From midori at ebi.ac.uk Fri Sep 11 04:00:33 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 11 Sep 2009 11:00:33 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200909111100.n8BB0Xgu007245@pigeon.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Tue Sep 15 04:00:38 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 15 Sep 2009 11:00:38 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200909151100.n8FB0cnL006330@pigeon.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Thu Sep 24 04:00:36 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 24 Sep 2009 11:00:36 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200909241100.n8OB0adY000376@pigeon.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Mon Sep 28 04:00:35 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 28 Sep 2009 11:00:35 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200909281100.n8SB0ZD3030128@pigeon.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Tue Sep 29 04:00:38 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 29 Sep 2009 11:00:38 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200909291100.n8TB0c7N016505@pigeon.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Tue Sep 29 07:30:37 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 29 Sep 2009 15:30:37 +0100 (BST) Subject: [Annotation] merging MF and BP terms Message-ID: Hi, We have two SF items in which merging function and process terms looks like a viable solution to a problem. One is an overly-specific, single-step "process" that is essentially equivalent to a "function" (in the GO sense); the other is a "function" term that is defined such that it doesn't describe a single activity, and is essentially the same as a process term. SF 2864212 - merge MF term RNA splicing factor activity, transesterification mechanism GO:0031202 into BP term RNA splicing, via transesterification reactions GO:0000375 For this one, we would merge the MF term into the BP term, and ensure that the merged term has is_a ancestry in the BP graph. I think that's all we would change. https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 SF 2864271 - merge BP term conversion of met-tRNAf to fmet-tRNA GO:0001718 into MF term methionyl-tRNA formyltransferase activity GO:0004479 https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 In this case, the proposal is to merge the process term into the function term, ensuring that the merged term has is_a ancestry only in the MF ontology,and has a part_of link to a process term. Specifically, the merged term would retain the name and ID from GO:0004479, and would be part_of translational initiation GO:0006413. Does anyone have any objections or other comments on these? thanks, m From dph at informatics.jax.org Tue Sep 29 07:40:22 2009 From: dph at informatics.jax.org (David Hill) Date: Tue, 29 Sep 2009 10:40:22 -0400 Subject: [Annotation] merging MF and BP terms In-Reply-To: References: Message-ID: <4AC21C56.8090208@informatics.jax.org> I just checked these out. This seems fine. In the first case, what would be the functions that are executed in the process 'RNA splicing, via transesterification reactions'? David Midori Harris wrote: > Hi, > > We have two SF items in which merging function and process terms looks > like a viable solution to a problem. One is an overly-specific, > single-step "process" that is essentially equivalent to a "function" > (in the GO sense); the other is a "function" term that is defined such > that it doesn't describe a single activity, and is essentially the > same as a process term. > > SF 2864212 - merge MF term > RNA splicing factor activity, transesterification mechanism GO:0031202 > > into BP term > RNA splicing, via transesterification reactions GO:0000375 > > For this one, we would merge the MF term into the BP term, and ensure > that the merged term has is_a ancestry in the BP graph. I think that's > all we would change. > > https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 > > > > SF 2864271 - merge BP term > > conversion of met-tRNAf to fmet-tRNA GO:0001718 > > into MF term > methionyl-tRNA formyltransferase activity GO:0004479 > > https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 > > > In this case, the proposal is to merge the process term into the > function term, ensuring that the merged term has is_a ancestry only in > the MF ontology,and has a part_of link to a process term. > Specifically, the merged term would retain the name and ID from > GO:0004479, and would be part_of translational initiation GO:0006413. > > Does anyone have any objections or other comments on these? > > thanks, > m > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation -- David P. Hill, Ph.D. Bioinformatics Scientist: Ontology Development Gene Ontology Consortium The Jackson Laboratory www.geneontology.org www.informatics.jax.org tel:207-288-6430 From midori at ebi.ac.uk Tue Sep 29 07:46:19 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 29 Sep 2009 15:46:19 +0100 (BST) Subject: [Annotation] merging MF and BP terms In-Reply-To: <4AC21C56.8090208@informatics.jax.org> References: <4AC21C56.8090208@informatics.jax.org> Message-ID: I think they would be the reactions described by the two is_a children of GO:0031202, 'first spliceosomal transesterification activity' (GO:0000384) and 'second spliceosomal transesterification activity' (GO:0000386). Karen C will know for sure. An alternative for the splicing case might be to alter the definition of GO:0031202, to something more activity-ish. Maybe "catalysis of either of the transesterification reactions that take place as part of spliceosomal mRNA splicing"? m On Tue, 29 Sep 2009, David Hill wrote: > I just checked these out. This seems fine. In the first case, what would be > the functions that are executed in the process 'RNA splicing, via > transesterification reactions'? > > David > > Midori Harris wrote: >> Hi, >> >> We have two SF items in which merging function and process terms looks like >> a viable solution to a problem. One is an overly-specific, single-step >> "process" that is essentially equivalent to a "function" (in the GO sense); >> the other is a "function" term that is defined such that it doesn't >> describe a single activity, and is essentially the same as a process term. >> >> SF 2864212 - merge MF term >> RNA splicing factor activity, transesterification mechanism GO:0031202 >> >> into BP term >> RNA splicing, via transesterification reactions GO:0000375 >> >> For this one, we would merge the MF term into the BP term, and ensure that >> the merged term has is_a ancestry in the BP graph. I think that's all we >> would change. >> >> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >> >> >> SF 2864271 - merge BP term >> >> conversion of met-tRNAf to fmet-tRNA GO:0001718 >> >> into MF term >> methionyl-tRNA formyltransferase activity GO:0004479 >> >> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >> >> In this case, the proposal is to merge the process term into the function >> term, ensuring that the merged term has is_a ancestry only in the MF >> ontology,and has a part_of link to a process term. Specifically, the merged >> term would retain the name and ID from GO:0004479, and would be part_of >> translational initiation GO:0006413. >> >> Does anyone have any objections or other comments on these? >> >> thanks, >> m >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation > > From dph at informatics.jax.org Tue Sep 29 07:53:28 2009 From: dph at informatics.jax.org (David Hill) Date: Tue, 29 Sep 2009 10:53:28 -0400 Subject: [Annotation] merging MF and BP terms In-Reply-To: References: <4AC21C56.8090208@informatics.jax.org> Message-ID: <4AC21F68.5010803@informatics.jax.org> Great, this makes sense. Those 2 is_a children should become part_of children of the process as long as they are only executed in this process. this would follow from the merge. David Midori Harris wrote: > I think they would be the reactions described by the two is_a children > of GO:0031202, 'first spliceosomal transesterification activity' > (GO:0000384) and 'second spliceosomal transesterification activity' > (GO:0000386). Karen C will know for sure. > > An alternative for the splicing case might be to alter the definition > of GO:0031202, to something more activity-ish. Maybe "catalysis of > either of the transesterification reactions that take place as part of > spliceosomal mRNA splicing"? > > m > > On Tue, 29 Sep 2009, David Hill wrote: > >> I just checked these out. This seems fine. In the first case, what >> would be the functions that are executed in the process 'RNA >> splicing, via transesterification reactions'? >> >> David >> >> Midori Harris wrote: >>> Hi, >>> >>> We have two SF items in which merging function and process terms >>> looks like a viable solution to a problem. One is an >>> overly-specific, single-step "process" that is essentially >>> equivalent to a "function" (in the GO sense); the other is a >>> "function" term that is defined such that it doesn't describe a >>> single activity, and is essentially the same as a process term. >>> >>> SF 2864212 - merge MF term >>> RNA splicing factor activity, transesterification mechanism >>> GO:0031202 >>> >>> into BP term >>> RNA splicing, via transesterification reactions GO:0000375 >>> >>> For this one, we would merge the MF term into the BP term, and >>> ensure that the merged term has is_a ancestry in the BP graph. I >>> think that's all we would change. >>> >>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >>> >>> >>> SF 2864271 - merge BP term >>> >>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>> >>> into MF term >>> methionyl-tRNA formyltransferase activity GO:0004479 >>> >>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >>> >>> In this case, the proposal is to merge the process term into the >>> function term, ensuring that the merged term has is_a ancestry only >>> in the MF ontology,and has a part_of link to a process term. >>> Specifically, the merged term would retain the name and ID from >>> GO:0004479, and would be part_of translational initiation GO:0006413. >>> >>> Does anyone have any objections or other comments on these? >>> >>> thanks, >>> m >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >> >> -- David P. Hill, Ph.D. Bioinformatics Scientist: Ontology Development Gene Ontology Consortium The Jackson Laboratory www.geneontology.org www.informatics.jax.org tel:207-288-6430 From midori at ebi.ac.uk Tue Sep 29 07:56:42 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 29 Sep 2009 15:56:42 +0100 (BST) Subject: [Annotation] merging MF and BP terms In-Reply-To: <4AC21F68.5010803@informatics.jax.org> References: <4AC21C56.8090208@informatics.jax.org> <4AC21F68.5010803@informatics.jax.org> Message-ID: Yep, the way the 2 children are named and defined is completely consistent with making them part_of the appropriate splicing BP term. m On Tue, 29 Sep 2009, David Hill wrote: > Great, this makes sense. Those 2 is_a children should become part_of children > of the process as long as they are only executed in this process. this would > follow from the merge. > > David > > Midori Harris wrote: >> I think they would be the reactions described by the two is_a children of >> GO:0031202, 'first spliceosomal transesterification activity' (GO:0000384) >> and 'second spliceosomal transesterification activity' (GO:0000386). Karen >> C will know for sure. >> >> An alternative for the splicing case might be to alter the definition of >> GO:0031202, to something more activity-ish. Maybe "catalysis of either of >> the