in MGI annotated to 'GPI anchor binding' are based on this keyword mapping. Looking at Amigo, I believe that every single experimentally based annotation to 'GPI anchor binding' is for a GPI anchored protein, so clearly other annotators use this term in this way. I would bet this term was put in the GO by someone who intended it to be used this way. And, as Karen so conveniently pointed out, the definitions of GO binding terms, including GPI anchor binding, do not specifically exclude covalent binding, so logically the annotations stand. I would also point out that neither the 'Annotation Guide' nor 'Molecular Function Ontology Guidelines' sections of the documentation on the Gene Ontology Consortium's official web pages exclude annotation of covalent binding or even mention it. We don't even exclude annotation of covalent binding in the much stricter MGI GO annotation guidelines (the written ones). However, since I know that you are now at least driven halfway up the wall by my argumentation, I am may be willing to compromise and propose that in addition to eliminating the SwissProt keyword mapping, that we obsolete the term 'GPI-anchor binding ; GO:0048503' itself. I know of no protein that binds GPI anchors specifically in a non-covalent way, although I agree it is a theoretical possibility, and the term clearly has only been a source of confusion to GO annotators, although the annotations are actually _useful_ for GO users, who might want to be able to easily find GPI-anchored proteins all at once. But forget about the users -- with luck they may figure out that 'anchored to external side of plasma membrane ; GO:0031362' can be used to find some GPI anchored proteins, although there is no SwissProt mapping to this term and this term is less specific than 'GPI anchor binding'. Rest assured Harold, I do not routinely annotate covalent binding, except in the case of 'GPI anchor binding' where I felt I was following the precedent of others in the GO and providing quite useful information to our users. Although I am open to doing so, I do not plan remove my experimentally correct annotations until further discussions of this issue have taken place. Thanks, Alex Harold Drabkin wrote: > Alex can you please look at the GPI anchor binding annotations that > you made here. The term should only be used for non-covalent binding, > not covalent attachment. Since you recently looked at the papers, you > are more familiar with what they were trying to show. > > hjd > > > > -------- Original Message -------- > Return-Path: > Received: from smtp.sanger.ac.uk (smtp.sanger.ac.uk > [193.62.203.215]) by mirkwood.informatics.jax.org (8.13.8/8.13.8) with > ESMTP id m0GIBhtp026890 for ; Wed, 16 Jan > 2008 13:11:43 -0500 (EST) (envelope-from val at sanger.ac.uk) > Received: from intmail1b.internal.sanger.ac.uk ([172.17.56.130] > helo=smtp.sanger.ac.uk) by routemail.internal.sanger.ac.uk with esmtp > (Exim 4.66) (envelope-from ) id 1JFCjl-0002W8-LF for > hjd at informatics.jax.org; Wed, 16 Jan 2008 18:11:41 +0000 > Received: from deskpro16317.dynamic.sanger.ac.uk ([172.20.8.72]) > by intmail1b.internal.sanger.ac.uk with esmtp (Exim 4.41) id > 1JFCjl-0003rb-Fm; Wed, 16 Jan 2008 18:11:41 +0000 > Received: from localhost.sanger.ac.uk ([127.0.0.1]) by > deskpro16317.dynamic.sanger.ac.uk with esmtp (Exim 4.50) id > 1JFCjl-0008GD-Ef; Wed, 16 Jan 2008 18:11:41 +0000 > Message-ID: <478E48DD.1010503 at sanger.ac.uk> > Date: Wed, 16 Jan 2008 18:11:41 +0000 > From: Valerie Wood > User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.8) > Gecko/20070113 Debian/1.7.8-1sarge10 > X-Accept-Language: en > MIME-Version: 1.0 > To: hjd at informatics.jax.org > CC: Valerie Wood > Subject: Re: [annotation] RNA trimethylguanosine cap binding query > References: <478E3631.2030208 at sanger.ac.uk> > <478E435E.30002 at informatics.jax.org> > In-Reply-To: <478E435E.30002 at informatics.jax.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: 7bit > X-PMX-Version: 5.4.0.320885, Antispam-Engine: 2.5.2.313940, > Antispam-Data: 2008.1.16.95857 > X-PerlMx-Spam: Gauge=IIIIIII, Probability=7%, Report='__CT 0, > __CTE 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, > __MIME_VERSION 0, __SANE_MSGID 0, __USER_AGENT 0' > Content-Length: 2374 > > > > *Hi Harold, > > mouse > Cd24a > uses *PMID: 14707049 for what seems to be a covalent GPI-binding > doesn't it? > > i'm sure there is 'mixed usage' > > or is there some other data in there (I just did a search on GPI) > > Val > > > > > > Harold Drabkin wrote: > >> Valerie Wood wrote: >> >>> I recently used the term RNA trimethylguanosine cap binding to >>> annotate pombe telomerase RNA and represent the fact that this is >>> trimethylguanosine capped, but on re-reading the definition I'm not >>> sure if this is correct? >>> Can I use this for the modification itself? or is it for gene >>> products which interact with a capped product? >> >> It represents some gene product that binds to the triMeG cap present >> on an mRNA. Not the gene product that makes the cap. A binding term >> should never be used for a covalent bond. Binding implies a >> reversible reaction at STP, with a Ka and Kd. >> >> GPI anchor binding it meant to be used for something that binds the >> the GPI anchor and not covalently linked to it. >> >>> >>> There do not appear to be any other annotations to this term >>> despite the fact that many RNAs are capped which is another reason >>> which made me suspect my usage may be wrong. >>> >>> Should the binding terms should only be used for non-covalent >>> modifications (although this is only in some of the binding defs?), >>> and does not represent the use of some terms. For instance GPI >>> anchor binding is used for a number of proteins which are GPI >>> anchored, in addition to proteins which bins the GPI moiety during >>> GPI anchor biosynthesis. >>> >>> Cheers >>> >>> Val >>> >>> Def: >>> Interacting selectively with the trimethylguanosine >>> (m(3)(2,2,7)-GTP) moiety located at the 5' end of some RNA >>> molecules. Such trimethylated cap structures, generally produced by >>> posttranscriptional modification of a 7-methylguanosine cap, are >>> often found on snRNAs and snoRNAs transcribed by RNA polymerase II, >>> but have also be found on snRNAs transcribed by RNA polymerase III. >>> They have also been found on a subset of the mRNA population in some >>> species, e.g. C. elegans. >>> >>> >> >> >> >> > > > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From midori at ebi.ac.uk Thu Jan 17 05:38:03 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 17 Jan 2008 13:38:03 +0000 (GMT) Subject: [annotation] osmosensor - SF 1873095 Message-ID: Hi, In SF 1873095, Donghui has requested a definition for osmosensor activity (GO:0005034). Can those who have used this term in annotations -- MGI, RGD, SGD and TAIR -- suggest anything? I'm even wondering whether it's a legitimate molecular function term, since a quick look at PubMed search results indicates that histidine kinases and adenylyl cyclases (possibly among other things) can be referred to as "osmosensors". This is the SF item: https://sourceforge.net/tracker/index.php?func=detail&aid=1873095&group_id=36855&atid=440764 These are the gene products currently annotated to GO:0005034: MGI MGI:1926945 Trpv4 (2 lines in file) RGD RGD:69337 Trpv4 (2) SGD S000002828 HKR1 SGD S000003246 MSB2 SGD S000000920 SHO1 SGD S000001409 SLN1 (2) TAIR gene:3713570 ATHK1 Thanks, Midori From hjd at informatics.jax.org Thu Jan 17 06:23:40 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Thu, 17 Jan 2008 09:23:40 -0500 Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478F29FD.8030501@informatics.jax.org> References: <478E8F41.60106@informatics.jax.org> <478E98C1.4030608@informatics.jax.org> <478F29FD.8030501@informatics.jax.org> Message-ID: <478F64EC.1040202@informatics.jax.org> To use binding for the creation of a covalent bond is just absolutely incorrect. This is just basic undergraduate chemistry. Modifying the definition is fine; I would add both statements. However, if anyone has used this in this way it is wrong. Those annotations should stricken when found. I cannot see any "but". Although we do not obviously have the time to revisit each one, in the cases Val found, they should be removed; they were incorrect use of the term binding. hjd Alexander Diehl wrote: > While I agree that common annotation practice has been to exclude > covalent bonds between gene products and other entities (including > other proteins), the fact that this has not be specifically excluded > by the definition of 1135 MF binding terms suggests to me the there > could be in fact be many annotations using these binding terms that > include covalent bonds. Per standard GO practice, we should obsolete > all 1135 binding terms, provide equivalent, but redefined new binding > terms, to force people to reexamine their annotations. > > Clearly, we are not going to do this. So in fact, I recommend that we > do not change the definitions at all, although perhaps we could add a > comment like, "Note that binding terms are not intended for annotation > of covalent bonds." > > -- Alex > > > Midori Harris wrote: >> Has this gone into SF? (hint, hint) >> >> should be easy to fix ... >> >> On Wed, 16 Jan 2008, Harold Drabkin wrote: >> >>> Hopefully a script can be designed to add this as a sentence to the >>> end of each definition! >>> >>> hjd >>> >>> Karen Christie wrote: >>>> while you're right that terms inherit from their parents, it's >>>> still probably better to fix it everywhere, so that people who only >>>> look at a specific term and not all its parents get the >>>> non-covalent idea clearly. >>>> >>>> -Karen >>>> >>>> >>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>> >>>>> I actually noticed that the core term, binding, with def of : >>>>> The selective, often stoichiometric, interaction of a molecule >>>>> with one or more specific sites on another molecule. >>>>> is missing the non-covalent idea; fixing it in this term should >>>>> suffice for it's children >>>>> >>>>> >>>>> The Oxford bible: binding: the act or process by which one >>>>> molecule attaches to another by noncovalent forces. >>>>> >>>>> >>>>> Valerie Wood wrote: >>>>>> yes thanks it seems obvious now, although I think I have some >>>>>> rogue annotations to fix for GPI binding to fix.! This might be >>>>>> obvious to everyone, but it might be worth adding 'non covalent' >>>>>> to all of the binding term defs just to emphasise. Its quite >>>>>> clear when you read the 'RNA trimethylguanosine cap binding def, >>>>>> but I'm not sure that it is for some of the others. thanks >>>>>> >>>>>> val >>>>>> > > From hjd at informatics.jax.org Thu Jan 17 06:34:38 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Thu, 17 Jan 2008 09:34:38 -0500 Subject: [Fwd: Re: [annotation] RNA trimethylguanosine cap binding query] In-Reply-To: <478F3450.9060104@informatics.jax.org> References: <478E4A28.8000202@informatics.jax.org> <478F3450.9060104@informatics.jax.org> Message-ID: <478F677E.1020006@informatics.jax.org> I don't believe there is such thing as "covalent binding". There is covalent bonding. Perhaps it is the term GPI anchor binding" that needs to be obsoleted and a new term, not a child of binding, be made to properly describe whatever is going on. hd Alexander Diehl wrote: > Harold, > > It is true I have made a number of annotations to the term 'GPI anchor > binding' for CD24a and Thy1. I was always a bit uncomfortable about > these annotations as they violated the idea of binding terms being for > non-covalent bonds only, but in fact I was only following the > precedent set by others in the GO for GPI-anchored proteins. You see > for as long as I have been in the GO, and perhaps for much longer, we > have had the SwissProt Keyword mapping, > > SP_KW:KW-0336 GPI-anchor > GO:GPI anchor binding ; GO:0048503 > > which basically means any protein identified by SwissProt curators as > having a GPI-anchor has been mapped to 'GPI-anchor binding'. Apart > from CD24a and Thy1, all the other genes in MGI annotated to 'GPI > anchor binding' are based on this keyword mapping. Looking at Amigo, > I believe that every single experimentally based annotation to 'GPI > anchor binding' is for a GPI anchored protein, so clearly other > annotators use this term in this way. I would bet this term was put > in the GO by someone who intended it to be used this way. And, as > Karen so conveniently pointed out, the definitions of GO binding > terms, including GPI anchor binding, do not specifically exclude > covalent binding, so logically the annotations stand. I would also > point out that neither the 'Annotation Guide' nor 'Molecular Function > Ontology Guidelines' sections of the documentation on the Gene > Ontology Consortium's official web pages exclude annotation of > covalent binding or even mention it. We don't even exclude annotation > of covalent binding in the much stricter MGI GO annotation guidelines > (the written ones). > > However, since I know that you are now at least driven halfway up the > wall by my argumentation, I am may be willing to compromise and > propose that in addition to eliminating the SwissProt keyword mapping, > that we obsolete the term 'GPI-anchor binding ; GO:0048503' itself. I > know of no protein that binds GPI anchors specifically in a > non-covalent way, although I agree it is a theoretical possibility, > and the term clearly has only been a source of confusion to GO > annotators, although the annotations are actually _useful_ for GO > users, who might want to be able to easily find GPI-anchored proteins > all at once. But forget about the users -- with luck they may figure > out that 'anchored to external side of plasma membrane ; GO:0031362' > can be used to find some GPI anchored proteins, although there is no > SwissProt mapping to this term and this term is less specific than > 'GPI anchor binding'. > > Rest assured Harold, I do not routinely annotate covalent binding, > except in the case of 'GPI anchor binding' where I felt I was > following the precedent of others in the GO and providing quite useful > information to our users. Although I am open to doing so, I do not > plan remove my experimentally correct annotations until further > discussions of this issue have taken place. > > Thanks, > > Alex > > > Harold Drabkin wrote: >> Alex can you please look at the GPI anchor binding annotations that >> you made here. The term should only be used for non-covalent binding, >> not covalent attachment. Since you recently looked at the papers, you >> are more familiar with what they were trying to show. >> >> hjd >> >> >> >> -------- Original Message -------- >> Return-Path: >> Received: from smtp.sanger.ac.uk (smtp.sanger.ac.uk >> [193.62.203.215]) by mirkwood.informatics.jax.org (8.13.8/8.13.8) >> with ESMTP id m0GIBhtp026890 for ; Wed, 16 >> Jan 2008 13:11:43 -0500 (EST) (envelope-from val at sanger.ac.uk) >> Received: from intmail1b.internal.sanger.ac.uk ([172.17.56.130] >> helo=smtp.sanger.ac.uk) by routemail.internal.sanger.ac.uk with esmtp >> (Exim 4.66) (envelope-from ) id 1JFCjl-0002W8-LF >> for hjd at informatics.jax.org; Wed, 