From midori at ebi.ac.uk Thu Oct 1 03:53:07 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 1 Oct 2009 11:53:07 +0100 (BST) Subject: [Go] Alert: proposal to merge MF GO:0031202 into BP GO:0000375 Message-ID: Dear GO, The proposal has been made to merge the molecular function term 'RNA splicing factor activity, transesterification mechanism ; GO:0031202' into the biological process term 'RNA splicing, via transesterification reactions ; GO:0000375'. The reason is that GO:0031202 is defined such that it doesn't describe a single activity, and is essentially the same as a process term. GO:0031202 groups two activities whose common feature is involvement in the same process. Note that annotations can be transferred to GO:0000375, but there is no single molecular function term to which all annotated gene products can be transferred. Instead, curators must choose one of these two terms (is_a children of GO:0031202 at present; they will become part_of GO:0000375): first spliceosomal transesterification activity ; GO:0000384 second spliceosomal transesterification activity ; GO:0000386 If there is not enough information available to choose either or both of GO:0000384 and GO:0000386, the annotation will have to be moved to the parent, 'catalytic activity ; GO:0003824'. Annotations to GO:0031202 exist as follows: file IEA non-IEA total gene_association.aspgd.gz 13 0 13 gene_association.cgd.gz 33 3 36 gene_association.dictyBase.gz 0 25 25 gene_association.fb.gz 0 30 30 gene_association.GeneDB_Pfalciparum.gz 0 21 21 gene_association.GeneDB_Spombe.gz 0 30 30 gene_association.GeneDB_Tbrucei.gz 0 10 10 gene_association.goa_human.gz 0 23 23 gene_association.goa_uniprot.gz 0 3 3 gene_association.goa_uniprot_noiea.gz 0 3 3 gene_association.mgi.gz 0 7 7 gene_association.PAMGO_Mgrisea.gz 0 2 2 gene_association.rgd.gz 0 4 4 gene_association.sgd.gz 0 109 109 gene_association.tair.gz 0 16 16 The term is used in one external mapping: Reactome:160901 RNA splicing factor activity, transesterification mechanism > GO:RNA splicing factor activity, transesterification mechanism ; GO:0031202 SourceForge link: https://sourceforge.net/tracker/?func=detail&aid=2864212&group_id=36855&atid=440764 This change has already been discussed on the ontology development and annotation mailing lists, but we are allowing time for additional comments (and annotation updates) until Friday, October 23, 2009. *** Unless objections are received by October 23, we will assume that you agree to this change. *** Midori From midori at ebi.ac.uk Thu Oct 1 11:00:55 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 1 Oct 2009 18:00:55 UT Subject: [Go] SourceForge Update Message-ID: <200910011800.n91I0t5C027259@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 jaiswalp at science.oregonstate.edu Thu Oct 1 11:37:25 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu, 01 Oct 2009 11:37:25 -0700 Subject: [Go] AmiGO: structural constituent of cell wall Message-ID: <4AC4F6E5.90000@science.oregonstate.edu> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005199&session_id=3810amigo1254420818 This term and some other sibling terms may require renaming of the terms. As I understand, 'constituent' means a component of or part of. E.g. The cell wall is composed of cellulose fiber, polysaccharides, and proteins. Means these components are in essence is_a structural constituent of cell wall and obviously these are not the function terms. The suggested function term could be 'structural integrity of a cell wall'. Though it may as well be a process term. Pankaj From midori at ebi.ac.uk Thu Oct 1 11:45:04 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 1 Oct 2009 19:45:04 +0100 (BST) Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC4F6E5.90000@science.oregonstate.edu> References: <4AC4F6E5.90000@science.oregonstate.edu> Message-ID: These terms have never been ideal; we've known about the problems with them literally for years. 'Structural integrity' is no more a molecular function than the present names; it's a biological quality. m On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005199&session_id=3810amigo1254420818 > > This term and some other sibling terms may require renaming of the terms. > > As I understand, 'constituent' means a component of or part of. E.g. The cell > wall is composed of cellulose fiber, polysaccharides, and proteins. Means > these components are in essence is_a structural constituent of cell wall and > obviously these are not the function terms. > > The suggested function term could be 'structural integrity of a cell wall'. > Though it may as well be a process term. > > Pankaj > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From jaiswalp at science.oregonstate.edu Thu Oct 1 11:49:32 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu, 01 Oct 2009 11:49:32 -0700 Subject: [Go] AmiGO: binding Message-ID: <4AC4F9BC.6090907@science.oregonstate.edu> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005488&session_id=3810amigo1254420818 The narrow synonym 'ligand' seems inappropriate. 'ligand' is used for "a substance (an atom or molecule or radical or ion) that forms a complex around a central atom" and it may require a physical/chemical bonding/binding. Therefore it is not used for 'binding' function. Pankaj From midori at ebi.ac.uk Thu Oct 1 11:53:39 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 1 Oct 2009 19:53:39 +0100 (BST) Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC4FA71.2070803@science.oregonstate.edu> References: <4AC4F6E5.90000@science.oregonstate.edu> <4AC4FA71.2070803@science.oregonstate.edu> Message-ID: I've wanted to for those aforementioned years. Let's see what the rest of the list says ... m On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > Can we retire them. > > Pankaj > > Midori Harris wrote: >> These terms have never been ideal; we've known about the problems with them >> literally for years. 'Structural integrity' is no more a molecular function >> than the present names; it's a biological quality. >> >> m >> >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> >>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005199&session_id=3810amigo1254420818 >>> >>> This term and some other sibling terms may require renaming of the terms. >>> >>> As I understand, 'constituent' means a component of or part of. E.g. The >>> cell wall is composed of cellulose fiber, polysaccharides, and proteins. >>> Means these components are in essence is_a structural constituent of cell >>> wall and obviously these are not the function terms. >>> >>> The suggested function term could be 'structural integrity of a cell >>> wall'. Though it may as well be a process term. >>> > From jaiswalp at science.oregonstate.edu Thu Oct 1 11:52:33 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu, 01 Oct 2009 11:52:33 -0700 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: References: <4AC4F6E5.90000@science.oregonstate.edu> Message-ID: <4AC4FA71.2070803@science.oregonstate.edu> Can we retire them. Pankaj Midori Harris wrote: > These terms have never been ideal; we've known about the problems with > them literally for years. 'Structural integrity' is no more a molecular > function than the present names; it's a biological quality. > > m > > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > >> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005199&session_id=3810amigo1254420818 >> >> >> This term and some other sibling terms may require renaming of the terms. >> >> As I understand, 'constituent' means a component of or part of. E.g. >> The cell wall is composed of cellulose fiber, polysaccharides, and >> proteins. Means these components are in essence is_a structural >> constituent of cell wall and obviously these are not the function terms. >> >> The suggested function term could be 'structural integrity of a cell >> wall'. Though it may as well be a process term. >> From mgiglio at SOM.UMARYLAND.EDU Thu Oct 1 12:20:26 2009 From: mgiglio at SOM.UMARYLAND.EDU (Gwinn Giglio, Michelle) Date: Thu, 01 Oct 2009 15:20:26 -0400 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: Message-ID: Hi, I don't see how we can retire these. Proteins that form the building blocks of a structure have this as their "function". It is not an "action", but it is still a "function". What is the function of a brick if not to form part of a wall? What would be the function for proteins like flagellin if these terms were obsoleted? Michelle On 10/1/09 2:53 PM, "Midori Harris" wrote: > I've wanted to for those aforementioned years. Let's see what the rest of > the list says ... > > m > > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > >> Can we retire them. >> >> Pankaj >> >> Midori Harris wrote: >>> These terms have never been ideal; we've known about the problems with them >>> literally for years. 