transesterification reactions that take place as part of spliceosomal >> mRNA splicing"? >> >> m >> >> On Tue, 29 Sep 2009, David Hill wrote: >> >>> I just checked these out. This seems fine. In the first case, what would >>> be the functions that are executed in the process 'RNA splicing, via >>> transesterification reactions'? >>> >>> David >>> >>> Midori Harris wrote: >>>> Hi, >>>> >>>> We have two SF items in which merging function and process terms looks >>>> like a viable solution to a problem. One is an overly-specific, >>>> single-step "process" that is essentially equivalent to a "function" (in >>>> the GO sense); the other is a "function" term that is defined such that >>>> it doesn't describe a single activity, and is essentially the same as a >>>> process term. >>>> >>>> SF 2864212 - merge MF term >>>> RNA splicing factor activity, transesterification mechanism GO:0031202 >>>> >>>> into BP term >>>> RNA splicing, via transesterification reactions GO:0000375 >>>> >>>> For this one, we would merge the MF term into the BP term, and ensure >>>> that the merged term has is_a ancestry in the BP graph. I think that's >>>> all we would change. >>>> >>>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >>>> >>>> SF 2864271 - merge BP term >>>> >>>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>>> >>>> into MF term >>>> methionyl-tRNA formyltransferase activity GO:0004479 >>>> >>>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >>>> In this case, the proposal is to merge the process term into the function >>>> term, ensuring that the merged term has is_a ancestry only in the MF >>>> ontology,and has a part_of link to a process term. Specifically, the >>>> merged term would retain the name and ID from GO:0004479, and would be >>>> part_of translational initiation GO:0006413. >>>> >>>> Does anyone have any objections or other comments on these? >>>> >>>> thanks, >>>> m >>>> _______________________________________________ >>>> Annotation mailing list >>>> Annotation at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> >>> > > From kchris at genome.stanford.edu Tue Sep 29 09:00:31 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Tue, 29 Sep 2009 09:00:31 -0700 (PDT) Subject: [Annotation] [Ontology-editors] merging MF and BP terms In-Reply-To: References: <4AC21C56.8090208@informatics.jax.org> <4AC21F68.5010803@informatics.jax.org> Message-ID: I'm looking at the graph of the function ontology: - molecular_function -- catalytic activity --- RNA splicing factor activity, transesterification mechanism ---- first spliceosomal transesterification activity ---- second spliceosomal transesterification activity and I'm wondering whether or not we need a grouping term for the two different catalytic activities of the spliceosome. Perhaps, it is better if there is not, so that if you only know that a gene product contributes to splicing, but not which reaction(s) it is specifically involved in/required for, then you only make a process annotation and give it "molecular_function" [unknown] for its function annotation. -Karen On Tue, 29 Sep 2009, Midori Harris wrote: > Yep, the way the 2 children are named and defined is completely consistent > with making them part_of the appropriate splicing BP term. > > m > > On Tue, 29 Sep 2009, David Hill wrote: > >> Great, this makes sense. Those 2 is_a children should become part_of >> children of the process as long as they are only executed in this process. >> this would follow from the merge. >> >> David >> >> Midori Harris wrote: >>> I think they would be the reactions described by the two is_a children of >>> GO:0031202, 'first spliceosomal transesterification activity' (GO:0000384) >>> and 'second spliceosomal transesterification activity' (GO:0000386). Karen >>> C will know for sure. >>> >>> An alternative for the splicing case might be to alter the definition of >>> GO:0031202, to something more activity-ish. Maybe "catalysis of either of >>> the transesterification reactions that take place as part of spliceosomal >>> mRNA splicing"? >>> >>> m >>> >>> On Tue, 29 Sep 2009, David Hill wrote: >>> >>>> I just checked these out. This seems fine. In the first case, what would >>>> be the functions that are executed in the process 'RNA splicing, via >>>> transesterification reactions'? >>>> >>>> David >>>> >>>> Midori Harris wrote: >>>>> Hi, >>>>> >>>>> We have two SF items in which merging function and process terms looks >>>>> like a viable solution to a problem. One is an overly-specific, >>>>> single-step "process" that is essentially equivalent to a "function" (in >>>>> the GO sense); the other is a "function" term that is defined such that >>>>> it doesn't describe a single activity, and is essentially the same as a >>>>> process term. >>>>> >>>>> SF 2864212 - merge MF term >>>>> RNA splicing factor activity, transesterification mechanism GO:0031202 >>>>> >>>>> into BP term >>>>> RNA splicing, via transesterification reactions GO:0000375 >>>>> >>>>> For this one, we would merge the MF term into the BP term, and ensure >>>>> that the merged term has is_a ancestry in the BP graph. I think that's >>>>> all we would change. >>>>> >>>>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >>>>> SF 2864271 - merge BP term >>>>> >>>>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>>>> >>>>> into MF term >>>>> methionyl-tRNA formyltransferase activity GO:0004479 >>>>> >>>>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >>>>> In this case, the proposal is to merge the process term into the >>>>> function term, ensuring that the merged term has is_a ancestry only in >>>>> the MF ontology,and has a part_of link to a process term. Specifically, >>>>> the merged term would retain the name and ID from GO:0004479, and would >>>>> be part_of translational initiation GO:0006413. >>>>> >>>>> Does anyone have any objections or other comments on these? >>>>> >>>>> thanks, >>>>> m >>>>> _______________________________________________ >>>>> Annotation mailing list >>>>> Annotation at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>> >>>> >> >> > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > From tberardi at acoma.stanford.edu Tue Sep 29 10:30:16 2009 From: tberardi at acoma.stanford.edu (Tanya Berardini) Date: Tue, 29 Sep 2009 10:30:16 -0700 Subject: [Annotation] [Ontology-editors] merging MF and BP terms In-Reply-To: References: <4AC21C56.8090208@informatics.jax.org> <4AC21F68.5010803@informatics.jax.org> Message-ID: <8e22ab960909291030v68447629td1fe0cb91d83b280@mail.gmail.com> On Tue, Sep 29, 2009 at 9:00 AM, Karen Christie wrote: > I'm looking at the graph of the function ontology: > > - molecular_function > -- catalytic activity > --- RNA splicing factor activity, transesterification mechanism > ---- first spliceosomal transesterification activity > ---- second spliceosomal transesterification activity > > and I'm wondering whether or not we need a grouping term for the two > different catalytic activities of the spliceosome. > Perhaps, it is better if there is not, so that if you only know that a gene > product contributes to splicing, but not which reaction(s) it is > specifically involved in/required for, then you only make a process > annotation and give it "molecular_function" [unknown] for its function > annotation. > Yes, I think this is appropriate especially since the two transesterification reactions are different. Tanya > > -Karen > > > > > On Tue, 29 Sep 2009, Midori Harris wrote: > > Yep, the way the 2 children are named and defined is completely consistent >> with making them part_of the appropriate splicing BP term. >> >> m >> >> On Tue, 29 Sep 2009, David Hill wrote: >> >> Great, this makes sense. Those 2 is_a children should become part_of >>> children of the process as long as they are only executed in this process. >>> this would follow from the merge. >>> >>> David >>> >>> Midori Harris wrote: >>> >>>> I think they would be the reactions described by the two is_a children >>>> of GO:0031202, 'first spliceosomal transesterification activity' >>>> (GO:0000384) and 'second spliceosomal transesterification activity' >>>> (GO:0000386). Karen C will know for sure. >>>> >>>> An alternative for the splicing case might be to alter the definition of >>>> GO:0031202, to something more activity-ish. Maybe "catalysis of either of >>>> the transesterification reactions that take place as part of spliceosomal >>>> mRNA splicing"? >>>> >>>> m >>>> >>>> On Tue, 29 Sep 2009, David Hill wrote: >>>> >>>> I just checked these out. This seems fine. In the first case, what >>>>> would be the functions that are executed in the process 'RNA splicing, via >>>>> transesterification reactions'? >>>>> >>>>> David >>>>> >>>>> Midori Harris wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> We have two SF items in which merging function and process terms looks >>>>>> like a viable solution to a problem. One is an overly-specific, single-step >>>>>> "process" that is essentially equivalent to a "function" (in the GO sense); >>>>>> the other is a "function" term that is defined such that it doesn't describe >>>>>> a single activity, and is essentially the same as a process term. >>>>>> >>>>>> SF 2864212 - merge MF term >>>>>> RNA splicing factor activity, transesterification mechanism >>>>>> GO:0031202 >>>>>> >>>>>> into BP term >>>>>> RNA splicing, via transesterification reactions GO:0000375 >>>>>> >>>>>> For this one, we would merge the MF term into the BP term, and ensure >>>>>> that the merged term has is_a ancestry in the BP graph. I think that's all >>>>>> we would change. >>>>>> >>>>>> >>>>>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764SF 2864271 - merge BP term >>>>>> >>>>>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>>>>> >>>>>> into MF term >>>>>> methionyl-tRNA formyltransferase activity GO:0004479 >>>>>> >>>>>> >>>>>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764In this case, the proposal is to merge the process term into the function >>>>>> term, ensuring that the merged term has is_a ancestry only in the MF >>>>>> ontology,and has a part_of link to a process term. Specifically, the merged >>>>>> term would retain the name and ID from GO:0004479, and would be part_of >>>>>> translational initiation GO:0006413. >>>>>> >>>>>> Does anyone have any objections or other comments on these? >>>>>> >>>>>> thanks, >>>>>> m >>>>>> _______________________________________________ >>>>>> Annotation mailing list >>>>>> Annotation at geneontology.org >>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>>>> >>>>> >>>>> >>>>> >>> >>> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> >> _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > -- Tanya Berardini TAIR Curator www.arabidopsis.