16 Jan 2008 18:11:41 +0000 >> Received: from deskpro16317.dynamic.sanger.ac.uk ([172.20.8.72]) >> by intmail1b.internal.sanger.ac.uk with esmtp (Exim 4.41) id >> 1JFCjl-0003rb-Fm; Wed, 16 Jan 2008 18:11:41 +0000 >> Received: from localhost.sanger.ac.uk ([127.0.0.1]) by >> deskpro16317.dynamic.sanger.ac.uk with esmtp (Exim 4.50) id >> 1JFCjl-0008GD-Ef; Wed, 16 Jan 2008 18:11:41 +0000 >> Message-ID: <478E48DD.1010503 at sanger.ac.uk> >> Date: Wed, 16 Jan 2008 18:11:41 +0000 >> From: Valerie Wood >> User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.8) >> Gecko/20070113 Debian/1.7.8-1sarge10 >> X-Accept-Language: en >> MIME-Version: 1.0 >> To: hjd at informatics.jax.org >> CC: Valerie Wood >> Subject: Re: [annotation] RNA trimethylguanosine cap binding query >> References: <478E3631.2030208 at sanger.ac.uk> >> <478E435E.30002 at informatics.jax.org> >> In-Reply-To: <478E435E.30002 at informatics.jax.org> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> Content-Transfer-Encoding: 7bit >> X-PMX-Version: 5.4.0.320885, Antispam-Engine: 2.5.2.313940, >> Antispam-Data: 2008.1.16.95857 >> X-PerlMx-Spam: Gauge=IIIIIII, Probability=7%, Report='__CT 0, >> __CTE 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, >> __MIME_VERSION 0, __SANE_MSGID 0, __USER_AGENT 0' >> Content-Length: 2374 >> >> >> >> *Hi Harold, >> >> mouse >> Cd24a >> uses *PMID: 14707049 for what seems to be a covalent GPI-binding >> doesn't it? >> >> i'm sure there is 'mixed usage' >> >> or is there some other data in there (I just did a search on GPI) >> >> Val >> >> >> >> >> >> Harold Drabkin wrote: >> >>> Valerie Wood wrote: >>> >>>> I recently used the term RNA trimethylguanosine cap binding to >>>> annotate pombe telomerase RNA and represent the fact that this is >>>> trimethylguanosine capped, but on re-reading the definition I'm >>>> not sure if this is correct? >>>> Can I use this for the modification itself? or is it for gene >>>> products which interact with a capped product? >>> >>> It represents some gene product that binds to the triMeG cap present >>> on an mRNA. Not the gene product that makes the cap. A binding term >>> should never be used for a covalent bond. Binding implies a >>> reversible reaction at STP, with a Ka and Kd. >>> >>> GPI anchor binding it meant to be used for something that binds the >>> the GPI anchor and not covalently linked to it. >>> >>>> >>>> There do not appear to be any other annotations to this term >>>> despite the fact that many RNAs are capped which is another reason >>>> which made me suspect my usage may be wrong. >>>> >>>> Should the binding terms should only be used for non-covalent >>>> modifications (although this is only in some of the binding defs?), >>>> and does not represent the use of some terms. For instance GPI >>>> anchor binding is used for a number of proteins which are GPI >>>> anchored, in addition to proteins which bins the GPI moiety during >>>> GPI anchor biosynthesis. >>>> >>>> Cheers >>>> >>>> Val >>>> >>>> Def: >>>> Interacting selectively with the trimethylguanosine >>>> (m(3)(2,2,7)-GTP) moiety located at the 5' end of some RNA >>>> molecules. Such trimethylated cap structures, generally produced by >>>> posttranscriptional modification of a 7-methylguanosine cap, are >>>> often found on snRNAs and snoRNAs transcribed by RNA polymerase II, >>>> but have also be found on snRNAs transcribed by RNA polymerase III. >>>> They have also been found on a subset of the mRNA population in >>>> some species, e.g. C. elegans. >>>> >>>> >>> >>> >>> >>> >> >> >> > > From val at sanger.ac.uk Thu Jan 17 06:40:24 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 17 Jan 2008 14:40:24 UT Subject: [annotation] RNA trimethylguanosine cap binding query Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080117/8a6159b8/attachment.pl From adiehl at informatics.jax.org Thu Jan 17 06:41:44 2008 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Thu, 17 Jan 2008 14:41:44 +0000 Subject: [Fwd: Re: [annotation] RNA trimethylguanosine cap binding query] In-Reply-To: <478F677E.1020006@informatics.jax.org> References: <478E4A28.8000202@informatics.jax.org> <478F3450.9060104@informatics.jax.org> <478F677E.1020006@informatics.jax.org> Message-ID: <478F6928.30700@informatics.jax.org> Harold, A quick google of "convalent binding" yields lots of hits, mostly of a scientific nature. I think this is a not-uncommon usage, undergraduate chemistry be damned. -- Alex Harold Drabkin wrote: > I don't believe there is such thing as "covalent binding". There is > covalent bonding. Perhaps it is the term GPI anchor binding" that > needs to be obsoleted and a new term, not a child of binding, be made > to properly describe whatever is going on. > > hd > > Alexander Diehl wrote: >> Harold, >> >> It is true I have made a number of annotations to the term 'GPI >> anchor binding' for CD24a and Thy1. I was always a bit uncomfortable >> about these annotations as they violated the idea of binding terms >> being for non-covalent bonds only, but in fact I was only following >> the precedent set by others in the GO for GPI-anchored proteins. You >> see for as long as I have been in the GO, and perhaps for much >> longer, we have had the SwissProt Keyword mapping, >> >> SP_KW:KW-0336 GPI-anchor > GO:GPI anchor binding ; GO:0048503 >> >> which basically means any protein identified by SwissProt curators as >> having a GPI-anchor has been mapped to 'GPI-anchor binding'. Apart >> from CD24a and Thy1, all the other genes in MGI annotated to 'GPI >> anchor binding' are based on this keyword mapping. Looking at Amigo, >> I believe that every single experimentally based annotation to 'GPI >> anchor binding' is for a GPI anchored protein, so clearly other >> annotators use this term in this way. I would bet this term was put >> in the GO by someone who intended it to be used this way. And, as >> Karen so conveniently pointed out, the definitions of GO binding >> terms, including GPI anchor binding, do not specifically exclude >> covalent binding, so logically the annotations stand. I would also >> point out that neither the 'Annotation Guide' nor 'Molecular Function >> Ontology Guidelines' sections of the documentation on the Gene >> Ontology Consortium's official web pages exclude annotation of >> covalent binding or even mention it. We don't even exclude >> annotation of covalent binding in the much stricter MGI GO annotation >> guidelines (the written ones). >> >> However, since I know that you are now at least driven halfway up the >> wall by my argumentation, I am may be willing to compromise and >> propose that in addition to eliminating the SwissProt keyword >> mapping, that we obsolete the term 'GPI-anchor binding ; GO:0048503' >> itself. I know of no protein that binds GPI anchors specifically in >> a non-covalent way, although I agree it is a theoretical possibility, >> and the term clearly has only been a source of confusion to GO >> annotators, although the annotations are actually _useful_ for GO >> users, who might want to be able to easily find GPI-anchored proteins >> all at once. But forget about the users -- with luck they may figure >> out that 'anchored to external side of plasma membrane ; GO:0031362' >> can be used to find some GPI anchored proteins, although there is no >> SwissProt mapping to this term and this term is less specific than >> 'GPI anchor binding'. >> >> Rest assured Harold, I do not routinely annotate covalent binding, >> except in the case of 'GPI anchor binding' where I felt I was >> following the precedent of others in the GO and providing quite >> useful information to our users. Although I am open to doing so, I >> do not plan remove my experimentally correct annotations until >> further discussions of this issue have taken place. >> >> Thanks, >> >> Alex >> >> >> Harold Drabkin wrote: >>> Alex can you please look at the GPI anchor binding annotations that >>> you made here. The term should only be used for non-covalent >>> binding, not covalent attachment. Since you recently looked at the >>> papers, you are more familiar with what they were trying to show. >>> >>> hjd >>> >>> >>> >>> -------- Original Message -------- >>> Return-Path: >>> Received: from smtp.sanger.ac.uk (smtp.sanger.ac.uk >>> [193.62.203.215]) by mirkwood.informatics.jax.org (8.13.8/8.13.8) >>> with ESMTP id m0GIBhtp026890 for ; Wed, 16 >>> Jan 2008 13:11:43 -0500 (EST) (envelope-from val at sanger.ac.uk) >>> Received: from intmail1b.internal.sanger.ac.uk ([172.17.56.130] >>> helo=smtp.sanger.ac.uk) by routemail.internal.sanger.ac.uk with >>> esmtp (Exim 4.66) (envelope-from ) id >>> 1JFCjl-0002W8-LF for hjd at informatics.jax.org; Wed, 16 Jan 2008 >>> 18:11:41 +0000 >>> Received: from deskpro16317.dynamic.sanger.ac.uk ([172.20.8.72]) >>> by intmail1b.internal.sanger.ac.uk with esmtp (Exim 4.41) id >>> 1JFCjl-0003rb-Fm; Wed, 16 Jan 2008 18:11:41 +0000 >>> Received: from localhost.sanger.ac.uk ([127.0.0.1]) by >>> deskpro16317.dynamic.sanger.ac.uk with esmtp (Exim 4.50) id >>> 1JFCjl-0008GD-Ef; Wed, 16 Jan 2008 18:11:41 +0000 >>> Message-ID: <478E48DD.1010503 at sanger.ac.uk> >>> Date: Wed, 16 Jan 2008 18:11:41 +0000 >>> From: Valerie Wood >>> User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.8) >>> Gecko/20070113 Debian/1.7.8-1sarge10 >>> X-Accept-Language: en >>> MIME-Version: 1.0 >>> To: hjd at informatics.jax.org >>> CC: Valerie Wood >>> Subject: Re: [annotation] RNA trimethylguanosine cap binding query >>> References: <478E3631.2030208 at sanger.ac.uk> >>> <478E435E.30002 at informatics.jax.org> >>> In-Reply-To: <478E435E.30002 at informatics.jax.org> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> Content-Transfer-Encoding: 7bit >>> X-PMX-Version: 5.4.0.320885, Antispam-Engine: 2.5.2.313940, >>> Antispam-Data: 2008.1.16.95857 >>> X-PerlMx-Spam: Gauge=IIIIIII, Probability=7%, Report='__CT 0, >>> __CTE 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, >>> __MIME_VERSION 0, __SANE_MSGID 0, __USER_AGENT 0' >>> Content-Length: 2374 >>> >>> >>> >>> *Hi Harold, >>> >>> mouse >>> Cd24a >>> uses *PMID: 14707049 for what seems to be a covalent GPI-binding >>> doesn't it? >>> >>> i'm sure there is 'mixed usage' >>> >>> or is there some other data in there (I just did a search on GPI) >>> >>> Val >>> >>> >>> >>> >>> >>> Harold Drabkin wrote: >>> >>>> Valerie Wood wrote: >>>> >>>>> I recently used the term RNA trimethylguanosine cap binding to >>>>> annotate pombe telomerase RNA and represent the fact that this is >>>>> trimethylguanosine capped, but on re-reading the definition I'm >>>>> not sure if this is correct? >>>>> Can I use this for the modification itself? or is it for gene >>>>> products which interact with a capped product? >>>> >>>> It represents some gene product that binds to the triMeG cap >>>> present on an mRNA. Not the gene product that makes the cap. A >>>> binding term should never be used for a covalent bond. Binding >>>> implies a reversible reaction at STP, with a Ka and Kd. >>>> >>>> GPI anchor binding it meant to be used for something that binds the >>>> the GPI anchor and not covalently linked to it. >>>> >>>>> >>>>> There do not appear to be any other annotations to this term >>>>> despite the fact that many RNAs are capped which is another >>>>> reason which made me suspect my usage may be wrong. >>>>> >>>>> Should the binding terms should only be used for non-covalent >>>>> modifications (although this is only in some of the binding >>>>> defs?), and does not represent the use of some terms. For >>>>> instance GPI anchor binding is used for a number of proteins which >>>>> are GPI anchored, in addition to proteins which bins the GPI >>>>> moiety during GPI anchor biosynthesis. >>>>> >>>>> Cheers >>>>> >>>>> Val >>>>> >>>>> Def: >>>>> Interacting selectively with the trimethylguanosine >>>>> (m(3)(2,2,7)-GTP) moiety located at the 5' end of some RNA >>>>> molecules. Such trimethylated cap structures, generally produced >>>>> by posttranscriptional modification of a 7-methylguanosine cap, >>>>> are often found on snRNAs and snoRNAs transcribed by RNA >>>>> polymerase II, but have also be found on snRNAs transcribed by RNA >>>>> polymerase III. They have also been found on a subset of the mRNA >>>>> population in some species, e.g. C. elegans. >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >>> >> >> > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From hjd at informatics.jax.org Thu Jan 17 06:48:37 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Thu, 17 Jan 2008 09:48:37 -0500 Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: References: Message-ID: <478F6AC5.6050504@informatics.jax.org> I do think that is the more sensible thing to do. hd Valerie Wood wrote: > Why don't we obsolete GPI binding and create a new term (it only has 31 manual annotations which appear to be mainly incorrect), plus the IEA mappings, which we have already established are wrong. > > I can't think of any other binding term which may have been used inconsistently in this way. I don't really know why we did this, but as now see I originally requested the term I will take the blame for establishing this bad practice. > > I have an alternative way to curate PTMs (and I guess most others do) so I'll just reannotate using this method. It would be useful to have a way to collect PTMs consistently with and between orgs, but as Karen C said, they don't belong in GO. > > We could then add a comment to all of the other binding terms to say that they are ONLY intended for non-covalent modifications. > > Would everyone be happy with this? > > Val > > > > > Harold Drabkin wrote: > >> To use binding for the creation of a covalent bond is just absolutely >> incorrect. This is just basic undergraduate chemistry. >> >> Modifying the definition is fine; I would add both statements. >> However, if anyone has used this in this way it is wrong. Those >> annotations should stricken when found. I cannot see any "but". >> Although we do not obviously have the time to revisit each one, in the >> cases Val found, they should be removed; they were incorrect use of the >> term binding. >> >> >> hjd >> >> Alexander Diehl wrote: >> >>> While I agree that common annotation practice has been to exclude >>> covalent bonds between gene products and other entities (including >>> other proteins), the fact that this has not be specifically excluded >>> by the definition of 1135 MF binding terms suggests to me the there >>> could be in fact be many annotations using these binding terms that >>> include covalent bonds. Per standard GO practice, we should obsolete >>> all 1135 binding terms, provide equivalent, but redefined new binding >>> terms, to force people to reexamine their annotations. >>> >>> Clearly, we are not going to do this. So in fact, I recommend that we >>> do not change the definitions at all, although perhaps we could add a >>> comment like, "Note that binding terms are not intended for annotation >>> of covalent bonds." >>> >>> -- Alex >>> >>> >>> Midori Harris wrote: >>> >>>> Has this gone into SF? (hint, hint) >>>> >>>> should be easy to fix ... >>>> >>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>> >>>> >>>>> Hopefully a script