'Structural integrity' is no more a molecular function >>> than the present names; it's a biological quality. >>> >>> m >>> >>> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>> >>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>> 9&session_id=3810amigo1254420818 >>>> >>>> This term and some other sibling terms may require renaming of the terms. >>>> >>>> As I understand, 'constituent' means a component of or part of. E.g. The >>>> cell wall is composed of cellulose fiber, polysaccharides, and proteins. >>>> Means these components are in essence is_a structural constituent of cell >>>> wall and obviously these are not the function terms. >>>> >>>> The suggested function term could be 'structural integrity of a cell >>>> wall'. Though it may as well be a process term. >>>> >> > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From hjd at informatics.jax.org Thu Oct 1 12:36:12 2009 From: hjd at informatics.jax.org (Harold Drabkin) Date: Thu, 01 Oct 2009 15:36:12 -0400 Subject: [Go] AmiGO: binding In-Reply-To: <4AC4F9BC.6090907@science.oregonstate.edu> References: <4AC4F9BC.6090907@science.oregonstate.edu> Message-ID: <4AC504AC.5050102@informatics.jax.org> Pankaj Jaiswal (OSU) wrote: > http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005488&session_id=3810amigo1254420818 > > > The narrow synonym 'ligand' seems inappropriate. 'ligand' is used for > "a substance (an atom or molecule or radical or ion) that forms a > complex around a central atom" and it may require a physical/chemical > bonding/binding. Therefore it is not used for 'binding' function. > > Pankaj > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go "ligand" is the that is bound; Thus a receptor binds (or has a function of binding) a ligand. If the entities that form any one binary interaction are both proteins, one can think of each of them being ligands of the other. However, in most types of biological experiments, a ligand is usually a non-protein entity. In any case, the term isn't really a synonym for the function binding. I thought this was one of those things that was a function, but then removed and made a synonym? h From jaiswalp at science.oregonstate.edu Thu Oct 1 12:40:38 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu, 01 Oct 2009 12:40:38 -0700 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: References: Message-ID: <4AC505B6.6080206@science.oregonstate.edu> Gwinn Giglio, Michelle wrote: > > Hi, > > I don't see how we can retire these. Proteins that form the building blocks > of a structure have this as their "function". It is not an "action", but it > is still a "function". > Is it necessary to assign a function? Can they live with only process and component terms associated to gene products. > What is the function of a brick if not to form part of a wall? > There is no defined function for the brick. Someone MAY use the brick in building the wall, but it is not necessary. If used it has a component part_of relationship. # rectangular block of clay baked by the sun or in a kiln; used as a building or paving material from: wordnetweb.princeton.edu/perl/webwn > What would be the function for proteins like flagellin if these terms were > obsoleted? > What do you think of this annotation? A generic top level MF term seems okay. http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 Missing GO term. cellular component --is_a structural protein/molecule > Michelle > > > > On 10/1/09 2:53 PM, "Midori Harris" wrote: > >> I've wanted to for those aforementioned years. Let's see what the rest of >> the list says ... >> >> m >> >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> >>> Can we retire them. >>> >>> Pankaj >>> >>> Midori Harris wrote: >>>> These terms have never been ideal; we've known about the problems with them >>>> literally for years. 'Structural integrity' is no more a molecular function >>>> than the present names; it's a biological quality. >>>> >>>> m >>>> >>>> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>> >>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>> 9&session_id=3810amigo1254420818 >>>>> >>>>> This term and some other sibling terms may require renaming of the terms. >>>>> >>>>> As I understand, 'constituent' means a component of or part of. E.g. The >>>>> cell wall is composed of cellulose fiber, polysaccharides, and proteins. >>>>> Means these components are in essence is_a structural constituent of cell >>>>> wall and obviously these are not the function terms. >>>>> >>>>> The suggested function term could be 'structural integrity of a cell >>>>> wall'. Though it may as well be a process term. >>>>> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org From adiehl at informatics.jax.org Thu Oct 1 12:39:44 2009 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Thu, 01 Oct 2009 15:39:44 -0400 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: References: Message-ID: <4AC50580.30209@informatics.jax.org> If the molecular function ontology is really the "molecular functioning" ontology, i.e. an ontology of molecular-level processes, is being a structural constituent a an actual process? -- Alex Gwinn Giglio, Michelle wrote: > Hi, > > I don't see how we can retire these. Proteins that form the building blocks > of a structure have this as their "function". It is not an "action", but it > is still a "function". > > What is the function of a brick if not to form part of a wall? > > What would be the function for proteins like flagellin if these terms were > obsoleted? > > Michelle > > > > On 10/1/09 2:53 PM, "Midori Harris" wrote: > > >> I've wanted to for those aforementioned years. Let's see what the rest of >> the list says ... >> >> m >> >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> >> >>> Can we retire them. >>> >>> Pankaj >>> >>> Midori Harris wrote: >>> >>>> These terms have never been ideal; we've known about the problems with them >>>> literally for years. 'Structural integrity' is no more a molecular function >>>> than the present names; it's a biological quality. >>>> >>>> m >>>> >>>> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>> >>>> >>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>> 9&session_id=3810amigo1254420818 >>>>> >>>>> This term and some other sibling terms may require renaming of the terms. >>>>> >>>>> As I understand, 'constituent' means a component of or part of. E.g. The >>>>> cell wall is composed of cellulose fiber, polysaccharides, and proteins. >>>>> Means these components are in essence is_a structural constituent of cell >>>>> wall and obviously these are not the function terms. >>>>> >>>>> The suggested function term could be 'structural integrity of a cell >>>>> wall'. Though it may as well be a process term. >>>>> >>>>> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > -- Alexander D. Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From Judith.Blake at jax.org Thu Oct 1 13:13:23 2009 From: Judith.Blake at jax.org (Judith Blake) Date: Thu, 1 Oct 2009 16:13:23 -0400 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: Message-ID: We need terms for these actions; we just need to find the right term. These are functions (or as I'm learning to say, functionings). Right now... 'structural constituent function for the cell wall'... Or 'structural constituent of the cell wall'. That would be the MF term, ya? judy On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" wrote: Hi, I don't see how we can retire these. Proteins that form the building blocks of a structure have this as their "function". It is not an "action", but it is still a "function". What is the function of a brick if not to form part of a wall? What would be the function for proteins like flagellin if these terms were obsoleted? Michelle On 10/1/09 2:53 PM, "Midori Harris" wrote: > I've wanted to for those aforementioned years. Let's see what the rest of > the list says ... > > m > > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > >> Can we retire them. >> >> Pankaj >> >> Midori Harris wrote: >>> These terms have never been ideal; we've known about the problems with them >>> literally for years. 'Structural integrity' is no more a molecular function >>> than the present names; it's a biological quality. >>> >>> m >>> >>> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>> >>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>> 9&session_id=3810amigo1254420818 >>>> >>>> This term and some other sibling terms may require renaming of the terms. >>>> >>>> As I understand, 'constituent' means a component of or part of. E.g. The >>>> cell wall is composed of cellulose fiber, polysaccharides, and proteins. >>>> Means these components are in essence is_a structural constituent of cell >>>> wall and obviously these are not the function terms. >>>> >>>> The suggested function term could be 'structural integrity of a cell >>>> wall'. Though it may as well be a process term. >>>> >> > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go _______________________________________________ Go mailing list Go at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaiswalp at science.oregonstate.edu Thu Oct 1 13:23:40 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu, 01 Oct 2009 13:23:40 -0700 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: References: Message-ID: <4AC50FCC.50400@science.oregonstate.edu> We may agree with the annotations such as http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 Alternative suggestions for terms would be MF is_a structural constitution provision is_a cell wall structural constitution provision Pankaj Judith Blake wrote: > We need terms for these actions; we just need to find the right term. > These are functions (or as I?m learning to say, functionings). Right > now... ?structural constituent function for the cell wall?... Or > ?structural constituent of the cell wall?. That would be the MF term, ya? > > judy > > > On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" > wrote: > > > > > Hi, > > I don't see how we can retire these. Proteins that form the > building blocks > of a structure have this as their "function". It is not an > "action", but it > is still a "function". > > What is the function of a brick if not to form part of a wall? > > What would be the function for proteins like flagellin if these > terms were > obsoleted? > > Michelle > > > > On 10/1/09 2:53 PM, "Midori Harris" wrote: > > > I've wanted to for those aforementioned years. Let's see what the > rest of > > the list says ... > > > > m > > > > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > > > > > Can we retire them. > > > > > > Pankaj > > > > > > Midori Harris wrote: > > >> These terms have never been ideal; we've known about the > problems with them > > >> literally for years. 