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From alanruttenberg at gmail.com Tue Sep 29 10:52:53 2009 From: alanruttenberg at gmail.com (Alan Ruttenberg) Date: Tue, 29 Sep 2009 13:52:53 -0400 Subject: [Annotation] merging MF and BP terms In-Reply-To: References: Message-ID: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> The problem is that this still confuses function with process. Functions are the things that the enzymes (using the term broadly) have that make the processes happen. If one goes into more detail, there are a variety of participants in the process (substrates, products, "cofactors"), but only one bearer of the function in a particular process. Every function has a corresponding process, its "realization". Functions are not parts of processes. The realizations of functions are. The functions have a physical basis in the structure of their bearers. The functions exist before any process happens. A molecule may have a function but never actually realize it. These distinctions have important consequences as people such as myself work on adding more detail to the GO. The processes get more detail by adding *participants*. Within those processes, when there is a molecule like an enzyme that functions in a particular way, it needs to be distinguished from the other participants in some way. The way that it is distinguished is by saying it bears a function. The heuristic that a molecular function is a "single step" process is misused, IMO. That it is a "single step" derives from the fact that in such descriptions there is a single molecule that has a function. The step is the process that surrounds execution of that function. As I said, getting this distinction clear is essential for future detailing of GO processes such as I and others do. Can we start to get this right here and now? -Alan On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris wrote: > Hi, > > We have two SF items in which merging function and process terms looks like > a viable solution to a problem. One is an overly-specific, single-step > "process" that is essentially equivalent to a "function" (in the GO sense); > the other is a "function" term that is defined such that it doesn't describe > a single activity, and is essentially the same as a process term. > > SF 2864212 - merge MF term > RNA splicing factor activity, transesterification mechanism GO:0031202 > > into BP term > RNA splicing, via transesterification reactions GO:0000375 > > For this one, we would merge the MF term into the BP term, and ensure that > the merged term has is_a ancestry in the BP graph. I think that's all we > would change. > > > https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 > > > SF 2864271 - merge BP term > > conversion of met-tRNAf to fmet-tRNA GO:0001718 > > into MF term > methionyl-tRNA formyltransferase activity GO:0004479 > > > https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 > > In this case, the proposal is to merge the process term into the function > term, ensuring that the merged term has is_a ancestry only in the MF > ontology,and has a part_of link to a process term. Specifically, the merged > term would retain the name and ID from GO:0004479, and would be part_of > translational initiation GO:0006413. > > Does anyone have any objections or other comments on these? > > thanks, > m > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > -------------- next part -------------- An HTML attachment was scrubbed... URL: From kchris at genome.stanford.edu Tue Sep 29 11:18:05 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Tue, 29 Sep 2009 11:18:05 -0700 (PDT) Subject: [Annotation] merging MF and BP terms In-Reply-To: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> References: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> Message-ID: I'd like to know you deal with multisubunit enzymes, where no one particular gene product has the catalytic activity. -Karen On Tue, 29 Sep 2009, Alan Ruttenberg wrote: > The problem is that this still confuses function with process. Functions are > the things that the enzymes (using the term broadly) have that make the > processes happen. If one goes into more detail, there are a variety of > participants in the process (substrates, products, "cofactors"), but only > one bearer of the function in a particular process. > Every function has a corresponding process, its "realization". > > Functions are not parts of processes. The realizations of functions are. > > The functions have a physical basis in the structure of their bearers. > > The functions exist before any process happens. A molecule may have a > function but never actually realize it. > > These distinctions have important consequences as people such as myself work > on adding more detail to the GO. The processes get more detail by adding > *participants*. Within those processes, when there is a molecule like an > enzyme that functions in a particular way, it needs to be distinguished from > the other participants in some way. The way that it is distinguished is by > saying it bears a function. > > The heuristic that a molecular function is a "single step" process is > misused, IMO. That it is a "single step" derives from the fact that in such > descriptions there is a single molecule that has a function. The step is the > process that surrounds execution of that function. > > As I said, getting this distinction clear is essential for future detailing > of GO processes such as I and others do. Can we start to get this right here > and now? > > -Alan > > > > On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris wrote: > >> Hi, >> >> We have two SF items in which merging function and process terms looks like >> a viable solution to a problem. One is an overly-specific, single-step >> "process" that is essentially equivalent to a "function" (in the GO sense); >> the other is a "function" term that is defined such that it doesn't describe >> a single activity, and is essentially the same as a process term. >> >> SF 2864212 - merge MF term >> RNA splicing factor activity, transesterification mechanism GO:0031202 >> >> into BP term >> RNA splicing, via transesterification reactions GO:0000375 >> >> For this one, we would merge the MF term into the BP term, and ensure that >> the merged term has is_a ancestry in the BP graph. I think that's all we >> would change. >> >> >> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >> >> >> SF 2864271 - merge BP term >> >> conversion of met-tRNAf to fmet-tRNA GO:0001718 >> >> into MF term >> methionyl-tRNA formyltransferase activity GO:0004479 >> >> >> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >> >> In this case, the proposal is to merge the process term into the function >> term, ensuring that the merged term has is_a ancestry only in the MF >> ontology,and has a part_of link to a process term. Specifically, the merged >> term would retain the name and ID from GO:0004479, and would be part_of >> translational initiation GO:0006413. >> >> Does anyone have any objections or other comments on these? >> >> thanks, >> m >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> > From Judith.Blake at jax.org Tue Sep 29 11:38:09 2009 From: Judith.Blake at jax.org (Judith Blake) Date: Tue, 29 Sep 2009 14:38:09 -0400 Subject: [Annotation] merging MF and BP terms In-Reply-To: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> Message-ID: Functions are occurrants. A function describes an action, biochemical, structural, whatever. Functions are part of processes. A variety of structures, encoded in a molecule, have the potential to realize a function. That is a property of the molecule, not of the function. A molecule can have encoded the potential of engaging in several functions. The confusion I think is that of the relationship between the gene product and a molecular function, and the molecular function and the biological process. Judy On 9/29/09 1:52 PM, "Alan Ruttenberg" wrote: The problem is that this still confuses function with process. Functions are the things that the enzymes (using the term broadly) have that make the processes happen. If one goes into more detail, there are a variety of participants in the process (substrates, products, "cofactors"), but only one bearer of the function in a particular process. Every function has a corresponding process, its "realization". Functions are not parts of processes. The realizations of functions are. The functions have a physical basis in the structure of their bearers. The functions exist before any process happens. A molecule may have a function but never actually realize it. These distinctions have important consequences as people such as myself work on adding more detail to the GO. The processes get more detail by adding *participants*. Within those processes, when there is a molecule like an enzyme that functions in a particular way, it needs to be distinguished from the other participants in some way. The way that it is distinguished is by saying it bears a function. The heuristic that a molecular function is a "single step" process is misused, IMO. That it is a "single step" derives from the fact that in such descriptions there is a single molecule that has a function. The step is the process that surrounds execution of that function. As I said, getting this distinction clear is essential for future detailing of GO processes such as I and others do. Can we start to get this right here and now? -Alan On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris wrote: Hi, We have two SF items in which merging function and process terms looks like a viable solution to a problem. One is an overly-specific, single-step "process" that is essentially equivalent to a "function" (in the GO sense); the other is a "function" term that is defined such that it doesn't describe a single activity, and is essentially the same as a process term. SF 2864212 - merge MF term RNA splicing factor activity, transesterification mechanism GO:0031202 into BP term RNA splicing, via transesterification reactions GO:0000375 For this one, we would merge the MF term into the BP term, and ensure that the merged term has is_a ancestry in the BP graph. I think that's all we would change. https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 SF 2864271 - merge BP term conversion of met-tRNAf to fmet-tRNA GO:0001718 into MF term methionyl-tRNA formyltransferase activity GO:0004479 https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 In this case, the proposal is to merge the process term into the function term, ensuring that the merged term has is_a ancestry only in the MF ontology,and has a part_of link to a process term. Specifically, the merged term would retain the name and ID from GO:0004479, and would be part_of translational initiation GO:0006413. Does anyone have any objections or other comments on these? thanks, m _______________________________________________ Annotation mailing list Annotation at geneontology.org http://fafner.stanford.edu/mailman/listinfo/annotation -------------- next part -------------- An HTML attachment was scrubbed... URL: From alanruttenberg at gmail.com Tue Sep 29 11:45:59 2009 From: alanruttenberg at gmail.com (Alan Ruttenberg) Date: Tue, 29 Sep 2009 14:45:59 -0400 Subject: [Annotation] merging MF and BP terms In-Reply-To: References: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> Message-ID: <29af5e2d0909291145p1e2af1d4q2e94a2a49103a130@mail.gmail.com> On Tue, Sep 29, 2009 at 2:38 PM, Judith Blake wrote: > > Functions are occurrants. A function describes an action, biochemical, > structural, whatever. > A function doesn't describe anything. Information artifact describe things. Sorry to be picky about words. It's my job. If you look at the papers on BFO you will see that functions are continuants and occurrents are disjoint from continuants. So functions are not occurrents. If the GO is using terminology at odds with BFO that needs to be fixed - we agreed at the last foundry meeting that we were all going to use a common upper level ontology. > > Functions are part of processes. > Function*ings* (i.e. realizations of functions) are part of processes. > > A variety of structures, encoded in a molecule, have the potential to > realize a function. > Type error: processes don't have potential. (concluded by substitution "potential to realize a function" + function is_a process => "potential to