can be designed to add this as a sentence to the >>>>> end of each definition! >>>>> >>>>> hjd >>>>> >>>>> Karen Christie wrote: >>>>> >>>>>> while you're right that terms inherit from their parents, it's >>>>>> still probably better to fix it everywhere, so that people who only >>>>>> look at a specific term and not all its parents get the >>>>>> non-covalent idea clearly. >>>>>> >>>>>> -Karen >>>>>> >>>>>> >>>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>>> >>>>>> >>>>>>> I actually noticed that the core term, binding, with def of : >>>>>>> The selective, often stoichiometric, interaction of a molecule >>>>>>> with one or more specific sites on another molecule. >>>>>>> is missing the non-covalent idea; fixing it in this term should >>>>>>> suffice for it's children >>>>>>> >>>>>>> >>>>>>> The Oxford bible: binding: the act or process by which one >>>>>>> molecule attaches to another by noncovalent forces. >>>>>>> >>>>>>> >>>>>>> Valerie Wood wrote: >>>>>>> >>>>>>>> yes thanks it seems obvious now, although I think I have some >>>>>>>> rogue annotations to fix for GPI binding to fix.! This might be >>>>>>>> obvious to everyone, but it might be worth adding 'non covalent' >>>>>>>> to all of the binding term defs just to emphasise. Its quite >>>>>>>> clear when you read the 'RNA trimethylguanosine cap binding def, >>>>>>>> but I'm not sure that it is for some of the others. thanks >>>>>>>> >>>>>>>> val >>>>>>>> >>>>>>>> >>> >> >> > > From adiehl at informatics.jax.org Thu Jan 17 06:48:55 2008 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Thu, 17 Jan 2008 14:48:55 +0000 Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: References: Message-ID: <478F6AD7.6020509@informatics.jax.org> Anyone for 'anchored to external side of plasma membrane via GPI anchor' as an is-a child of 'anchored to external side of plasma membrane ; GO:0031362', or even 'anchored to membrane via GPI anchor'? I would be quite happy with this solution, and we could remap the SwissProt keyword 'GPI-anchor'. Thanks, Alex Valerie Wood wrote: > Why don't we obsolete GPI binding and create a new term (it only has 31 manual annotations which appear to be mainly incorrect), plus the IEA mappings, which we have already established are wrong. > > I can't think of any other binding term which may have been used inconsistently in this way. I don't really know why we did this, but as now see I originally requested the term I will take the blame for establishing this bad practice. > > I have an alternative way to curate PTMs (and I guess most others do) so I'll just reannotate using this method. It would be useful to have a way to collect PTMs consistently with and between orgs, but as Karen C said, they don't belong in GO. > > We could then add a comment to all of the other binding terms to say that they are ONLY intended for non-covalent modifications. > > Would everyone be happy with this? > > Val > > > > > Harold Drabkin wrote: > >> To use binding for the creation of a covalent bond is just absolutely >> incorrect. This is just basic undergraduate chemistry. >> >> Modifying the definition is fine; I would add both statements. >> However, if anyone has used this in this way it is wrong. Those >> annotations should stricken when found. I cannot see any "but". >> Although we do not obviously have the time to revisit each one, in the >> cases Val found, they should be removed; they were incorrect use of the >> term binding. >> >> >> hjd >> >> Alexander Diehl wrote: >> >>> While I agree that common annotation practice has been to exclude >>> covalent bonds between gene products and other entities (including >>> other proteins), the fact that this has not be specifically excluded >>> by the definition of 1135 MF binding terms suggests to me the there >>> could be in fact be many annotations using these binding terms that >>> include covalent bonds. Per standard GO practice, we should obsolete >>> all 1135 binding terms, provide equivalent, but redefined new binding >>> terms, to force people to reexamine their annotations. >>> >>> Clearly, we are not going to do this. So in fact, I recommend that we >>> do not change the definitions at all, although perhaps we could add a >>> comment like, "Note that binding terms are not intended for annotation >>> of covalent bonds." >>> >>> -- Alex >>> >>> >>> Midori Harris wrote: >>> >>>> Has this gone into SF? (hint, hint) >>>> >>>> should be easy to fix ... >>>> >>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>> >>>> >>>>> Hopefully a script can be designed to add this as a sentence to the >>>>> end of each definition! >>>>> >>>>> hjd >>>>> >>>>> Karen Christie wrote: >>>>> >>>>>> while you're right that terms inherit from their parents, it's >>>>>> still probably better to fix it everywhere, so that people who only >>>>>> look at a specific term and not all its parents get the >>>>>> non-covalent idea clearly. >>>>>> >>>>>> -Karen >>>>>> >>>>>> >>>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>>> >>>>>> >>>>>>> I actually noticed that the core term, binding, with def of : >>>>>>> The selective, often stoichiometric, interaction of a molecule >>>>>>> with one or more specific sites on another molecule. >>>>>>> is missing the non-covalent idea; fixing it in this term should >>>>>>> suffice for it's children >>>>>>> >>>>>>> >>>>>>> The Oxford bible: binding: the act or process by which one >>>>>>> molecule attaches to another by noncovalent forces. >>>>>>> >>>>>>> >>>>>>> Valerie Wood wrote: >>>>>>> >>>>>>>> yes thanks it seems obvious now, although I think I have some >>>>>>>> rogue annotations to fix for GPI binding to fix.! This might be >>>>>>>> obvious to everyone, but it might be worth adding 'non covalent' >>>>>>>> to all of the binding term defs just to emphasise. Its quite >>>>>>>> clear when you read the 'RNA trimethylguanosine cap binding def, >>>>>>>> but I'm not sure that it is for some of the others. thanks >>>>>>>> >>>>>>>> val >>>>>>>> >>>>>>>> >>> >> >> > > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From FMcCarthy at cvm.msstate.edu Thu Jan 17 07:24:08 2008 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Thu, 17 Jan 2008 09:24:08 -0600 Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478F6AD7.6020509@informatics.jax.org> References: <478F6AD7.6020509@informatics.jax.org> Message-ID: Alexander Diehl on Thursday, January 17, 2008 at 8:48 AM +0000 wrote: >Anyone for 'anchored to external side of plasma membrane via GPI anchor' >as an is-a child of 'anchored to external side of plasma membrane ; >GO:0031362', or even 'anchored to membrane via GPI anchor'? I would be >quite happy with this solution, and we could remap the SwissProt keyword >'GPI-anchor'. My undergraduate chemistry may be a bit rusty but this sounds like a good biological solution. I'm in favour. Fiona The AgBase Databases Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031 http://www.agbase.msstate.edu/ From kchris at genome.Stanford.EDU Thu Jan 17 07:31:48 2008 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Thu, 17 Jan 2008 07:31:48 -0800 (PST) Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478F6AC5.6050504@informatics.jax.org> References: <478F6AC5.6050504@informatics.jax.org> Message-ID: sounds sensible to me too -Karen On Thu, 17 Jan 2008, Harold Drabkin wrote: > I do think that is the more sensible thing to do. > hd > > > Valerie Wood wrote: >> Why don't we obsolete GPI binding and create a new term (it only has 31 >> manual annotations which appear to be mainly incorrect), plus the IEA >> mappings, which we have already established are