'Structural integrity' is no more a > molecular function > > >> than the present names; it's a biological quality. > > >> > > >> m > > >> > > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > > >> > > >>> > http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 > > >>> 9&session_id=3810amigo1254420818 > > >>> > > >>> This term and some other sibling terms may require renaming of > the terms. > > >>> > > >>> As I understand, 'constituent' means a component of or part of. > E.g. The > > >>> cell wall is composed of cellulose fiber, polysaccharides, and > proteins. > > >>> Means these components are in essence is_a structural > constituent of cell > > >>> wall and obviously these are not the function terms. > > >>> > > >>> The suggested function term could be 'structural integrity of a > cell > > >>> wall'. Though it may as well be a process term. > > >>> > > > > > _______________________________________________ > > Go mailing list > > Go at geneontology.org > > http://fafner.stanford.edu/mailman/listinfo/go > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org From kchris at genome.stanford.edu Thu Oct 1 13:42:46 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Thu, 1 Oct 2009 13:42:46 -0700 (PDT) Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC50FCC.50400@science.oregonstate.edu> References: <4AC50FCC.50400@science.oregonstate.edu> Message-ID: While we're on the subject of "structural constituent of x", what about the function term "structural constituent of ribosome"? This seems to express exactly the same information as the component term "ribosome". Personally, I would think that the ribosome itself has one or more molecular activities, that should be represented in the F ontology, but that merely being a component of the ribosome is not a function and that this term is redundant with the component term. -Karen On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > We may agree with the annotations such as > http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 > > Alternative suggestions for terms would be > > MF > is_a structural constitution provision > is_a cell wall structural constitution provision > > Pankaj > > Judith Blake wrote: >> We need terms for these actions; we just need to find the right term. >> These are functions (or as I?m learning to say, functionings). Right >> now... ?structural constituent function for the cell wall?... Or >> ?structural constituent of the cell wall?. That would be the MF term, ya? >> >> judy >> >> >> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >> wrote: >> >> >> >> >> Hi, >> >> I don't see how we can retire these. Proteins that form the >> building blocks >> of a structure have this as their "function". It is not an >> "action", but it >> is still a "function". >> >> What is the function of a brick if not to form part of a wall? >> >> What would be the function for proteins like flagellin if these >> terms were >> obsoleted? >> >> Michelle >> >> >> >> On 10/1/09 2:53 PM, "Midori Harris" wrote: >> >> > I've wanted to for those aforementioned years. Let's see what the >> rest of >> > the list says ... >> > >> > m >> > >> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> > >> > > Can we retire them. >> > > >> > > Pankaj >> > > >> > > Midori Harris wrote: >> > >> These terms have never been ideal; we've known about the >> problems with them >> > >> literally for years. 'Structural integrity' is no more a >> molecular function >> > >> than the present names; it's a biological quality. >> > >> >> > >> m >> > >> >> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> > >> >> > >>> >> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >> > >>> 9&session_id=3810amigo1254420818 >> > >>> >> > >>> This term and some other sibling terms may require renaming of >> the terms. >> > >>> >> > >>> As I understand, 'constituent' means a component of or part of. >> E.g. The >> > >>> cell wall is composed of cellulose fiber, polysaccharides, and >> proteins. >> > >>> Means these components are in essence is_a structural >> constituent of cell >> > >>> wall and obviously these are not the function terms. >> > >>> >> > >>> The suggested function term could be 'structural integrity of a >> cell >> > >>> wall'. Though it may as well be a process term. >> > >>> >> > > >> > _______________________________________________ >> > Go mailing list >> > Go at geneontology.org >> > http://fafner.stanford.edu/mailman/listinfo/go >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > -- > Pankaj Jaiswal > Assistant Professor > Dept. of Botany and Plant Pathology > 3082 Cordley Hall > Oregon State University > Corvallis, OR, 97331-2902, USA > > Ph.: +1-541-737-8471 > Fax: +1-541-737-3573 > Web: www.gramene.org > www.plantontology.org > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From jimhu at tamu.edu Thu Oct 1 13:49:40 2009 From: jimhu at tamu.edu (Jim Hu) Date: Thu, 1 Oct 2009 15:49:40 -0500 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC50FCC.50400@science.oregonstate.edu> References: <4AC50FCC.50400@science.oregonstate.edu> Message-ID: <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> - "constitution provision" is really awkward. - I don't understand how functioning as a structural protein is an action. - why not just have structural component as a high level term to distinguish from the implication that function is unknown if there are no MF terms, but infer what it's a structural component of from the CC terms? For Michelle's example, flagellin would get GO:0005198 ! structural molecule activity (function) GO:0009420 ! bacterial-type flagellum filament (component) Jim On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: > We may agree with the annotations such as > http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 > > Alternative suggestions for terms would be > > MF > is_a structural constitution provision > is_a cell wall structural constitution provision > > Pankaj > > Judith Blake wrote: >> We need terms for these actions; we just need to find the right >> term. These are functions (or as I?m learning to say, >> functionings). Right now... ?structural constituent function for >> the cell wall?... Or ?structural constituent of the cell wall?. >> That would be the MF term, ya? >> judy >> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" > > wrote: >> Hi, >> I don't see how we can retire these. Proteins that form the >> building blocks >> of a structure have this as their "function". It is not an >> "action", but it >> is still a "function". >> What is the function of a brick if not to form part of a wall? >> What would be the function for proteins like flagellin if these >> terms were >> obsoleted? >> Michelle >> On 10/1/09 2:53 PM, "Midori Harris" wrote: >> > I've wanted to for those aforementioned years. Let's see what >> the >> rest of >> > the list says ... >> > >> > m >> > >> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> > >> > > Can we retire them. >> > > >> > > Pankaj >> > > >> > > Midori Harris wrote: >> > >> These terms have never been ideal; we've known about the >> problems with them >> > >> literally for years. 'Structural integrity' is no more a >> molecular function >> > >> than the present names; it's a biological quality. >> > >> >> > >> m >> > >> >> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> > >> >> > >>> >> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >> > >>> 9&session_id=3810amigo1254420818 >> > >>> >> > >>> This term and some other sibling terms may require >> renaming of >> the terms. >> > >>> >> > >>> As I understand, 'constituent' means a component of or >> part of. >> E.g. The >> > >>> cell wall is composed of cellulose fiber, polysaccharides, >> and >> proteins. >> > >>> Means these components are in essence is_a structural >> constituent of cell >> > >>> wall and obviously these are not the function terms. >> > >>> >> > >>> The suggested function term could be 'structural integrity >> of a >> cell >> > >>> wall'. Though it may as well be a process term. >> > >>> >> > > >> > _______________________________________________ >> > Go mailing list >> > Go at geneontology.org >> > http://fafner.stanford.edu/mailman/listinfo/go >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > -- > Pankaj Jaiswal > Assistant Professor > Dept. of Botany and Plant Pathology > 3082 Cordley Hall > Oregon State University > Corvallis, OR, 97331-2902, USA > > Ph.: +1-541-737-8471 > Fax: +1-541-737-3573 > Web: www.gramene.org > www.plantontology.org > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Judith.Blake at jax.org Thu Oct 1 13:54:57 2009 From: Judith.Blake at jax.org (Judith Blake) Date: Thu, 1 Oct 2009 16:54:57 -0400 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: Message-ID: This is an old discussion :) I remember that we decided on this at a Bar Harbor meeting after rigorous discussion about how to annotate gene products that were