realize a process". The error is that it is the functions that are the potentials. Potentials are realized. The realizations are processes. We discussed this very recently with Michael and he agreed. > That is a property of the molecule, not of the function. > What is the reference of "That"? > A molecule can have encoded the potential of engaging in several > functions. > Absolutely. (as long as you rewrite "functions" -> "functionings" (i.e. processes).) A molecule can bear multiple functions is the way we would say this. The confusion I think is that of the relationship between the gene product > and a molecular function, and the molecular function and the biological > process. > And what do you say these are. I (and BFO) are clear: The relation between a molecular function and a gene product is "inheres". The relation between molecular function and a biological process is "realized_by". -Alan > > Judy > > > > > On 9/29/09 1:52 PM, "Alan Ruttenberg" wrote: > > The problem is that this still confuses function with process. Functions > are the things that the enzymes (using the term broadly) have that make the > processes happen. If one goes into more detail, there are a variety of > participants in the process (substrates, products, "cofactors"), but only > one bearer of the function in a particular process. > > Every function has a corresponding process, its "realization". > > Functions are not parts of processes. The realizations of functions are. > > The functions have a physical basis in the structure of their bearers. > > The functions exist before any process happens. A molecule may have a > function but never actually realize it. > > These distinctions have important consequences as people such as myself > work on adding more detail to the GO. The processes get more detail by > adding *participants*. Within those processes, when there is a molecule like > an enzyme that functions in a particular way, it needs to be distinguished > from the other participants in some way. The way that it is distinguished is > by saying it bears a function. > > The heuristic that a molecular function is a "single step" process is > misused, IMO. That it is a "single step" derives from the fact that in such > descriptions there is a single molecule that has a function. The step is the > process that surrounds execution of that function. > > As I said, getting this distinction clear is essential for future detailing > of GO processes such as I and others do. Can we start to get this right here > and now? > > -Alan > > > > On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris wrote: > > Hi, > > We have two SF items in which merging function and process terms looks like > a viable solution to a problem. One is an overly-specific, single-step > "process" that is essentially equivalent to a "function" (in the GO sense); > the other is a "function" term that is defined such that it doesn't describe > a single activity, and is essentially the same as a process term. > > SF 2864212 - merge MF term > RNA splicing factor activity, transesterification mechanism GO:0031202 > > into BP term > RNA splicing, via transesterification reactions GO:0000375 > > For this one, we would merge the MF term into the BP term, and ensure that > the merged term has is_a ancestry in the BP graph. I think that's all we > would change. > > > https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 > > > SF 2864271 - merge BP term > > conversion of met-tRNAf to fmet-tRNA GO:0001718 > > into MF term > methionyl-tRNA formyltransferase activity GO:0004479 > > > https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 > > In this case, the proposal is to merge the process term into the function > term, ensuring that the merged term has is_a ancestry only in the MF > ontology,and has a part_of link to a process term. Specifically, the merged > term would retain the name and ID from GO:0004479, and would be part_of > translational initiation GO:0006413. > > Does anyone have any objections or other comments on these? > > thanks, > m > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alanruttenberg at gmail.com Tue Sep 29 11:39:30 2009 From: alanruttenberg at gmail.com (Alan Ruttenberg) Date: Tue, 29 Sep 2009 14:39:30 -0400 Subject: [Annotation] merging MF and BP terms In-Reply-To: References: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> Message-ID: <29af5e2d0909291139n125fe58bpfdc59b449affa481@mail.gmail.com> On Tue, Sep 29, 2009 at 2:18 PM, Karen Christie wrote: > I'd like to know you deal with multisubunit enzymes, where no one > particular gene product has the catalytic activity. > I think that the function is then ascribed to either the complex as a whole, or to the part of the complex that is responsible for the activity. The schema is: Complex has_part protein 1 has_part protein 2 ... Complex bears function (reverse function inheres in complex) function realized in process which implies: Complex participates in process. In addition, typically there will be other participants in the process. For example the mRNA that is being spliced. If we are at the point where we need to argue about which part of the complex bears the function then we are in good shape. -Alan > -Karen > > > > On Tue, 29 Sep 2009, Alan Ruttenberg wrote: > > The problem is that this still confuses function with process. Functions >> are >> the things that the enzymes (using the term broadly) have that make the >> processes happen. If one goes into more detail, there are a variety of >> participants in the process (substrates, products, "cofactors"), but only >> one bearer of the function in a particular process. >> Every function has a corresponding process, its "realization". >> >> Functions are not parts of processes. The realizations of functions are. >> >> The functions have a physical basis in the structure of their bearers. >> >> The functions exist before any process happens. A molecule may have a >> function but never actually realize it. >> >> These distinctions have important consequences as people such as myself >> work >> on adding more detail to the GO. The processes get more detail by adding >> *participants*. Within those processes, when there is a molecule like an >> enzyme that functions in a particular way, it needs to be distinguished >> from >> the other participants in some way. The way that it is distinguished is by >> saying it bears a function. >> >> The heuristic that a molecular function is a "single step" process is >> misused, IMO. That it is a "single step" derives from the fact that in >> such >> descriptions there is a single molecule that has a function. The step is >> the >> process that surrounds execution of that function. >> >> As I said, getting this distinction clear is essential for future >> detailing >> of GO processes such as I and others do. Can we start to get this right >> here >> and now? >> >> -Alan >> >> >> >> On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris wrote: >> >> Hi, >>> >>> We have two SF items in which merging function and process terms looks >>> like >>> a viable solution to a problem. One is an overly-specific, single-step >>> "process" that is essentially equivalent to a "function" (in the GO >>> sense); >>> the other is a "function" term that is defined such that it doesn't >>> describe >>> a single activity, and is essentially the same as a process term. >>> >>> SF 2864212 - merge MF term >>> RNA splicing factor activity, transesterification mechanism GO:0031202 >>> >>> into BP term >>> RNA splicing, via transesterification reactions GO:0000375 >>> >>> For this one, we would merge the MF term into the BP term, and ensure >>> that >>> the merged term has is_a ancestry in the BP graph. I think that's all we >>> would change. >>> >>> >>> >>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >>> >>> >>> SF 2864271 - merge BP term >>> >>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>> >>> into MF term >>> methionyl-tRNA formyltransferase activity GO:0004479 >>> >>> >>> >>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >>> >>> In this case, the proposal is to merge the process term into the function >>> term, ensuring that the merged term has is_a ancestry only in the MF >>> ontology,and has a part_of link to a process term. Specifically, the >>> merged >>> term would retain the name and ID from GO:0004479, and would be part_of >>> translational initiation GO:0006413. >>> >>> Does anyone have any objections or other comments on these? >>> >>> thanks, >>> m >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From cherry at stanford.edu Tue Sep 29 12:55:56 2009 From: cherry at stanford.edu (cherry at stanford.edu) Date: Tue, 29 Sep 2009 12:55:56 -0700 (PDT) Subject: [Annotation] Gene Ontology Email lists unavailable Oct 2nd Message-ID: <200909291955.n8TJtuM6025452@fafner.Stanford.EDU> The mailserver that provides the Gene Ontology mailing lists will be down this weekend. All lists and the web site for the mailing lists will be unavailable from noon (Pacific) October 2nd and back before noon (Pacific) October 4rd. You are subscribed to the one of the GOC lists. I apologize for the trouble if you receive this message more than once. All subscriptions to all lists are being sent this message. If you happen to send an email during the down time you do not need to send the message again. It is normal for mailservers to keep trying for five days. Your message will simply be delayed. The main GO web sites and tools are not affected and will be available. Cheers, Mike Cherry From kchris at genome.stanford.edu Tue Sep 29 15:11:20 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Tue, 29 Sep 2009 15:11:20 -0700 (PDT) Subject: [Annotation] merging MF and BP terms In-Reply-To: <29af5e2d0909291139n125fe58bpfdc59b449affa481@mail.gmail.com> References: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> <29af5e2d0909291139n125fe58bpfdc59b449affa481@mail.gmail.com> Message-ID: These two function terms were created with the intent to represent the two catalytic activites that occur in large spliceosomal complexes. Based on the current understanding, I would ascribe these functions to a complex as a whole. There is not yet evidence that would allow ascribing either catalytic activity to a smaller portion of either relevant complex and they're certainly not catalyzed by a single gene product. We have recently revised the component ontology and now also represent the two specific complexes that carry out each of these two catalytic activities, these two terms and their child terms: - catalytic step 1 spliceosome - catalytic step 2 spliceosome In process, we have these terms: - generation of catalytic spliceosome for first transesterification step - generation of catalytic spliceosome for second transesterification step So, I think we are doing this (splicing) right (finally). In process, we represent the big picture, including some specific stages like generation of particular complexes in the cycle. In complex, we represent the various identifiable complexes that researchers recognize. In function, we represent only the two catalytic activities. As named/phrased, the existing function grouping term directly above the two specific function terms (first/second spliceosomal transesterification activity) basically just means "be involved with splicing", which I agree is equivalent to the existing process term. So, I agree that the current function term (GO:0031202) should be merged into the corresponding process term, as proposed. If we do need a grouping term in the function ontology for these