wrong. >> >> I can't think of any other binding term which may have been used >> inconsistently in this way. I don't really know why we did this, but as now >> see I originally requested the term I will take the blame for establishing >> this bad practice. >> I have an alternative way to curate PTMs (and I guess most others do) so >> I'll just reannotate using this method. It would be useful to have a way to >> collect PTMs consistently with and between orgs, but as Karen C said, they >> don't belong in GO. >> >> We could then add a comment to all of the other binding terms to say that >> they are ONLY intended for non-covalent modifications. >> >> Would everyone be happy with this? >> >> Val >> >> >> >> >> Harold Drabkin wrote: >>> To use binding for the creation of a covalent bond is just absolutely >>> incorrect. This is just basic undergraduate chemistry. >>> Modifying the definition is fine; I would add both statements. However, >>> if anyone has used this in this way it is wrong. Those annotations should >>> stricken when found. I cannot see any "but". Although we do not >>> obviously have the time to revisit each one, in the cases Val found, they >>> should be removed; they were incorrect use of the term binding. >>> >>> >>> hjd >>> >>> Alexander Diehl wrote: >>> >>>> While I agree that common annotation practice has been to exclude >>>> covalent bonds between gene products and other entities (including other >>>> proteins), the fact that this has not be specifically excluded by the >>>> definition of 1135 MF binding terms suggests to me the there could be in >>>> fact be many annotations using these binding terms that include covalent >>>> bonds. Per standard GO practice, we should obsolete all 1135 binding >>>> terms, provide equivalent, but redefined new binding terms, to force >>>> people to reexamine their annotations. >>>> >>>> Clearly, we are not going to do this. So in fact, I recommend that we do >>>> not change the definitions at all, although perhaps we could add a >>>> comment like, "Note that binding terms are not intended for annotation of >>>> covalent bonds." >>>> >>>> -- Alex >>>> >>>> >>>> Midori Harris wrote: >>>> >>>>> Has this gone into SF? (hint, hint) >>>>> >>>>> should be easy to fix ... >>>>> >>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>> >>>>> >>>>>> Hopefully a script can be designed to add this as a sentence to the end >>>>>> of each definition! >>>>>> >>>>>> hjd >>>>>> >>>>>> Karen Christie wrote: >>>>>> >>>>>>> while you're right that terms inherit from their parents, it's still >>>>>>> probably better to fix it everywhere, so that people who only look at >>>>>>> a specific term and not all its parents get the non-covalent idea >>>>>>> clearly. >>>>>>> >>>>>>> -Karen >>>>>>> >>>>>>> >>>>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>>>> >>>>>>> >>>>>>>> I actually noticed that the core term, binding, with def of : The >>>>>>>> selective, often stoichiometric, interaction of a molecule with one >>>>>>>> or more specific sites on another molecule. >>>>>>>> is missing the non-covalent idea; fixing it in this term should >>>>>>>> suffice for it's children >>>>>>>> >>>>>>>> >>>>>>>> The Oxford bible: binding: the act or process by which one molecule >>>>>>>> attaches to another by noncovalent forces. >>>>>>>> >>>>>>>> >>>>>>>> Valerie Wood wrote: >>>>>>>> >>>>>>>>> yes thanks it seems obvious now, although I think I have some rogue >>>>>>>>> annotations to fix for GPI binding to fix.! This might be obvious to >>>>>>>>> everyone, but it might be worth adding 'non covalent' to all of the >>>>>>>>> binding term defs just to emphasise. Its quite clear when you read >>>>>>>>> the 'RNA trimethylguanosine cap binding def, but I'm not sure that >>>>>>>>> it is for some of the others. thanks >>>>>>>>> >>>>>>>>> val >>>>>>>>> >>>>>>>>> >>>> >>> >>> >> >> From kchris at genome.Stanford.EDU Thu Jan 17 07:41:29 2008 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Thu, 17 Jan 2008 07:41:29 -0800 (PST) Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: <478F6AD7.6020509@informatics.jax.org> References: <478F6AD7.6020509@informatics.jax.org> Message-ID: Considering that we already have "anchored to external side of plasma membrane", it doesn't seem out of line to make a more specific child term. Are there other anchors other than GPI anchors? -Karen On Thu, 17 Jan 2008, Alexander Diehl wrote: > Anyone for 'anchored to external side of plasma membrane via GPI anchor' as > an is-a child of 'anchored to external side of plasma membrane ; GO:0031362', > or even 'anchored to membrane via GPI anchor'? I would be quite happy with > this solution, and we could remap the SwissProt keyword 'GPI-anchor'. > > Thanks, > > Alex > > > > Valerie Wood wrote: >> Why don't we obsolete GPI binding and create a new term (it only has 31 >> manual annotations which appear to be mainly incorrect), plus the IEA >> mappings, which we have already established are wrong. >> >> I can't think of any other binding term which may have been used >> inconsistently in this way. I don't really know why we did this, but as now >> see I originally requested the term I will take the blame for establishing >> this bad practice. >> I have an alternative way to curate PTMs (and I guess most others do) so >> I'll just reannotate using this method. It would be useful to have a way to >> collect PTMs consistently with and between orgs, but as Karen C said, they >> don't belong in GO. >> >> We could then add a comment to all of the other binding terms to say that >> they are ONLY intended for non-covalent modifications. >> >> Would everyone be happy with this? >> >> Val >> >> >> >> >> Harold Drabkin wrote: >>> To use binding for the creation of a covalent bond is just absolutely >>> incorrect. This is just basic undergraduate chemistry. >>> Modifying the definition is fine; I would add both statements. However, >>> if anyone has used this in this way it is wrong. Those annotations should >>> stricken when found. I cannot see any "but". Although we do not >>> obviously have the time to revisit each one, in the cases Val found, they >>> should be removed; they were incorrect use of the term binding. >>> >>> >>> hjd >>> >>> Alexander Diehl wrote: >>> >>>> While I agree that common annotation practice has been to exclude >>>> covalent bonds between gene products and other entities (including other >>>> proteins), the fact that this has not be specifically excluded by the >>>> definition of 1135 MF binding terms suggests to me the there could be in >>>> fact be many annotations using these binding terms that include covalent >>>> bonds. Per standard GO practice, we should obsolete all 1135 binding >>>> terms, provide equivalent, but redefined new binding terms, to force >>>> people to reexamine their annotations. >>>> >>>> Clearly, we are not going to do this. So in fact, I recommend that we do >>>> not change the definitions at all, although perhaps we could add a >>>> comment like, "Note that binding terms are not intended for annotation of >>>> covalent bonds." >>>> >>>> -- Alex >>>> >>>> >>>> Midori Harris wrote: >>>> >>>>> Has this gone into SF? (hint, hint) >>>>> >>>>> should be easy to fix ... >>>>> >>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>> >>>>> >>>>>> Hopefully a script can be designed to add this as a sentence to the end >>>>>> of each definition! >>>>>> >>>>>> hjd >>>>>> >>>>>> Karen Christie wrote: >>>>>> >>>>>>> while you're right that terms inherit from their parents, it's still >>>>>>> probably better to fix it everywhere, so that people who only look at >>>>>>> a specific term and not all its parents get the non-covalent idea >>>>>>> clearly. >>>>>>> >>>>>>> -Karen >>>>>>> >>>>>>> >>>>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>>>> >>>>>>> >>>>>>>> I actually noticed that the core term, binding, with def of : The >>>>>>>> selective, often stoichiometric, interaction of a molecule with one >>>>>>>> or more specific sites on another molecule. >>>>>>>> is missing the non-covalent idea; fixing it in this term should >>>>>>>> suffice for it's children >>>>>>>> >>>>>>>> >>>>>>>> The Oxford bible: binding: the act or process by which one molecule >>>>>>>> attaches to another by noncovalent forces. >>>>>>>> >>>>>>>> >>>>>>>> Valerie Wood wrote: >>>>>>>> >>>>>>>>> yes thanks it seems obvious now, although I think I have some rogue >>>>>>>>> annotations to fix for GPI binding to fix.! This might be obvious to >>>>>>>>> everyone, but it might be worth adding 'non covalent' to all of the >>>>>>>>> binding term defs just to emphasise. Its quite clear when you read >>>>>>>>> the 'RNA trimethylguanosine cap binding def, but I'm not sure that >>>>>>>>> it is for some of the others. thanks >>>>>>>>> >>>>>>>>> val >>>>>>>>> >>>>>>>>> >>>> >>> >>> >> >> > > > -- > Alexander Diehl, Ph.D. > Senior Scientific Curator > Mouse Genome Informatics > The Jackson Laboratory > 600 Main Street > Bar Harbor, ME 04609 > > email: adiehl at informatics.jax.org > work: +1 (207) 288-6427 > fax: +1 (207) 288-6131 > From midori at ebi.ac.uk Thu Jan 17 07:44:41 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 17 Jan 2008 15:44:41 +0000 (GMT) Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: References: <478F6AD7.6020509@informatics.jax.org> Message-ID: Well, there are myristoyl group anchors too, if I recall correctly. But I'm not convinced that the type of anchor is really cellular component territory, so I'm inclined to avoid the more specific term(s) on those grounds. m On Thu, 17 Jan 2008, Karen Christie wrote: > Considering that we already have "anchored to external side of plasma > membrane", it doesn't seem out of line to make a more specific child term. > Are there other anchors other than GPI anchors? > > -Karen > > > On Thu, 17 Jan 2008, Alexander Diehl wrote: > >> Anyone for 'anchored to external side of plasma membrane via GPI anchor' as >> an is-a child of 'anchored to external side of plasma membrane ; >> GO:0031362', or even 'anchored to membrane via GPI anchor'? I would be >> quite happy with this solution, and we could remap the SwissProt keyword >> 'GPI-anchor'. >> >> Thanks, >> >> Alex >> >> >> >> Valerie Wood wrote: >>> Why don't we obsolete GPI binding and create a new term (it only has 31 >>> manual annotations which appear to be mainly incorrect), plus the IEA >>> mappings, which we have already established are wrong. >>> >>> I can't think of any other binding term which may have been used >>> inconsistently in this way. I don't really know why we did this, but as >>> now see I originally requested the term I will take the blame for >>> establishing this bad practice. I have an alternative way to curate PTMs >>> (and I guess most others do) so I'll just reannotate using this method. It >>> would be useful to have a way to collect PTMs consistently with and >>> between orgs, but as Karen C said, they don't belong in GO. >>> >>> We could then add a comment to all of the other binding terms to say that >>> they are ONLY intended for non-covalent modifications. >>> >>> Would everyone be happy with this? >>> >>> Val >>> >>> >>> >>> >>> Harold Drabkin wrote: >>>> To use binding for the creation of a covalent bond is just absolutely >>>> incorrect. This is just basic undergraduate chemistry. Modifying the >>>> definition is fine; I would add both statements. However, if anyone has >>>> used this in this way it is wrong. Those annotations should stricken when >>>> found. I cannot see any "but". Although we do not obviously have the >>>> time to revisit each one, in the cases Val found, they should be >>>> removed; they were incorrect use of the term binding. >>>> >>>> >>>> hjd >>>> >>>> Alexander Diehl wrote: >>>> >>>>> While I agree that common annotation practice has been to exclude >>>>> covalent bonds between gene products and other entities (including other >>>>> proteins), the fact that this has not be specifically excluded by the >>>>> definition of 1135 MF binding terms suggests to me the there could be in >>>>> fact be many annotations using these binding terms that include covalent >>>>> bonds. Per standard GO practice, we should obsolete all 1135 binding >>>>> terms, provide equivalent, but redefined new binding terms, to force >>>>> people to reexamine their annotations. >>>>> >>>>> Clearly, we are not going to do this. So in fact, I recommend that we >>>>> do not change the definitions at all, although perhaps we could add a >>>>> comment like, "Note that binding terms are not intended for annotation >>>>> of covalent bonds." >>>>> >>>>> -- Alex >>>>> >>>>> >>>>> Midori Harris wrote: >>>>> >>>>>> Has this gone into SF? (hint, hint) >>>>>> >>>>>> should be easy to fix ... >>>>>> >>>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>>> >>>>>> >>>>>>> Hopefully a script can be designed to add this as a sentence to the >>>>>>> end of each definition! >>>>>>> >>>>>>> hjd >>>>>>> >>>>>>> Karen Christie wrote: >>>>>>> >>>>>>>> while you're right that terms inherit from their parents, it's still >>>>>>>> probably better to fix it everywhere, so that people who only look at >>>>>>>> a specific term and not all its parents get the non-covalent idea >>>>>>>> clearly. >>>>>>>> >>>>>>>> -Karen >>>>>>>> >>>>>>>> >>>>>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>>>>> >>>>>>>> >>>>>>>>> I actually noticed that the core term, binding, with def of : The >>>>>>>>> selective, often stoichiometric, interaction of a molecule with one >>>>>>>>> or more specific sites on another molecule. >>>>>>>>> is missing the non-covalent idea; fixing it in this term should >>>>>>>>> suffice for it's children >>>>>>>>> >>>>>>>>> >>>>>>>>> The Oxford bible: binding: the act or process by which one molecule >>>>>>>>> attaches to another by noncovalent forces. >>>>>>>>> >>>>>>>>> >>>>>>>>> Valerie Wood wrote: >>>>>>>>> >>>>>>>>>> yes thanks it seems obvious now, although I think I have some rogue >>>>>>>>>> annotations to fix for GPI binding to fix.! This might be obvious >>>>>>>>>> to everyone, but it might be worth adding 'non covalent' to all of >>>>>>>>>> the binding term defs just to emphasise. Its quite clear when you >>>>>>>>>> read the 'RNA trimethylguanosine cap binding def, but I'm not sure >>>>>>>>>> that it is for some of the others. thanks >>>>>>>>>> >>>>>>>>>> val >>>>>>>>>> >>>>>>>>>> >>>>> >>>> >>>> >>> >>> >> >> >> -- >> Alexander Diehl, Ph.D. >> Senior Scientific Curator >> Mouse Genome Informatics >> The Jackson Laboratory >> 600 Main Street >> Bar Harbor, ME 04609 >> >> email: adiehl at informatics.jax.org >> work: +1 (207) 288-6427 >> fax: +1 (207) 288-6131 >> > From jodi at genome.Stanford.EDU Thu Jan 17 08:01:17 2008 From: jodi at genome.Stanford.EDU (Jodi Hirschman) Date: Thu, 17 Jan 2008 11:01:17 -0500 Subject: [annotation] osmosensor - SF 1873095 In-Reply-To: References: Message-ID: <33A4447B-7D1A-4A57-A6F8-799D93076E4A@genome.stanford.edu> Hi, I proposed a definition and added it to the SF item: > https://sourceforge.net/tracker/index.php? > func=detail&aid=1873095&group_id=36855&atid=440764 but I also question whether this term is legit. Seems like BP terms like GO: 47484 'regulation of response to osmotic stress' are