members of a complex. and the issue was that the catalytic activity functioning part of the ribosome is the result of the activity of a peptide that is a member of the ribosome. The structural activity functioning part of the ribosome is the result of the activity of other peptides. Where we are going with all this, I think, is that we will have CC-MF links and complexes will be annotated to a MF and gp have a relationship of some sort to the CC. Judy On 10/1/09 4:42 PM, "Karen Christie" wrote: While we're on the subject of "structural constituent of x", what about the function term "structural constituent of ribosome"? This seems to express exactly the same information as the component term "ribosome". Personally, I would think that the ribosome itself has one or more molecular activities, that should be represented in the F ontology, but that merely being a component of the ribosome is not a function and that this term is redundant with the component term. -Karen On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > We may agree with the annotations such as > http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 > > Alternative suggestions for terms would be > > MF > is_a structural constitution provision > is_a cell wall structural constitution provision > > Pankaj > > Judith Blake wrote: >> We need terms for these actions; we just need to find the right term. >> These are functions (or as I'm learning to say, functionings). Right >> now... 'structural constituent function for the cell wall'... Or >> 'structural constituent of the cell wall'. That would be the MF term, ya? >> >> judy >> >> >> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >> wrote: >> >> >> >> >> Hi, >> >> I don't see how we can retire these. Proteins that form the >> building blocks >> of a structure have this as their "function". It is not an >> "action", but it >> is still a "function". >> >> What is the function of a brick if not to form part of a wall? >> >> What would be the function for proteins like flagellin if these >> terms were >> obsoleted? >> >> Michelle >> >> >> >> On 10/1/09 2:53 PM, "Midori Harris" wrote: >> >> > I've wanted to for those aforementioned years. Let's see what the >> rest of >> > the list says ... >> > >> > m >> > >> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> > >> > > Can we retire them. >> > > >> > > Pankaj >> > > >> > > Midori Harris wrote: >> > >> These terms have never been ideal; we've known about the >> problems with them >> > >> literally for years. 'Structural integrity' is no more a >> molecular function >> > >> than the present names; it's a biological quality. >> > >> >> > >> m >> > >> >> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >> > >> >> > >>> >> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >> > >>> 9&session_id=3810amigo1254420818 >> > >>> >> > >>> This term and some other sibling terms may require renaming of >> the terms. >> > >>> >> > >>> As I understand, 'constituent' means a component of or part of. >> E.g. The >> > >>> cell wall is composed of cellulose fiber, polysaccharides, and >> proteins. >> > >>> Means these components are in essence is_a structural >> constituent of cell >> > >>> wall and obviously these are not the function terms. >> > >>> >> > >>> The suggested function term could be 'structural integrity of a >> cell >> > >>> wall'. Though it may as well be a process term. >> > >>> >> > > >> > _______________________________________________ >> > Go mailing list >> > Go at geneontology.org >> > http://fafner.stanford.edu/mailman/listinfo/go >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > -- > Pankaj Jaiswal > Assistant Professor > Dept. of Botany and Plant Pathology > 3082 Cordley Hall > Oregon State University > Corvallis, OR, 97331-2902, USA > > Ph.: +1-541-737-8471 > Fax: +1-541-737-3573 > Web: www.gramene.org > www.plantontology.org > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaiswalp at science.oregonstate.edu Thu Oct 1 14:01:33 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu, 01 Oct 2009 14:01:33 -0700 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> Message-ID: <4AC518AD.6050000@science.oregonstate.edu> I think you got it. Also, just for a reasoning purpose we may need a term in GO:CC for structural part/component of part-X. Because here we are defining that it is a structural component of CC, but have no logical definition for structural_part in CC. Pankaj Jim Hu wrote: > - "constitution provision" is really awkward. > - I don't understand how functioning as a structural protein is an action. > - why not just have structural component as a high level term to > distinguish from the implication that function is unknown if there are > no MF terms, but infer what it's a structural component of from the CC > terms? For Michelle's example, flagellin would get > > GO:0005198 ! structural molecule activity (function) > GO:0009420 ! bacterial-type flagellum filament (component) > > Jim > > On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: > >> We may agree with the annotations such as >> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >> >> Alternative suggestions for terms would be >> >> MF >> is_a structural constitution provision >> is_a cell wall structural constitution provision >> >> Pankaj >> >> Judith Blake wrote: >>> We need terms for these actions; we just need to find the right term. >>> These are functions (or as I?m learning to say, functionings). >>> Right now... ?structural constituent function for the cell wall?... >>> Or ?structural constituent of the cell wall?. That would be the MF >>> term, ya? >>> judy >>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>> wrote: >>> Hi, >>> I don't see how we can retire these. Proteins that form the >>> building blocks >>> of a structure have this as their "function". It is not an >>> "action", but it >>> is still a "function". >>> What is the function of a brick if not to form part of a wall? >>> What would be the function for proteins like flagellin if these >>> terms were >>> obsoleted? >>> Michelle >>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>> > I've wanted to for those aforementioned years. Let's see what the >>> rest of From kchris at genome.stanford.edu Thu Oct 1 14:04:59 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Thu, 1 Oct 2009 14:04:59 -0700 (PDT) Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: References: Message-ID: Yes, it is an old discussion, but we have also just come up with a proposal to effectively remove the equally old F term for "splicing factor activity" from the F ontology. I think the ribosome may merit similar treatment. The actual activity of the ribosome, peptide-bond formation, or whatever better way there may be to say that, is a function, so maybe we can represent that. But just being a component of the ribosome is not a function, and it is basically making an identical statement to the component annotation. -Karen On Thu, 1 Oct 2009, Judith Blake wrote: > This is an old discussion :) I remember that we decided on this at a > Bar Harbor meeting after rigorous discussion about how to annotate gene > products that were members of a complex. > > and the issue was that the catalytic activity functioning part of the > ribosome is the result of the activity of a peptide that is a member of > the ribosome. The structural activity functioning part of the ribosome > is the result of the activity of other peptides. > > Where we are going with all this, I think, is that we will have CC-MF > links and complexes will be annotated to a MF and gp have a relationship > of some sort to the CC. > > Judy > > > > > On 10/1/09 4:42 PM, "Karen Christie" wrote: > > While we're on the subject of "structural constituent of x", what about > the function term "structural constituent of ribosome"? This seems to > express exactly the same information as the component term "ribosome". > > Personally, I would think that the ribosome itself has one or more > molecular activities, that should be represented in the F ontology, but > that merely being a component of the ribosome is not a function and that > this term is redundant with the component term. > > -Karen > > > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: > >> We may agree with the annotations such as >> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >> >> Alternative suggestions for terms would be >> >> MF >> is_a structural constitution provision >> is_a cell wall structural constitution provision >> >> Pankaj >> >> Judith Blake wrote: >>> We need terms for these actions; we just need to find the right term. >>> These are functions (or as I'm learning to say, functionings). Right >>> now... 'structural constituent function for the cell wall'... Or >>> 'structural constituent of the cell wall'. That would be the MF term, ya? >>> >>> judy >>> >>> >>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>> wrote: >>> >>> >>> >>> >>> Hi, >>> >>> I don't see how we can retire these. Proteins that form the >>> building blocks >>> of a structure have this as their "function". It is not an >>> "action", but it >>> is still a "function". >>> >>> What is the function of a brick if not to form part of a wall? >>> >>> What would be the function for proteins like flagellin if these >>> terms were >>> obsoleted? >>> >>> Michelle >>> >>> >>> >>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>> >>> > I've wanted to for those aforementioned years. Let's see what the >>> rest of >>> > the list says ... >>> > >>> > m >>> > >>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>> > >>> >> Can we retire them. >>> >> >>> >> Pankaj >>> >> >>> >> Midori Harris wrote: >>> >>> These terms have never been ideal; we've known about the >>> problems with them >>> >>> literally for years. 