two function terms, it should be a generalized function, something like "transesterification activity", not something process specific as the current one is. -Karen P.S. In terms of proceeding with this, we'll need to make sure we give annotation groups an appropriate heads up since there will no function term that has an equivalent meaning where you could do a direct replace. The two child terms of GO:0031202 are more specific. Thus reannotation will require reading for each gene to determine whether to annotate to either of these two specific terms or to the root node for function. I think it would be appropriate to have a longer lead time than two weeks to allow groups to work on this before essentially removing the term from function. SGD has about 60 genes annotated to this term, excluding computational annotations. On Tue, 29 Sep 2009, Alan Ruttenberg wrote: > On Tue, Sep 29, 2009 at 2:18 PM, Karen Christie > wrote: > >> I'd like to know you deal with multisubunit enzymes, where no one >> particular gene product has the catalytic activity. >> > > I think that the function is then ascribed to either the complex as a whole, > or to the part of the complex that is responsible for the activity. > > The schema is: > > Complex > has_part protein 1 > has_part protein 2 > ... > > Complex bears function (reverse function inheres in complex) > > function realized in process > > which implies: > > Complex participates in process. > > In addition, typically there will be other participants in the process. For > example the mRNA that is being spliced. > > If we are at the point where we need to argue about which part of the > complex bears the function then we are in good shape. > > -Alan > > > >> -Karen >> >> >> >> On Tue, 29 Sep 2009, Alan Ruttenberg wrote: >> >> The problem is that this still confuses function with process. Functions >>> are >>> the things that the enzymes (using the term broadly) have that make the >>> processes happen. If one goes into more detail, there are a variety of >>> participants in the process (substrates, products, "cofactors"), but only >>> one bearer of the function in a particular process. >>> Every function has a corresponding process, its "realization". >>> >>> Functions are not parts of processes. The realizations of functions are. >>> >>> The functions have a physical basis in the structure of their bearers. >>> >>> The functions exist before any process happens. A molecule may have a >>> function but never actually realize it. >>> >>> These distinctions have important consequences as people such as myself >>> work >>> on adding more detail to the GO. The processes get more detail by adding >>> *participants*. Within those processes, when there is a molecule like an >>> enzyme that functions in a particular way, it needs to be distinguished >>> from >>> the other participants in some way. The way that it is distinguished is by >>> saying it bears a function. >>> >>> The heuristic that a molecular function is a "single step" process is >>> misused, IMO. That it is a "single step" derives from the fact that in >>> such >>> descriptions there is a single molecule that has a function. The step is >>> the >>> process that surrounds execution of that function. >>> >>> As I said, getting this distinction clear is essential for future >>> detailing >>> of GO processes such as I and others do. Can we start to get this right >>> here >>> and now? >>> >>> -Alan >>> >>> >>> >>> On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris wrote: >>> >>> Hi, >>>> >>>> We have two SF items in which merging function and process terms looks >>>> like >>>> a viable solution to a problem. One is an overly-specific, single-step >>>> "process" that is essentially equivalent to a "function" (in the GO >>>> sense); >>>> the other is a "function" term that is defined such that it doesn't >>>> describe >>>> a single activity, and is essentially the same as a process term. >>>> >>>> SF 2864212 - merge MF term >>>> RNA splicing factor activity, transesterification mechanism GO:0031202 >>>> >>>> into BP term >>>> RNA splicing, via transesterification reactions GO:0000375 >>>> >>>> For this one, we would merge the MF term into the BP term, and ensure >>>> that >>>> the merged term has is_a ancestry in the BP graph. I think that's all we >>>> would change. >>>> >>>> >>>> >>>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >>>> >>>> >>>> SF 2864271 - merge BP term >>>> >>>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>>> >>>> into MF term >>>> methionyl-tRNA formyltransferase activity GO:0004479 >>>> >>>> >>>> >>>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >>>> >>>> In this case, the proposal is to merge the process term into the function >>>> term, ensuring that the merged term has is_a ancestry only in the MF >>>> ontology,and has a part_of link to a process term. Specifically, the >>>> merged >>>> term would retain the name and ID from GO:0004479, and would be part_of >>>> translational initiation GO:0006413. >>>> >>>> Does anyone have any objections or other comments on these? >>>> >>>> thanks, >>>> m >>>> _______________________________________________ >>>> Annotation mailing list >>>> Annotation at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>> >>>> >>> > From midori at ebi.ac.uk Wed Sep 30 04:00:38 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 30 Sep 2009 11:00:38 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200909301100.n8UB0cwT002995@pigeon.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Sep 30 04:04:50 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 30 Sep 2009 12:04:50 +0100 (BST) Subject: [Annotation] merging MF and BP terms In-Reply-To: References: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> <29af5e2d0909291139n125fe58bpfdc59b449affa481@mail.gmail.com> Message-ID: How long will you need? Especially if it's more than the usual two weeks, I'd like to get an alert out soon. m On Tue, 29 Sep 2009, Karen Christie wrote: > These two function terms were created with the intent to represent the two > catalytic activites that occur in large spliceosomal complexes. Based on the > current understanding, I would ascribe these functions to a complex as a > whole. There is not yet evidence that would allow ascribing either catalytic > activity to a smaller portion of either relevant complex and they're > certainly not catalyzed by a single gene product. > > We have recently revised the component ontology and now also represent the > two specific complexes that carry out each of these two catalytic activities, > these two terms and their child terms: > - catalytic step 1 spliceosome > - catalytic step 2 spliceosome > > In process, we have these terms: > - generation of catalytic spliceosome for first transesterification step > - generation of catalytic spliceosome for second transesterification step > > So, I think we are doing this (splicing) right (finally). In process, we > represent the big picture, including some specific stages like generation of > particular complexes in the cycle. In complex, we represent the various > identifiable complexes that researchers recognize. In function, we represent > only the two catalytic activities. > > As named/phrased, the existing function grouping term directly above the two > specific function terms (first/second spliceosomal transesterification > activity) basically just means "be involved with splicing", which I agree is > equivalent to the existing process term. So, I agree that the current > function term (GO:0031202) should be merged into the corresponding process > term, as proposed. > > If we do need a grouping term in the function ontology for these two function > terms, it should be a generalized function, something like > "transesterification activity", not something process specific as the current > one is. > > -Karen > > P.S. In terms of proceeding with this, we'll need to make sure we give > annotation groups an appropriate heads up since there will no function term > that has an equivalent meaning where you could do a direct replace. The two > child terms of GO:0031202 are more specific. Thus reannotation will require > reading for each gene to determine whether to annotate to either of these two > specific terms or to the root node for function. I think it would be > appropriate to have a longer lead time than two weeks to allow groups to work > on this before essentially removing the term from function. SGD has about 60 > genes annotated to this term, excluding computational annotations. > > > > On Tue, 29 Sep 2009, Alan Ruttenberg wrote: > >> On Tue, Sep 29, 2009 at 2:18 PM, Karen Christie >> wrote: >> >>> I'd like to know you deal with multisubunit enzymes, where no one >>> particular gene product has the catalytic activity. >>> >> >> I think that the function is then ascribed to either the complex as a >> whole, >> or to the part of the complex that is responsible for the activity. >> >> The schema is: >> >> Complex >> has_part protein 1 >> has_part protein 2 >> ... >> >> Complex bears function (reverse function inheres in complex) >> >> function realized in process >> >> which implies: >> >> Complex participates in process. >> >> In addition, typically there will be other participants in the process. For >> example the mRNA that is being spliced. >> >> If we are at the point where we need to argue about which part of the >> complex bears the function then we are in good shape. >> >> -Alan >> >> >> >>> -Karen >>> >>> >>> >>> On Tue, 29 Sep 2009, Alan Ruttenberg wrote: >>> >>> The problem is that this still confuses function with process. Functions >>>> are >>>> the things that the enzymes (using the term broadly) have that make the >>>> processes happen. If one goes into more detail, there are a variety of >>>> participants in the process (substrates, products, "cofactors"), but only >>>> one bearer of the function in a particular process. >>>> Every function has a corresponding process, its "realization". >>>> >>>> Functions are not parts of processes. The realizations of functions are. >>>> >>>> The functions have a physical basis in the structure of their bearers. >>>> >>>> The functions exist before any process happens. A molecule may have a >>>> function but never actually realize it. >>>> >>>> These distinctions have important consequences as people such as myself >>>> work >>>> on adding more detail to the GO. The processes get more detail by adding >>>> *participants*. Within those processes, when there is a molecule like an >>>> enzyme that functions in a particular way, it needs to be distinguished >>>> from >>>> the other participants in some way. The way that it is distinguished is >>>> by >>>> saying it bears a function. >>>> >>>> The heuristic that a molecular function is a "single step" process is >>>> misused, IMO. That it is a "single step" derives from the fact that in >>>> such >>>> descriptions there is a single molecule that has a function. The step is >>>> the >>>> process that surrounds execution of that function. >>>> >>>> As I said, getting this distinction clear is essential for future >>>> detailing >>>> of GO processes such as I and others do. Can we start to get this right >>>> here >>>> and now? >>>> >>>> -Alan >>>> >>>> >>>> >>>> On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris wrote: >>>> >>>> Hi, >>>>> >>>>> We have two SF items in which merging function and process terms looks >>>>> like >>>>> a viable solution to a problem. One is an overly-specific, single-step >>>>> "process" that is essentially equivalent to a "function" (in