better. Jodi On Jan 17, 2008, at 8:38 AM, Midori Harris wrote: > Hi, > > In SF 1873095, Donghui has requested a definition for osmosensor > activity (GO:0005034). Can those who have used this term in > annotations -- MGI, RGD, SGD and TAIR -- suggest anything? I'm even > wondering whether it's a legitimate molecular function term, since > a quick look at PubMed search results indicates that histidine > kinases and adenylyl cyclases (possibly among other things) can be > referred to as "osmosensors". > > This is the SF item: > https://sourceforge.net/tracker/index.php? > func=detail&aid=1873095&group_id=36855&atid=440764 > > These are the gene products currently annotated to GO:0005034: > MGI MGI:1926945 Trpv4 (2 lines in file) > RGD RGD:69337 Trpv4 (2) > SGD S000002828 HKR1 > SGD S000003246 MSB2 > SGD S000000920 SHO1 > SGD S000001409 SLN1 (2) > TAIR gene:3713570 ATHK1 > > Thanks, > Midori From kchris at genome.Stanford.EDU Thu Jan 17 08:04:56 2008 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Thu, 17 Jan 2008 08:04:56 -0800 (PST) Subject: [annotation] RNA trimethylguanosine cap binding query In-Reply-To: References: <478F6AD7.6020509@informatics.jax.org> Message-ID: I see your point. Perhaps the existing term "anchored to external side of plasma membrane" is as far as component should go. To go farther with what type of molecule is used for the anchor, would be the domain of some other ontology. -Karen On Thu, 17 Jan 2008, Midori Harris wrote: > Well, there are myristoyl group anchors too, if I recall correctly. But I'm > not convinced that the type of anchor is really cellular component territory, > so I'm inclined to avoid the more specific term(s) on those grounds. > > m > > On Thu, 17 Jan 2008, Karen Christie wrote: > >> Considering that we already have "anchored to external side of plasma >> membrane", it doesn't seem out of line to make a more specific child term. >> Are there other anchors other than GPI anchors? >> >> -Karen >> >> >> On Thu, 17 Jan 2008, Alexander Diehl wrote: >> >>> Anyone for 'anchored to external side of plasma membrane via GPI anchor' >>> as an is-a child of 'anchored to external side of plasma membrane ; >>> GO:0031362', or even 'anchored to membrane via GPI anchor'? I would be >>> quite happy with this solution, and we could remap the SwissProt keyword >>> 'GPI-anchor'. >>> >>> Thanks, >>> >>> Alex >>> >>> >>> >>> Valerie Wood wrote: >>>> Why don't we obsolete GPI binding and create a new term (it only has 31 >>>> manual annotations which appear to be mainly incorrect), plus the IEA >>>> mappings, which we have already established are wrong. >>>> >>>> I can't think of any other binding term which may have been used >>>> inconsistently in this way. I don't really know why we did this, but as >>>> now see I originally requested the term I will take the blame for >>>> establishing this bad practice. I have an alternative way to curate PTMs >>>> (and I guess most others do) so I'll just reannotate using this method. >>>> It would be useful to have a way to collect PTMs consistently with and >>>> between orgs, but as Karen C said, they don't belong in GO. >>>> >>>> We could then add a comment to all of the other binding terms to say that >>>> they are ONLY intended for non-covalent modifications. >>>> >>>> Would everyone be happy with this? >>>> >>>> Val >>>> >>>> >>>> >>>> >>>> Harold Drabkin wrote: >>>>> To use binding for the creation of a covalent bond is just absolutely >>>>> incorrect. This is just basic undergraduate chemistry. Modifying the >>>>> definition is fine; I would add both statements. However, if anyone has >>>>> used this in this way it is wrong. Those annotations should stricken >>>>> when found. I cannot see any "but". Although we do not obviously have >>>>> the time to revisit each one, in the cases Val found, they should be >>>>> removed; they were incorrect use of the term binding. >>>>> >>>>> >>>>> hjd >>>>> >>>>> Alexander Diehl wrote: >>>>> >>>>>> While I agree that common annotation practice has been to exclude >>>>>> covalent bonds between gene products and other entities (including >>>>>> other proteins), the fact that this has not be specifically excluded by >>>>>> the definition of 1135 MF binding terms suggests to me the there could >>>>>> be in fact be many annotations using these binding terms that include >>>>>> covalent bonds. Per standard GO practice, we should obsolete all 1135 >>>>>> binding terms, provide equivalent, but redefined new binding terms, to >>>>>> force people to reexamine their annotations. >>>>>> >>>>>> Clearly, we are not going to do this. So in fact, I recommend that we >>>>>> do not change the definitions at all, although perhaps we could add a >>>>>> comment like, "Note that binding terms are not intended for annotation >>>>>> of covalent bonds." >>>>>> >>>>>> -- Alex >>>>>> >>>>>> >>>>>> Midori Harris wrote: >>>>>> >>>>>>> Has this gone into SF? (hint, hint) >>>>>>> >>>>>>> should be easy to fix ... >>>>>>> >>>>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>>>> >>>>>>> >>>>>>>> Hopefully a script can be designed to add this as a sentence to the >>>>>>>> end of each definition! >>>>>>>> >>>>>>>> hjd >>>>>>>> >>>>>>>> Karen Christie wrote: >>>>>>>> >>>>>>>>> while you're right that terms inherit from their parents, it's still >>>>>>>>> probably better to fix it everywhere, so that people who only look >>>>>>>>> at a specific term and not all its parents get the non-covalent idea >>>>>>>>> clearly. >>>>>>>>> >>>>>>>>> -Karen >>>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>> I actually noticed that the core term, binding, with def of : >>>>>>>>>> The selective, often stoichiometric, interaction of a molecule with >>>>>>>>>> one or more specific sites on another molecule. >>>>>>>>>> is missing the non-covalent idea; fixing it in this term should >>>>>>>>>> suffice for it's children >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The Oxford bible: binding: the act or process by which one molecule >>>>>>>>>> attaches to another by noncovalent forces. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Valerie Wood wrote: >>>>>>>>>> >>>>>>>>>>> yes thanks it seems obvious now, although I think I have some >>>>>>>>>>> rogue annotations to fix for GPI binding to fix.! This might be >>>>>>>>>>> obvious to everyone, but it might be worth adding 'non covalent' >>>>>>>>>>> to all of the binding term defs just to emphasise. Its quite clear >>>>>>>>>>> when you read the 'RNA trimethylguanosine cap binding def, but I'm >>>>>>>>>>> not sure that it is for some of the others. thanks >>>>>>>>>>> >>>>>>>>>>> val >>>>>>>>>>> >>>>>>>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >>> -- >>> Alexander Diehl, Ph.D. >>> Senior Scientific Curator >>> Mouse Genome Informatics >>> The Jackson Laboratory >>> 600 Main Street >>> Bar Harbor, ME 04609 >>> >>> email: adiehl at informatics.jax.org >>> work: +1 (207) 288-6427 >>> fax: +1 (207) 288-6131 >>> >> > From val at sanger.ac.uk Thu Jan 17 10:46:24 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 17 Jan 2008 18:46:24 UT Subject: [annotation] RNA trimethylguanosine cap binding query Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20080117/4759e9c8/attachment.pl From midori at ebi.ac.uk Mon Jan 21 22:00:05 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 22 Jan 2008 06:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200801220600.m0M605q1260958@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20080122/2e40de8a/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... 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