'Structural integrity' is no more a >>> molecular function >>> >>> than the present names; it's a biological quality. >>> >>> >>> >>> m >>> >>> >>> >>> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>> >>> >>> >>>> >>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>> >>>> 9&session_id=3810amigo1254420818 >>> >>>> >>> >>>> This term and some other sibling terms may require renaming of >>> the terms. >>> >>>> >>> >>>> As I understand, 'constituent' means a component of or part of. >>> E.g. The >>> >>>> cell wall is composed of cellulose fiber, polysaccharides, and >>> proteins. >>> >>>> Means these components are in essence is_a structural >>> constituent of cell >>> >>>> wall and obviously these are not the function terms. >>> >>>> >>> >>>> The suggested function term could be 'structural integrity of a >>> cell >>> >>>> wall'. Though it may as well be a process term. >>> >>>> >>> >> >>> > _______________________________________________ >>> > Go mailing list >>> > Go at geneontology.org >>> > http://fafner.stanford.edu/mailman/listinfo/go >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >> >> -- >> Pankaj Jaiswal >> Assistant Professor >> Dept. of Botany and Plant Pathology >> 3082 Cordley Hall >> Oregon State University >> Corvallis, OR, 97331-2902, USA >> >> Ph.: +1-541-737-8471 >> Fax: +1-541-737-3573 >> Web: www.gramene.org >> www.plantontology.org >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > From cjm at berkeleybop.org Thu Oct 1 15:26:09 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 1 Oct 2009 23:26:09 +0100 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> Message-ID: On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: > - "constitution provision" is really awkward. > - I don't understand how functioning as a structural protein is an > action. > - why not just have structural component as a high level term to > distinguish from the implication that function is unknown if there > are no MF terms, but infer what it's a structural component of from > the CC terms? For Michelle's example, flagellin would get > > GO:0005198 ! structural molecule activity (function) > GO:0009420 ! bacterial-type flagellum filament (component) two annotations say less than a single annotation to the compositional term (either pre-composed in the ontology, or post-composed in the annotation using col16). > Jim > > On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: > >> We may agree with the annotations such as >> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >> >> Alternative suggestions for terms would be >> >> MF >> is_a structural constitution provision >> is_a cell wall structural constitution provision >> >> Pankaj >> >> Judith Blake wrote: >>> We need terms for these actions; we just need to find the right >>> term. These are functions (or as I?m learning to say, >>> functionings). Right now... ?structural constituent function for >>> the cell wall?... Or ?structural constituent of the cell wall?. >>> That would be the MF term, ya? >>> judy >>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >> > wrote: >>> Hi, >>> I don't see how we can retire these. Proteins that form the >>> building blocks >>> of a structure have this as their "function". It is not an >>> "action", but it >>> is still a "function". >>> What is the function of a brick if not to form part of a wall? >>> What would be the function for proteins like flagellin if these >>> terms were >>> obsoleted? >>> Michelle >>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>> > I've wanted to for those aforementioned years. Let's see what >>> the >>> rest of >>> > the list says ... >>> > >>> > m >>> > >>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>> > >>> > > Can we retire them. >>> > > >>> > > Pankaj >>> > > >>> > > Midori Harris wrote: >>> > >> These terms have never been ideal; we've known about the >>> problems with them >>> > >> literally for years. 'Structural integrity' is no more a >>> molecular function >>> > >> than the present names; it's a biological quality. >>> > >> >>> > >> m >>> > >> >>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>> > >> >>> > >>> >>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>> > >>> 9&session_id=3810amigo1254420818 >>> > >>> >>> > >>> This term and some other sibling terms may require >>> renaming of >>> the terms. >>> > >>> >>> > >>> As I understand, 'constituent' means a component of or >>> part of. >>> E.g. The >>> > >>> cell wall is composed of cellulose fiber, polysaccharides, >>> and >>> proteins. >>> > >>> Means these components are in essence is_a structural >>> constituent of cell >>> > >>> wall and obviously these are not the function terms. >>> > >>> >>> > >>> The suggested function term could be 'structural integrity >>> of a >>> cell >>> > >>> wall'. Though it may as well be a process term. >>> > >>> >>> > > >>> > _______________________________________________ >>> > Go mailing list >>> > Go at geneontology.org >>> > http://fafner.stanford.edu/mailman/listinfo/go >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> -- >> Pankaj Jaiswal >> Assistant Professor >> Dept. of Botany and Plant Pathology >> 3082 Cordley Hall >> Oregon State University >> Corvallis, OR, 97331-2902, USA >> >> Ph.: +1-541-737-8471 >> Fax: +1-541-737-3573 >> Web: www.gramene.org >> www.plantontology.org >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > ===================================== > Jim Hu > Associate Professor > Dept. of Biochemistry and Biophysics > 2128 TAMU > Texas A&M Univ. > College Station, TX 77843-2128 > 979-862-4054 > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From cjm at berkeleybop.org Thu Oct 1 15:34:15 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 1 Oct 2009 23:34:15 +0100 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC50580.30209@informatics.jax.org> References: <4AC50580.30209@informatics.jax.org> Message-ID: <7A5593B2-3A43-421C-AB03-79006EE222D2@berkeleybop.org> One answer is that MF consists *mostly* of terms representing molecular-level processes (e.g. all activity terms) but also contains some terms representing quality / bfo-function type things (e.g. structural constituent terms). cf Amelia's presentation from St Croix. On Oct 1, 2009, at 8:39 PM, Alexander Diehl wrote: > If the molecular function ontology is really the "molecular > functioning" ontology, i.e. an ontology of molecular-level > processes, is being a structural constituent a an actual process? > > -- Alex > > > Gwinn Giglio, Michelle wrote: >> Hi, >> >> I don't see how we can retire these. Proteins that form the >> building blocks >> of a structure have this as their "function". It is not an >> "action", but it >> is still a "function". >> >> What is the function of a brick if not to form part of a wall? >> >> What would be the function for proteins like flagellin if these >> terms were >> obsoleted? >> >> Michelle >> >> >> >> On 10/1/09 2:53 PM, "Midori Harris" wrote: >> >> >>> I've wanted to for those aforementioned years. Let's see what the >>> rest of >>> the list says ... >>> >>> m >>> >>> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>> >>> >>>> Can we retire them. >>>> >>>> Pankaj >>>> >>>> Midori Harris wrote: >>>> >>>>> These terms have never been ideal; we've known about the >>>>> problems with them >>>>> literally for years. 'Structural integrity' is no more a >>>>> molecular function >>>>> than the present names; it's a biological quality. >>>>> >>>>> m >>>>> >>>>> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>> >>>>> >>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>>> 9&session_id=3810amigo1254420818 >>>>>> >>>>>> This term and some other sibling terms may require renaming of >>>>>> the terms. >>>>>> >>>>>> As I understand, 'constituent' means a component of or part of. >>>>>> E.g. The >>>>>> cell wall is composed of cellulose fiber, polysaccharides, and >>>>>> proteins. >>>>>> Means these components are in essence is_a structural >>>>>> constituent of cell >>>>>> wall and obviously these are not the function terms. >>>>>> >>>>>> The suggested function term could be 'structural integrity of a >>>>>> cell >>>>>> wall'. Though it may as well be a process term. >>>>>> >>>>>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > > -- > Alexander D. Diehl, Ph.D. > Senior Scientific Curator > Mouse Genome Informatics > The Jackson Laboratory > 600 Main Street > Bar Harbor, ME 04609 > > email: adiehl at informatics.jax.org > work: +1 (207) 288-6427 > fax: +1 (207) 288-6131 > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From dph at informatics.jax.org Thu Oct 1 15:42:22 2009 From: dph at informatics.jax.org (David Hill) Date: Thu, 01 Oct 2009 18:42:22 -0400 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> Message-ID: <4AC5304E.6080100@informatics.jax.org> If we stick with the idea that all molecular functions are parts of biological processes, then we must ask what is the function of a gene product that has a role 'structural constituent of x' with respect to a biological process. We have many processes that are 'x structural organization'. In this sense, structural organization refers to the physical shaping of a structure. I think we need to have a function for a gene