the GO >>>>> sense); >>>>> the other is a "function" term that is defined such that it doesn't >>>>> describe >>>>> a single activity, and is essentially the same as a process term. >>>>> >>>>> SF 2864212 - merge MF term >>>>> RNA splicing factor activity, transesterification mechanism GO:0031202 >>>>> >>>>> into BP term >>>>> RNA splicing, via transesterification reactions GO:0000375 >>>>> >>>>> For this one, we would merge the MF term into the BP term, and ensure >>>>> that >>>>> the merged term has is_a ancestry in the BP graph. I think that's all we >>>>> would change. >>>>> >>>>> >>>>> >>>>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >>>>> >>>>> >>>>> SF 2864271 - merge BP term >>>>> >>>>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>>>> >>>>> into MF term >>>>> methionyl-tRNA formyltransferase activity GO:0004479 >>>>> >>>>> >>>>> >>>>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >>>>> >>>>> In this case, the proposal is to merge the process term into the >>>>> function >>>>> term, ensuring that the merged term has is_a ancestry only in the MF >>>>> ontology,and has a part_of link to a process term. Specifically, the >>>>> merged >>>>> term would retain the name and ID from GO:0004479, and would be part_of >>>>> translational initiation GO:0006413. >>>>> >>>>> Does anyone have any objections or other comments on these? >>>>> >>>>> thanks, >>>>> m >>>>> _______________________________________________ >>>>> Annotation mailing list >>>>> Annotation at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>>> >>>>> >>>> >> > From Judith.Blake at jax.org Wed Sep 30 04:10:59 2009 From: Judith.Blake at jax.org (Judith Blake) Date: Wed, 30 Sep 2009 07:10:59 -0400 Subject: [Annotation] merging MF and BP terms In-Reply-To: Message-ID: Hi Karen, all, I want to remind/inform all that the Protein Ontology (PRO) is now funded to represent explicit complexes that detail exact proteins that make up the complex. These could be annotated to a specific function term. The objective too is to have a relationship between the specific complex represented in PRO and the complex class represented in GO. Ultimately, the site of specific complex activity will need to be included in the terminology term I think (xref to cell type or tissue?). We would want to curate the specific complex. The example below is from Serneels, et.al., gamma-Secretase heterogeneity in the Aph1 subunit: relevance for Alzheimer's disease. Science. 2009 May 1;324(5927):639-42 The gamma-secretase complex plays a role in Alzheimer's disease and cancer progression. The development of clinically useful inhibitors, however, is complicated by the role of the gamma-secretase complex in regulated intramembrane proteolysis of Notch and other essential proteins. Different gamma-secretase complexes containing different Presenilin or Aph1 protein subunits are present in various tissues. Here we show that these complexes have heterogeneous biochemical and physiological properties. Specific inactivation of the Aph1B gamma-secretase in a mouse Alzheimer's disease model led to improvements of Alzheimer's disease-relevant phenotypic features without any Notch-related side effects. The Aph1B complex contributes to total gamma-secretase activity in the human brain, and thus specific targeting of Aph1B-containing gamma-secretase complexes may help generate less toxic therapies for Alzheimer's disease. Judy On 9/29/09 6:11 PM, "Karen Christie" wrote: These two function terms were created with the intent to represent the two catalytic activites that occur in large spliceosomal complexes. Based on the current understanding, I would ascribe these functions to a complex as a whole. There is not yet evidence that would allow ascribing either catalytic activity to a smaller portion of either relevant complex and they're certainly not catalyzed by a single gene product. We have recently revised the component ontology and now also represent the two specific complexes that carry out each of these two catalytic activities, these two terms and their child terms: - catalytic step 1 spliceosome - catalytic step 2 spliceosome In process, we have these terms: - generation of catalytic spliceosome for first transesterification step - generation of catalytic spliceosome for second transesterification step So, I think we are doing this (splicing) right (finally). In process, we represent the big picture, including some specific stages like generation of particular complexes in the cycle. In complex, we represent the various identifiable complexes that researchers recognize. In function, we represent only the two catalytic activities. As named/phrased, the existing function grouping term directly above the two specific function terms (first/second spliceosomal transesterification activity) basically just means "be involved with splicing", which I agree is equivalent to the existing process term. So, I agree that the current function term (GO:0031202) should be merged into the corresponding process term, as proposed. If we do need a grouping term in the function ontology for these two function terms, it should be a generalized function, something like "transesterification activity", not something process specific as the current one is. -Karen P.S. In terms of proceeding with this, we'll need to make sure we give annotation groups an appropriate heads up since there will no function term that has an equivalent meaning where you could do a direct replace. The two child terms of GO:0031202 are more specific. Thus reannotation will require reading for each gene to determine whether to annotate to either of these two specific terms or to the root node for function. I think it would be appropriate to have a longer lead time than two weeks to allow groups to work on this before essentially removing the term from function. SGD has about 60 genes annotated to this term, excluding computational annotations. On Tue, 29 Sep 2009, Alan Ruttenberg wrote: > On Tue, Sep 29, 2009 at 2:18 PM, Karen Christie > wrote: > >> I'd like to know you deal with multisubunit enzymes, where no one >> particular gene product has the catalytic activity. >> > > I think that the function is then ascribed to either the complex as a whole, > or to the part of the complex that is responsible for the activity. > > The schema is: > > Complex > has_part protein 1 > has_part protein 2 > ... > > Complex bears function (reverse function inheres in complex) > > function realized in process > > which implies: > > Complex participates in process. > > In addition, typically there will be other participants in the process. For > example the mRNA that is being spliced. > > If we are at the point where we need to argue about which part of the > complex bears the function then we are in good shape. > > -Alan > > > >> -Karen >> >> >> >> On Tue, 29 Sep 2009, Alan Ruttenberg wrote: >> >> The problem is that this still confuses function with process. Functions >>> are >>> the things that the enzymes (using the term broadly) have that make the >>> processes happen. If one goes into more detail, there are a variety of >>> participants in the process (substrates, products, "cofactors"), but only >>> one bearer of the function in a particular process. >>> Every function has a corresponding process, its "realization". >>> >>> Functions are not parts of processes. The realizations of functions are. >>> >>> The functions have a physical basis in the structure of their bearers. >>> >>> The functions exist before any process happens. A molecule may have a >>> function but never actually realize it. >>> >>> These distinctions have important consequences as people such as myself >>> work >>> on adding more detail to the GO. The processes get more detail by adding >>> *participants*. Within those processes, when there is a molecule like an >>> enzyme that functions in a particular way, it needs to be distinguished >>> from >>> the other participants in some way. The way that it is distinguished is by >>> saying it bears a function. >>> >>> The heuristic that a molecular function is a "single step" process is >>> misused, IMO. That it is a "single step" derives from the fact that in >>> such >>> descriptions there is a single molecule that has a function. The step is >>> the >>> process that surrounds execution of that function. >>> >>> As I said, getting this distinction clear is essential for future >>> detailing >>> of GO processes such as I and others do. Can we start to get this right >>> here >>> and now? >>> >>> -Alan >>> >>> >>> >>> On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris wrote: >>> >>> Hi, >>>> >>>> We have two SF items in which merging function and process terms looks >>>> like >>>> a viable solution to a problem. One is an overly-specific, single-step >>>> "process" that is essentially equivalent to a "function" (in the GO >>>> sense); >>>> the other is a "function" term that is defined such that it doesn't >>>> describe >>>> a single activity, and is essentially the same as a process term. >>>> >>>> SF 2864212 - merge MF term >>>> RNA splicing factor activity, transesterification mechanism GO:0031202 >>>> >>>> into BP term >>>> RNA splicing, via transesterification reactions GO:0000375 >>>> >>>> For this one, we would merge the MF term into the BP term, and ensure >>>> that >>>> the merged term has is_a ancestry in the BP graph. I think that's all we >>>> would change. >>>> >>>> >>>> >>>> https://sourceforge.net/tracker/?func=detail=2864212_id=36855=440764 >>>> >>>> >>>> SF 2864271 - merge BP term >>>> >>>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>>> >>>> into MF term >>>> methionyl-tRNA formyltransferase activity GO:0004479 >>>> >>>> >>>> >>>> https://sourceforge.net/tracker/?func=detail=2864271_id=36855=440764 >>>> >>>> In this case, the proposal is to merge the process term into the function >>>> term, ensuring that the merged term has is_a ancestry only in the MF >>>> ontology,and has a part_of link to a process term. Specifically, the >>>> merged >>>> term would retain the name and ID from GO:0004479, and would be part_of >>>> translational initiation GO:0006413. >>>> >>>> Does anyone have any objections or other comments on these? >>>> >>>> thanks, >>>> m >>>> _______________________________________________ >>>> Annotation mailing list >>>> Annotation at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>> >>>> >>> > _______________________________________________ Annotation mailing list Annotation at geneontology.org http://fafner.stanford.edu/mailman/listinfo/annotation -------------- next part -------------- An HTML attachment was scrubbed... URL: From kchris at genome.stanford.edu Wed Sep 30 13:36:10 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Wed, 30 Sep 2009 13:36:10 -0700 (PDT) Subject: [Annotation] merging MF and BP terms In-Reply-To: References: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> <29af5e2d0909291139n125fe58bpfdc59b449affa481@mail.gmail.com> Message-ID: Hi Midori, I checked with our GO annotation team and they think two weeks is enough, but are starting now rather than waiting till it goes through to avoid having no function annotations for those genes once this term is gone from Function. I know the standard email states when there are annotations. Perhaps it could also explicitly state when there is no comparable replacement term for annotation. thanks for considering annotation needs in this ontology change! -Karen On Wed, 30 Sep 2009, Midori Harris wrote: > How long will you need? Especially if it's more than the usual two weeks, > I'd like to get an alert out soon. > > m > > On Tue, 29 Sep 2009, Karen Christie wrote: > >> These two function terms were created with the intent to represent the two >> catalytic activites that occur in large spliceosomal complexes. Based on >> the current understanding, I would ascribe these functions to a complex as >> a whole. There is not yet evidence that would allow ascribing either >> catalytic activity to a smaller portion of either relevant complex and >> they're certainly not catalyzed by a single gene product. >> >> We have recently revised the component ontology and now also represent the >> two specific complexes that carry out each of these two catalytic >> activities, these two terms and their child terms: >> - catalytic step 1 spliceosome >> - catalytic step 2 spliceosome >> >> In process, we have these terms: >> - generation of catalytic spliceosome for first transesterification step >> - generation of catalytic spliceosome for second transesterification step >> >> So, I think we are doing this (splicing) right (finally). In process, we >> represent the big picture, including some specific stages like generation >> of particular complexes in the cycle. In complex, we represent the various >> identifiable complexes that researchers recognize. In function, we >> represent only the two catalytic activities. >> >> As named/phrased, the existing function grouping term directly above the >> two specific function terms (first/second spliceosomal transesterification >> activity) basically just means "be involved with splicing", which I agree >> is equivalent to the existing process term. So, I agree that the current >> function term (GO:0031202) should be merged into the corresponding process >> term, as proposed. >> >> If we do need a grouping term in the function ontology for these two >> function terms, it should be a generalized function, something like >> "transesterification activity", not something process specific as the >> current one is. >> >> -Karen >> >> P.S. In terms of proceeding with this, we'll need to make sure we give >> annotation groups an appropriate heads up since there will no function term >> that has an equivalent meaning where you could do a direct replace. The two >> child terms of GO:0031202 are more specific. Thus reannotation will require >> reading for each gene to determine whether to annotate to either of these >> two specific terms or to the root node for function. I think it would be >> appropriate to have a longer lead time than two weeks to allow groups to >> work on this before essentially removing the term from function. SGD has >> about 60 genes annotated to this term, excluding computational annotations. >> >> >> >> On Tue, 29 Sep 2009, Alan Ruttenberg wrote: >> >>> On Tue, Sep 29, 2009 at 2:18 PM, Karen Christie >>> wrote: >>> >>>> I'd like to know you deal with multisubunit enzymes, where no one >>>> particular gene product has the catalytic activity. >>>> >>> >>> I think that the function is then ascribed to either the complex as a >>> whole, >>> or to the part of the complex that is responsible for the activity. >>> >>> The schema is: >>> >>> Complex >>> has_part protein 1 >>> has_part protein 2 >>> ... >>> >>> Complex bears function (reverse function inheres in complex) >>> >>> function realized in process >>> >>> which implies: >>> >>> Complex participates in process. >>> >>> In addition, typically there will be other participants in the process. >>> For >>> example the mRNA that is being spliced. >>> >>> If we are at the point where we need to argue about which part of the >>> complex bears the function then we are in good shape. >>> >>> -Alan >>> >>> >>> >>>> -Karen >>>> >>>> >>>> >>>> On Tue, 29 Sep 2009, Alan Ruttenberg wrote: >>>> >>>> The problem is that this still confuses function with process. Functions >>>>> are >>>>> the things that the enzymes (using the term broadly) have that make the >>>>> processes happen. If one goes into more detail, there are a variety of >>>>> participants in the process (substrates, products, "cofactors"), but >>>>> only >>>>> one bearer of the function in a particular process. >>>>> Every function has a corresponding process, its "realization". >>>>> >>>>> Functions are not parts of processes. The realizations of functions are. >>>>> >>>>> The functions have a physical basis in the structure of their bearers. >>>>> >>>>> The functions exist before any process happens. A molecule may have a >>>>> function but never actually realize it. >>>>> >>>>> These distinctions have important consequences as people such as myself >>>>> work >>>>> on adding more detail to the GO. The processes get more detail by adding >>>>> *participants*. Within those processes, when there is a molecule like an >>>>> enzyme that functions in a particular way, it needs to be distinguished >>>>> from >>>>> the other participants in some way. The way that it is distinguished is >>>>> by >>>>> saying it bears a function. >>>>> >>>>> The heuristic that a molecular function is a "single step" process is >>>>> misused, IMO. That it is a "single step" derives from the fact that in >>>>> such >>>>> descriptions there is a single molecule that has a function. The step is >>>>> the >>>>> process that surrounds execution of that function. >>>>> >>>>> As I said, getting this distinction clear is essential for future >>>>> detailing >>>>> of GO processes such as I and others do. Can we start to get this right >>>>> here >>>>> and now? >>>>> >>>>> -Alan >>>>> >>>>> >>>>> >>>>> On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris >>>>> wrote: >>>>> >>>>> Hi, >>>>>> >>>>>> We have two SF items in which merging function and process terms looks >>>>>> like >>>>>> a viable solution to a problem. One is an overly-specific, single-step >>>>>> "process" that is essentially equivalent to a "function" (in the GO >>>>>> sense); >>>>>> the other is a "function" term that is defined such that it doesn't >>>>>> describe >>>>>> a single activity, and is essentially the same as a process term. >>>>>> >>>>>> SF 2864212 - merge MF term >>>>>> RNA splicing factor activity, transesterification mechanism GO:0031202 >>>>>> >>>>>> into BP term >>>>>> RNA splicing, via transesterification reactions GO:0000375 >>>>>> >>>>>> For this one, we would merge the MF term into the BP term, and ensure >>>>>> that >>>>>> the merged term has is_a ancestry in the BP graph. I think that's all >>>>>> we >>>>>> would change. >>>>>> >>>>>> >>>>>> >>>>>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >>>>>> >>>>>> >>>>>> SF 2864271 - merge BP term >>>>>> >>>>>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>>>>> >>>>>> into MF term >>>>>> methionyl-tRNA formyltransferase activity GO:0004479 >>>>>> >>>>>> >>>>>> >>>>>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >>>>>> >>>>>> In this case, the proposal is to merge the process term into the >>>>>> function >>>>>> term, ensuring that the merged term has is_a ancestry only in the MF >>>>>> ontology,and has a part_of link to a process term. Specifically, the >>>>>> merged >>>>>> term would retain the name and ID from GO:0004479, and would be part_of >>>>>> translational initiation GO:0006413. >>>>>> >>>>>> Does anyone have any objections or other comments on these? >>>>>> >>>>>> thanks, >>>>>> m >>>>>> _______________________________________________ >>>>>> Annotation mailing list >>>>>> Annotation at geneontology.org >>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>>>> >>>>>> >>>>> >>> >> > From hjd at informatics.jax.org Wed Sep 30 14:55:54 2009 From: hjd at informatics.jax.org (Harold Drabkin) Date: Wed, 30 Sep 2009 17:55:54 -0400 Subject: [Annotation] merging MF and BP terms In-Reply-To: References: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> <29af5e2d0909291139n125fe58bpfdc59b449affa481@mail.gmail.com> Message-ID: <4AC3D3EA.9020202@informatics.jax.org> Karen Christie wrote: > Hi Midori, > > I checked with our GO annotation team and they think two weeks is > enough, but are starting now rather than waiting till it goes through > to avoid having no function annotations for those genes once this term > is gone from Function. > > I know the standard email states when there are annotations. Perhaps > it could also explicitly state when there is no comparable replacement > term for annotation. This ^ is a good idea to save time! > > thanks for considering annotation needs in this ontology change! > > -Karen > > > > On Wed, 30 Sep 2009, Midori Harris wrote: > >> How long will you need? Especially if it's more than the usual two >> weeks, >> I'd like to get an alert out soon. >> >> m >> >> On Tue, 29 Sep 2009, Karen Christie wrote: >> >>> These two function terms were created with the intent to represent >>> the two catalytic activites that occur in large spliceosomal >>> complexes. Based on the current understanding, I would ascribe these >>> functions to a complex as a whole. There is not yet evidence that >>> would allow ascribing either catalytic activity to a smaller portion >>> of either relevant complex and they're certainly not catalyzed by a >>> single gene product. >>> >>> We have recently revised the component ontology and now also >>> represent the two specific complexes that carry out each of these >>> two catalytic activities, these two terms and their child terms: >>> - catalytic step 1 spliceosome >>> - catalytic step 2 spliceosome >>> >>> In process, we have these terms: >>> - generation of catalytic spliceosome for first transesterification >>> step >>> - generation of catalytic spliceosome for second transesterification >>> step >>> >>> So, I think we are doing this (splicing) right (finally). In >>> process, we represent the big picture, including some specific >>> stages like generation of particular complexes in the cycle. In >>> complex, we represent the various identifiable complexes that >>> researchers recognize. In function, we represent only the two >>> catalytic activities. >>> >>> As named/phrased, the existing function grouping term directly above >>> the two specific function terms (first/second spliceosomal >>> transesterification activity) basically just means "be involved with >>> splicing", which I agree is equivalent to the existing process term. >>> So, I agree that the current function term (GO:0031202) should be >>> merged into the corresponding process term, as proposed. >>> >>> If we do need a grouping term in the function ontology for these two >>> function terms, it should be a generalized function, something like >>> "transesterification activity", not something process specific as >>> the current one is. >>> >>> -Karen >>> >>> P.S. In terms of proceeding with this, we'll need to make sure we >>> give annotation groups an appropriate heads up since there will no >>> function term that has an equivalent meaning where you could do a >>> direct replace. The two child terms of GO:0031202 are more specific. >>> Thus reannotation will require reading for each gene to determine >>> whether to annotate to either of these two specific terms or to the >>> root node for function. I think it would be appropriate to have a >>> longer lead time than two weeks to allow groups to work on this >>> before essentially removing the term from function. SGD has about 60 >>> genes annotated to this term, excluding computational annotations. >>> >>> >>> >>> On Tue, 29 Sep 2009, Alan Ruttenberg wrote: >>> >>>> On Tue, Sep 29, 2009 at 2:18 PM, Karen Christie >>>> wrote: >>>> >>>>> I'd like to know you deal with multisubunit enzymes, where no one >>>>> particular gene product has the catalytic