product like actin. It is like a brick. A brick contributes to the structural organization of a building. We could describe the function of actin as 'molecular function involved in microfilament structural organization'. We need to decide whether the current 'structural' functions are worthy. Are they providing a function that contributes to a meaningful physical organization of a structure? For those of you who are old enough in GO, we had a similar argument about an old molecular function called 'tRNA'. We renamed the term 'triplet codon-amino acid adapter activity' and defined it with respect to its role in a process: The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis.. David Chris Mungall wrote: > > On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: > >> - "constitution provision" is really awkward. >> - I don't understand how functioning as a structural protein is an >> action. >> - why not just have structural component as a high level term to >> distinguish from the implication that function is unknown if there >> are no MF terms, but infer what it's a structural component of from >> the CC terms? For Michelle's example, flagellin would get >> >> GO:0005198 ! structural molecule activity (function) >> GO:0009420 ! bacterial-type flagellum filament (component) > > two annotations say less than a single annotation to the compositional > term (either pre-composed in the ontology, or post-composed in the > annotation using col16). > >> Jim >> >> On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: >> >>> We may agree with the annotations such as >>> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >>> >>> >>> Alternative suggestions for terms would be >>> >>> MF >>> is_a structural constitution provision >>> is_a cell wall structural constitution provision >>> >>> Pankaj >>> >>> Judith Blake wrote: >>>> We need terms for these actions; we just need to find the right >>>> term. These are functions (or as I?m learning to say, >>>> functionings). Right now... ?structural constituent function for >>>> the cell wall?... Or ?structural constituent of the cell wall?. >>>> That would be the MF term, ya? >>>> judy >>>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>>> wrote: >>>> Hi, >>>> I don't see how we can retire these. Proteins that form the >>>> building blocks >>>> of a structure have this as their "function". It is not an >>>> "action", but it >>>> is still a "function". >>>> What is the function of a brick if not to form part of a wall? >>>> What would be the function for proteins like flagellin if these >>>> terms were >>>> obsoleted? >>>> Michelle >>>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>>> > I've wanted to for those aforementioned years. Let's see what the >>>> rest of >>>> > the list says ... >>>> > >>>> > m >>>> > >>>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>> > >>>> > > Can we retire them. >>>> > > >>>> > > Pankaj >>>> > > >>>> > > Midori Harris wrote: >>>> > >> These terms have never been ideal; we've known about the >>>> problems with them >>>> > >> literally for years. 'Structural integrity' is no more a >>>> molecular function >>>> > >> than the present names; it's a biological quality. >>>> > >> >>>> > >> m >>>> > >> >>>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>> > >> >>>> > >>> >>>> >>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>> >>>> > >>> 9&session_id=3810amigo1254420818 >>>> > >>> >>>> > >>> This term and some other sibling terms may require renaming of >>>> the terms. >>>> > >>> >>>> > >>> As I understand, 'constituent' means a component of or part >>>> of. >>>> E.g. The >>>> > >>> cell wall is composed of cellulose fiber, polysaccharides, and >>>> proteins. >>>> > >>> Means these components are in essence is_a structural >>>> constituent of cell >>>> > >>> wall and obviously these are not the function terms. >>>> > >>> >>>> > >>> The suggested function term could be 'structural integrity >>>> of a >>>> cell >>>> > >>> wall'. Though it may as well be a process term. >>>> > >>> >>>> > > >>>> > _______________________________________________ >>>> > Go mailing list >>>> > Go at geneontology.org >>>> > http://fafner.stanford.edu/mailman/listinfo/go >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> -- >>> Pankaj Jaiswal >>> Assistant Professor >>> Dept. of Botany and Plant Pathology >>> 3082 Cordley Hall >>> Oregon State University >>> Corvallis, OR, 97331-2902, USA >>> >>> Ph.: +1-541-737-8471 >>> Fax: +1-541-737-3573 >>> Web: www.gramene.org >>> www.plantontology.org >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> ===================================== >> Jim Hu >> Associate Professor >> Dept. of Biochemistry and Biophysics >> 2128 TAMU >> Texas A&M Univ. >> College Station, TX 77843-2128 >> 979-862-4054 >> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go -- 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 kchris at genome.stanford.edu Thu Oct 1 16:13:52 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Thu, 1 Oct 2009 16:13:52 -0700 (PDT) Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC5304E.6080100@informatics.jax.org> References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> <4AC5304E.6080100@informatics.jax.org> Message-ID: sort of brainstorming here, just thinking trying to think through a possible way to distinguish between things we do and do not need to represent in Function... it may not work, but it seems interesting to try to think it through and share with the group to see if this is a useful way of thinking about this issue... Perhaps we should think about the idea of distinguishing between something that is a structural constitent of something that is itself considered for its structural role, vs a structural constituent of something that once assembled has a catalytic role. Actin is a constituent of a type of filament. While the filament is a dynamic structure, in terms of being assembled on one end and disassembled on the other, it is basically a structure that other gene products use to move things around, and more... Similarly, flagellin is a unit of something that is basically a structure, the flagellum. I realize the flagellum does have a larger role in terms of motility, but that's implemented through motor proteins rotating a long filament, which itself is basically structural. The cell wall is also largely structural. However, things like the spliceosome and the ribosome, while very large as complexes go, are not generally considered to be structural constitents of the cell. Both of these things have catalytic roles. It seems that we do need to represent the catalytic activity that is ascribed to the complex (we already do this for the spliceosome). But I don't think we need to represent being a member of a very large complex as a function. -Karen On Thu, 1 Oct 2009, David Hill wrote: > If we stick with the idea that all molecular functions are parts of > biological processes, then we must ask what is the function of a gene product > that has a role 'structural constituent of x' with respect to a biological > process. We have many processes that are 'x structural organization'. In this > sense, structural organization refers to the physical shaping of a structure. > > I think we need to have a function for a gene product like actin. It is like > a brick. A brick contributes to the structural organization of a building. We > could describe the function of actin as 'molecular function involved in > microfilament structural organization'. We need to decide whether the current > 'structural' functions are worthy. Are they providing a function that > contributes to a meaningful physical organization of a structure? > > For those of you who are old enough in GO, we had a similar argument about an > old molecular function called 'tRNA'. We renamed the term 'triplet > codon-amino acid adapter activity' and defined it with respect to its role in > a process: The codon binding activity of a tRNA that positions an activated > amino acid, mediating its insertion at the correct point in the sequence of a > nascent polypeptide chain during protein synthesis.. > > David > > > > Chris Mungall wrote: >> >> On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: >> >>> - "constitution provision" is really awkward. >>> - I don't understand how functioning as a structural protein is an action. >>> - why not just have structural component as a high level term to >>> distinguish from the implication that function is unknown if there are no >>> MF terms, but infer what it's a structural component of from the CC terms? >>> For Michelle's example, flagellin would get >>> >>> GO:0005198 ! structural molecule activity (function) >>> GO:0009420 ! bacterial-type flagellum filament (component) >> >> two annotations say less than a single annotation to the compositional term >> (either pre-composed in the ontology, or post-composed in the annotation >> using col16). >> >>> Jim >>> >>> On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: >>> >>>> We may agree with the annotations such as >>>> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >>>> >>>> Alternative suggestions for terms would be >>>> >>>> MF >>>> is_a structural constitution provision >>>> is_a cell wall structural constitution provision >>>> >>>> Pankaj >>>> >>>> Judith Blake wrote: >>>>> We need terms for these actions; we just need to find the right term. >>>>> These are functions (or as I?m learning to say, functionings). Right >>>>> now... ?structural constituent function for the cell wall?... Or >>>>> ?structural constituent of the cell wall?. That would be the MF term, >>>>> ya? >>>>> judy >>>>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>>>> wrote: >>>>> Hi, >>>>> I don't see how we can retire these. Proteins that form the >>>>> building blocks >>>>> of a structure have this as their "function". It is not an >>>>> "action", but it >>>>> is still a "function". >>>>> What is the function of a brick if not to form part of a wall? >>>>> What would be the function for proteins like flagellin if these >>>>> terms were >>>>> obsoleted? >>>>> Michelle >>>>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>>>> > I've wanted to for those aforementioned years. Let's see what the >>>>> rest of >>>>> > the list says ... >>>>> > >>>>> > m >>>>> > >>>>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>> > >>>>> > > Can we retire them. >>>>> > > >>>>> > > Pankaj >>>>> > > >>>>> > > Midori Harris wrote: >>>>> > >> These terms have never been ideal; we've known about the >>>>> problems with them >>>>> > >> literally for years. 'Structural integrity' is no more a >>>>> molecular function >>>>> > >> than the present names; it's a biological quality. >>>>> > >> >>>>> > >> m >>>>> > >> >>>>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>> > >> >>>>> > >>> >>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>> > >>> 9&session_id=3810amigo1254420818 >>>>> > >>> >>>>> > >>> This term and some other sibling terms may require renaming of >>>>> the terms. >>>>> > >>> >>>>> > >>> As I understand, 'constituent' means a component of or part of. >>>>> E.g. The >>>>> > >>> cell wall is composed of cellulose fiber, polysaccharides, and >>>>> proteins. >>>>> > >>> Means these components are in essence is_a structural >>>>> constituent of cell >>>>> > >>> wall and obviously these are not the function terms. >>>>> > >>> >>>>> > >>> The suggested function term could be 'structural integrity of a >>>>> cell >>>>> > >>> wall'. Though it may as well be a process term. >>>>> > >>> >>>>> > > >>>>> > _______________________________________________ >>>>> > Go mailing list >>>>> > Go at geneontology.org >>>>> > http://fafner.stanford.edu/mailman/listinfo/go >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>>> -- >>>> Pankaj Jaiswal >>>> Assistant Professor >>>> Dept. of Botany and Plant Pathology >>>> 3082 Cordley Hall >>>> Oregon State University >>>> Corvallis, OR, 97331-2902, USA >>>> >>>> Ph.: +1-541-737-8471 >>>> Fax: +1-541-737-3573 >>>> Web: www.gramene.org >>>> www.plantontology.org >>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> ===================================== >>> Jim Hu >>> Associate Professor >>> Dept. of Biochemistry and Biophysics >>> 2128 TAMU >>> Texas A&M Univ. >>> College Station, TX 77843-2128 >>> 979-862-4054 >>> >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > -- > 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 > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From dph at informatics.jax.org Thu Oct 1 18:52:07 2009 From: dph at informatics.jax.org (David Hill) Date: Thu, 01 Oct 2009 21:52:07 -0400 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> <4AC5304E.6080100@informatics.jax.org> Message-ID: <4AC55CC7.30808@informatics.jax.org> Karen, I think this is a good way to think about this. If there are no gene products that contribute to the ribosome like a brick contributes to a chimney, play a role in its physical organization, then we ditch the function 'structural constituent of ribosome' or whatever other name we choose for these kinds of terms. Karen Christie wrote: > sort of brainstorming here, just thinking trying to think through a > possible way to distinguish between things we do and do not need to > represent in Function... it may not work, but it seems interesting to > try to think it through and share with the group to see if this is a > useful way of thinking about this issue... > > Perhaps we should think about the idea of distinguishing between > something that is a structural constitent of something that is itself > considered for its structural role, vs a structural constituent of > something that once assembled has a catalytic role. > > Actin is a constituent of a type of filament. While the filament is a > dynamic structure, in terms of being assembled on one end and > disassembled on the other, it is basically a structure that other gene > products use to move things around, and more... Similarly, flagellin > is a unit of something that is basically a structure, the flagellum. I > realize the flagellum does have a larger role in terms of motility, > but that's implemented through motor proteins rotating a long > filament, which itself is basically structural. The cell wall is also > largely structural. > > However, things like the spliceosome and the ribosome, while very > large as complexes go, are not generally considered to be structural > constitents of the cell. Both of these things have catalytic roles. It > seems that we do need to represent the catalytic activity that is > ascribed to the complex (we already do this for the spliceosome). But > I don't think we need to represent being a member of a very large > complex as a function. > > -Karen > > > > > On Thu, 1 Oct 2009, David Hill wrote: > >> If we stick with the idea that all molecular functions are parts of >> biological processes, then we must ask what is the function of a gene >> product that has a role 'structural constituent of x' with respect to >> a biological process. We have many processes that are 'x structural >> organization'. In this sense, structural organization refers to the >> physical shaping of a structure. >> >> I think we need to have a function for a gene product like actin. It >> is like a brick. A brick contributes to the structural organization >> of a building. We could describe the function of actin as 'molecular >> function involved in microfilament structural organization'. We need >> to decide whether the current 'structural' functions are worthy. Are >> they providing a function that contributes to a meaningful physical >> organization of a structure? >> >> For those of you who are old enough in GO, we had a similar argument >> about an old molecular function called 'tRNA'. We renamed the term >> 'triplet codon-amino acid adapter activity' and defined it with >> respect to its role in a process: The codon binding activity of a >> tRNA that positions an activated amino acid, mediating its insertion >> at the correct point in the sequence of a nascent polypeptide chain >> during protein synthesis.. >> >> David >> >> >> >> Chris Mungall wrote: >>> >>> On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: >>> >>>> - "constitution provision" is really awkward. >>>> - I don't understand how functioning as a structural protein is an >>>> action. >>>> - why not just have structural component as a high level term to >>>> distinguish from the implication that function is unknown if there >>>> are no MF terms, but infer what it's a structural component of from >>>> the CC terms? For Michelle's example, flagellin would get >>>> >>>> GO:0005198 ! structural molecule activity (function) >>>> GO:0009420 ! bacterial-type flagellum filament (component) >>> >>> two annotations say less than a single annotation to the >>> compositional term (either pre-composed in the ontology, or >>> post-composed in the annotation using col16). >>> >>>> Jim >>>> >>>> On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: >>>> >>>>> We may agree with the annotations such as >>>>> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >>>>> >>>>> Alternative suggestions for terms would be >>>>> >>>>> MF >>>>> is_a structural constitution provision >>>>> is_a cell wall structural constitution provision >>>>> >>>>> Pankaj >>>>> >>>>> Judith Blake wrote: >>>>>> We need terms for these actions; we just need to find the right >>>>>> term. These are functions (or as I?m learning to say, >>>>>> functionings). Right now... ?structural constituent function >>>>>> for the cell wall?... Or ?structural constituent of the cell >>>>>> wall?. That would be the MF term, ya? >>>>>> judy >>>>>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>>>>> wrote: >>>>>> Hi, >>>>>> I don't see how we can retire these. Proteins that form the >>>>>> building blocks >>>>>> of a structure have this as their "function". It is not an >>>>>> "action", but it >>>>>> is still a "function". >>>>>> What is the function of a brick if not to form part of a wall? >>>>>> What would be the function for proteins like flagellin if these >>>>>> terms were >>>>>> obsoleted? >>>>>> Michelle >>>>>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>>>>> > I've wanted to for those aforementioned years. Let's see >>>>>> what the >>>>>> rest of >>>>>> > the list says ... >>>>>> > >>>>>> > m >>>>>> > >>>>>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>> > >>>>>> > > Can we retire them. >>>>>> > > >>>>>> > > Pankaj >>>>>> > > >>>>>> > > Midori Harris wrote: >>>>>> > >> These terms have never been ideal; we've known about the >>>>>> problems with them >>>>>> > >> literally for years. 