activity. >>>>> >>>> >>>> I think that the function is then ascribed to either the complex as >>>> a whole, >>>> or to the part of the complex that is responsible for the activity. >>>> >>>> The schema is: >>>> >>>> Complex >>>> has_part protein 1 >>>> has_part protein 2 >>>> ... >>>> >>>> Complex bears function (reverse function inheres in complex) >>>> >>>> function realized in process >>>> >>>> which implies: >>>> >>>> Complex participates in process. >>>> >>>> In addition, typically there will be other participants in the >>>> process. For >>>> example the mRNA that is being spliced. >>>> >>>> If we are at the point where we need to argue about which part of the >>>> complex bears the function then we are in good shape. >>>> >>>> -Alan >>>> >>>> >>>> >>>>> -Karen >>>>> >>>>> >>>>> >>>>> On Tue, 29 Sep 2009, Alan Ruttenberg wrote: >>>>> >>>>> The problem is that this still confuses function with process. >>>>> Functions >>>>>> are >>>>>> the things that the enzymes (using the term broadly) have that >>>>>> make the >>>>>> processes happen. If one goes into more detail, there are a >>>>>> variety of >>>>>> participants in the process (substrates, products, "cofactors"), >>>>>> but only >>>>>> one bearer of the function in a particular process. >>>>>> Every function has a corresponding process, its "realization". >>>>>> >>>>>> Functions are not parts of processes. The realizations of >>>>>> functions are. >>>>>> >>>>>> The functions have a physical basis in the structure of their >>>>>> bearers. >>>>>> >>>>>> The functions exist before any process happens. A molecule may >>>>>> have a >>>>>> function but never actually realize it. >>>>>> >>>>>> These distinctions have important consequences as people such as >>>>>> myself >>>>>> work >>>>>> on adding more detail to the GO. The processes get more detail by >>>>>> adding >>>>>> *participants*. Within those processes, when there is a molecule >>>>>> like an >>>>>> enzyme that functions in a particular way, it needs to be >>>>>> distinguished >>>>>> from >>>>>> the other participants in some way. The way that it is >>>>>> distinguished is by >>>>>> saying it bears a function. >>>>>> >>>>>> The heuristic that a molecular function is a "single step" >>>>>> process is >>>>>> misused, IMO. That it is a "single step" derives from the fact >>>>>> that in >>>>>> such >>>>>> descriptions there is a single molecule that has a function. The >>>>>> step is >>>>>> the >>>>>> process that surrounds execution of that function. >>>>>> >>>>>> As I said, getting this distinction clear is essential for future >>>>>> detailing >>>>>> of GO processes such as I and others do. Can we start to get this >>>>>> right >>>>>> here >>>>>> and now? >>>>>> >>>>>> -Alan >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris >>>>>> wrote: >>>>>> >>>>>> Hi, >>>>>>> >>>>>>> We have two SF items in which merging function and process terms >>>>>>> looks >>>>>>> like >>>>>>> a viable solution to a problem. One is an overly-specific, >>>>>>> single-step >>>>>>> "process" that is essentially equivalent to a "function" (in the GO >>>>>>> sense); >>>>>>> the other is a "function" term that is defined such that it doesn't >>>>>>> describe >>>>>>> a single activity, and is essentially the same as a process term. >>>>>>> >>>>>>> SF 2864212 - merge MF term >>>>>>> RNA splicing factor activity, transesterification mechanism >>>>>>> GO:0031202 >>>>>>> >>>>>>> into BP term >>>>>>> RNA splicing, via transesterification reactions GO:0000375 >>>>>>> >>>>>>> For this one, we would merge the MF term into the BP term, and >>>>>>> ensure >>>>>>> that >>>>>>> the merged term has is_a ancestry in the BP graph. I think >>>>>>> that's all we >>>>>>> would change. >>>>>>> >>>>>>> >>>>>>> >>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 >>>>>>> >>>>>>> >>>>>>> >>>>>>> SF 2864271 - merge BP term >>>>>>> >>>>>>> conversion of met-tRNAf to fmet-tRNA GO:0001718 >>>>>>> >>>>>>> into MF term >>>>>>> methionyl-tRNA formyltransferase activity GO:0004479 >>>>>>> >>>>>>> >>>>>>> >>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 >>>>>>> >>>>>>> >>>>>>> In this case, the proposal is to merge the process term into the >>>>>>> function >>>>>>> term, ensuring that the merged term has is_a ancestry only in >>>>>>> the MF >>>>>>> ontology,and has a part_of link to a process term. Specifically, >>>>>>> the >>>>>>> merged >>>>>>> term would retain the name and ID from GO:0004479, and would be >>>>>>> part_of >>>>>>> translational initiation GO:0006413. >>>>>>> >>>>>>> Does anyone have any objections or other comments on these? >>>>>>> >>>>>>> thanks, >>>>>>> m >>>>>>> _______________________________________________ >>>>>>> Annotation mailing list >>>>>>> Annotation at geneontology.org >>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>>>>>> >>>>>>> >>>>>> >>>> >>> >> > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation From suzi at fruitfly.org Wed Sep 30 17:30:19 2009 From: suzi at fruitfly.org (Suzanna Lewis) Date: Wed, 30 Sep 2009 17:30:19 -0700 Subject: [Annotation] merging MF and BP terms In-Reply-To: <29af5e2d0909291145p1e2af1d4q2e94a2a49103a130@mail.gmail.com> References: <29af5e2d0909291052v3b9821ele28f6229ac2b7232@mail.gmail.com> <29af5e2d0909291145p1e2af1d4q2e94a2a49103a130@mail.gmail.com> Message-ID: <4AE49577-109D-4104-B40C-5E10FA5CE1B2@fruitfly.org> Alan has it right. Functions are not occurents, Function*ings* are. But I think that the solution that David, Karen, and Midori have proposed is fine. We've consciously collapsed (to avoid repeating things) the "Function*ings* are part of processes" into a single artifact, a relationship (i.e. their is no information artifact for Function*ings* itself, it is implicit) that is for now called "part_of" (if I remember correctly). The name of this relationship may not be ideal, but we are trying to be clear about its intended usage. Chris & David first proposed this at the St. Croix meeting. And I seem to remember that David and I talked about this (and many other things, such as the nature of the implied relationship between an instance and a type when anyone makes an annotation) again at the relation ontology meeting in Denver. -S On Sep 29, 2009, at 11:45 AM, Alan Ruttenberg wrote: > > > On Tue, Sep 29, 2009 at 2:38 PM, Judith Blake > wrote: > > Functions are occurrants. A function describes an action, > biochemical, structural, whatever. > > A function doesn't describe anything. Information artifact describe > things. > Sorry to be picky about words. It's my job. > If you look at the papers on BFO you will see that functions are > continuants and occurrents are disjoint from continuants. So > functions are not occurrents. If the GO is using terminology at odds > with BFO that needs to be fixed - we agreed at the last foundry > meeting that we were all going to use a common upper level ontology. > > > Functions are part of processes. > > Function*ings* (i.e. realizations of functions) are part of processes. > > A variety of structures, encoded in a molecule, have the potential > to realize a function. > > Type error: processes don't have potential. (concluded by > substitution "potential to realize a function" + function is_a > process => "potential to realize a process". > > The error is that it is the functions that are the potentials. > Potentials are realized. The realizations are processes. > > We discussed this very recently with Michael and he agreed. > > That is a property of the molecule, not of the function. > > What is the reference of "That"? > > A molecule can have encoded the potential of engaging in several > functions. > > Absolutely. (as long as you rewrite "functions" -> > "functionings" (i.e. processes).) > > A molecule can bear multiple functions is the way we would say this. > > The confusion I think is that of the relationship between the gene > product and a molecular function, and the molecular function and the > biological process. > > And what do you say these are. I (and BFO) are clear: The relation > between a molecular function and a gene product is "inheres". The > relation between molecular function and a biological process is > "realized_by". > > -Alan > > > > Judy > > > > > On 9/29/09 1:52 PM, "Alan Ruttenberg" > wrote: > > The problem is that this still confuses function with process. > Functions are the things that the enzymes (using the term broadly) > have that make the processes happen. If one goes into more detail, > there are a variety of participants in the process (substrates, > products, "cofactors"), but only one bearer of the function in a > particular process. > > Every function has a corresponding process, its "realization". > > Functions are not parts of processes. The realizations of functions > are. > > The functions have a physical basis in the structure of their bearers. > > The functions exist before any process happens. A molecule may have > a function but never actually realize it. > > These distinctions have important consequences as people such as > myself work on adding more detail to the GO. The processes get more > detail by adding *participants*. Within those processes, when there > is a molecule like an enzyme that functions in a particular way, it > needs to be distinguished from the other participants in some way. > The way that it is distinguished is by saying it bears a function. > > The heuristic that a molecular function is a "single step" process > is misused, IMO. That it is a "single step" derives from the fact > that in such descriptions there is a single molecule that has a > function. The step is the process that surrounds execution of that > function. > > As I said, getting this distinction clear is essential for future > detailing of GO processes such as I and others do. Can we start to > get this right here and now? > > -Alan > > > > On Tue, Sep 29, 2009 at 10:30 AM, Midori Harris > wrote: > Hi, > > We have two SF items in which merging function and process terms > looks like a viable solution to a problem. One is an overly- > specific, single-step "process" that is essentially equivalent to a > "function" (in the GO sense); the other is a "function" term that is > defined such that it doesn't describe a single activity, and is > essentially the same as a process term. > > SF 2864212 - merge MF term > RNA splicing factor activity, transesterification mechanism GO: > 0031202 > > into BP term > RNA splicing, via transesterification reactions GO:0000375 > > For this one, we would merge the MF term into the BP term, and > ensure that the merged term has is_a ancestry in the BP graph. I > think that's all we would change. > > https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 > > > SF 2864271 - merge BP term > > conversion of met-tRNAf to fmet-tRNA GO:0001718 > > into MF term > methionyl-tRNA formyltransferase activity GO:0004479 > > https://sourceforge.net/tracker/?func=detail&aid=2864271&group_id=36855&atid=440764 > > In this case, the proposal is to merge the process term into the > function term, ensuring that the merged term has is_a ancestry only > in the MF ontology,and has a part_of link to a process term. > Specifically, the merged term would retain the name and ID from GO: > 0004479, and would be part_of translational initiation GO:0006413. > > Does anyone have any objections or other comments on these? > > thanks, > m > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > > > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation -------------- next part -------------- An HTML attachment was scrubbed... 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