'Structural integrity' is no more a >>>>>> molecular function >>>>>> > >> than the present names; it's a biological quality. >>>>>> > >> >>>>>> > >> m >>>>>> > >> >>>>>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>> > >> >>>>>> > >>> >>>>>> >>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>>> >>>>>> > >>> 9&session_id=3810amigo1254420818 >>>>>> > >>> >>>>>> > >>> This term and some other sibling terms may require >>>>>> renaming of >>>>>> the terms. >>>>>> > >>> >>>>>> > >>> As I understand, 'constituent' means a component of or >>>>>> part of. >>>>>> E.g. The >>>>>> > >>> cell wall is composed of cellulose fiber, >>>>>> polysaccharides, and >>>>>> proteins. >>>>>> > >>> Means these components are in essence is_a structural >>>>>> constituent of cell >>>>>> > >>> wall and obviously these are not the function terms. >>>>>> > >>> >>>>>> > >>> The suggested function term could be 'structural >>>>>> integrity of a >>>>>> cell >>>>>> > >>> wall'. Though it may as well be a process term. >>>>>> > >>> >>>>>> > > >>>>>> > _______________________________________________ >>>>>> > Go mailing list >>>>>> > Go at geneontology.org >>>>>> > http://fafner.stanford.edu/mailman/listinfo/go >>>>>> _______________________________________________ >>>>>> Go mailing list >>>>>> Go at geneontology.org >>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>> >>>>> -- >>>>> Pankaj Jaiswal >>>>> Assistant Professor >>>>> Dept. of Botany and Plant Pathology >>>>> 3082 Cordley Hall >>>>> Oregon State University >>>>> Corvallis, OR, 97331-2902, USA >>>>> >>>>> Ph.: +1-541-737-8471 >>>>> Fax: +1-541-737-3573 >>>>> Web: www.gramene.org >>>>> www.plantontology.org >>>>> >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>>> ===================================== >>>> Jim Hu >>>> Associate Professor >>>> Dept. of Biochemistry and Biophysics >>>> 2128 TAMU >>>> Texas A&M Univ. >>>> College Station, TX 77843-2128 >>>> 979-862-4054 >>>> >>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> -- >> 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 >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> -- 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 kchris at genome.stanford.edu Thu Oct 1 21:29:07 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Thu, 1 Oct 2009 21:29:07 -0700 (PDT) Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC55CC7.30808@informatics.jax.org> References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> <4AC5304E.6080100@informatics.jax.org> <4AC55CC7.30808@informatics.jax.org> Message-ID: Actually, considering that the ribosome has a catalytic function, I think that, similarly to other complexes where we represent their catalytic function in the F ontology, that this is the only function of the ribosome that needs to be represented in the F ontology. If we need to represent the "function" of being a member of the complex, then we may as well start having function terms like "structural constituent of RNA polymerase", "structural constituent of spliceosome", "structrual constituent of TFIIH core complex", etc. I don't think being a member of a complex is a function, and that's basically what our current F term for "structural constituent of ribosome" is equivalent to. It just seems really odd that for most complexes with a catalytic activity, we represent that catalytic activity in the function ontology (DNA & RNA polymerases, metabolic enzymes, etc.), but with the ribosome, we try to represent the "function" of individual gene products in forming the ribosome complex itself. However, for a comparably large ribonucleoprotein complex, that also has a catalytic activity, e.g. the spliceosome, we do not have a comparable term for "structural constituent of the spliceosome". I think the "brick" type function may well be valid for structures like walls (e.g. cell wall) and other things that are themselves structural, but I don't see why we need to represent a "brick" function for members of a catalytic complex. -Karen On Thu, 1 Oct 2009, David Hill wrote: > Karen, > > I think this is a good way to think about this. If there are no gene products > that contribute to the ribosome like a brick contributes to a chimney, play a > role in its physical organization, then we ditch the function 'structural > constituent of ribosome' or whatever other name we choose for these kinds of > terms. > > > > > Karen Christie wrote: >> sort of brainstorming here, just thinking trying to think through a >> possible way to distinguish between things we do and do not need to >> represent in Function... it may not work, but it seems interesting to try >> to think it through and share with the group to see if this is a useful way >> of thinking about this issue... >> >> Perhaps we should think about the idea of distinguishing between something >> that is a structural constitent of something that is itself considered for >> its structural role, vs a structural constituent of something that once >> assembled has a catalytic role. >> >> Actin is a constituent of a type of filament. While the filament is a >> dynamic structure, in terms of being assembled on one end and disassembled >> on the other, it is basically a structure that other gene products use to >> move things around, and more... Similarly, flagellin is a unit of something >> that is basically a structure, the flagellum. I realize the flagellum does >> have a larger role in terms of motility, but that's implemented through >> motor proteins rotating a long filament, which itself is basically >> structural. The cell wall is also largely structural. >> >> However, things like the spliceosome and the ribosome, while very large as >> complexes go, are not generally considered to be structural constitents of >> the cell. Both of these things have catalytic roles. It seems that we do >> need to represent the catalytic activity that is ascribed to the complex >> (we already do this for the spliceosome). But I don't think we need to >> represent being a member of a very large complex as a function. >> >> -Karen >> >> >> >> >> On Thu, 1 Oct 2009, David Hill wrote: >> >>> If we stick with the idea that all molecular functions are parts of >>> biological processes, then we must ask what is the function of a gene >>> product that has a role 'structural constituent of x' with respect to a >>> biological process. We have many processes that are 'x structural >>> organization'. In this sense, structural organization refers to the >>> physical shaping of a structure. >>> >>> I think we need to have a function for a gene product like actin. It is >>> like a brick. A brick contributes to the structural organization of a >>> building. We could describe the function of actin as 'molecular function >>> involved in microfilament structural organization'. We need to decide >>> whether the current 'structural' functions are worthy. Are they providing >>> a function that contributes to a meaningful physical organization of a >>> structure? >>> >>> For those of you who are old enough in GO, we had a similar argument about >>> an old molecular function called 'tRNA'. We renamed the term 'triplet >>> codon-amino acid adapter activity' and defined it with respect to its role >>> in a process: The codon binding activity of a tRNA that positions an >>> activated amino acid, mediating its insertion at the correct point in the >>> sequence of a nascent polypeptide chain during protein synthesis.. >>> >>> David >>> >>> >>> >>> Chris Mungall wrote: >>>> >>>> On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: >>>> >>>>> - "constitution provision" is really awkward. >>>>> - I don't understand how functioning as a structural protein is an >>>>> action. >>>>> - why not just have structural component as a high level term to >>>>> distinguish from the implication that function is unknown if there are >>>>> no MF terms, but infer what it's a structural component of from the CC >>>>> terms? For Michelle's example, flagellin would get >>>>> >>>>> GO:0005198 ! structural molecule activity (function) >>>>> GO:0009420 ! bacterial-type flagellum filament (component) >>>> >>>> two annotations say less than a single annotation to the compositional >>>> term (either pre-composed in the ontology, or post-composed in the >>>> annotation using col16). >>>> >>>>> Jim >>>>> >>>>> On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: >>>>> >>>>>> We may agree with the annotations such as >>>>>> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >>>>>> Alternative suggestions for terms would be >>>>>> >>>>>> MF >>>>>> is_a structural constitution provision >>>>>> is_a cell wall structural constitution provision >>>>>> >>>>>> Pankaj >>>>>> >>>>>> Judith Blake wrote: >>>>>>> We need terms for these actions; we just need to find the right term. >>>>>>> These are functions (or as I?m learning to say, functionings). Right >>>>>>> now... ?structural constituent function for the cell wall?... Or >>>>>>> ?structural constituent of the cell wall?. That would be the MF >>>>>>> term, ya? >>>>>>> judy >>>>>>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>>>>>> wrote: >>>>>>> Hi, >>>>>>> I don't see how we can retire these. Proteins that form the >>>>>>> building blocks >>>>>>> of a structure have this as their "function". It is not an >>>>>>> "action", but it >>>>>>> is still a "function". >>>>>>> What is the function of a brick if not to form part of a wall? >>>>>>> What would be the function for proteins like flagellin if these >>>>>>> terms were >>>>>>> obsoleted? >>>>>>> Michelle >>>>>>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>>>>>> > I've wanted to for those aforementioned years. Let's see what the >>>>>>> rest of >>>>>>> > the list says ... >>>>>>> > >>>>>>> > m >>>>>>> > >>>>>>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>>> > >>>>>>> > > Can we retire them. >>>>>>> > > >>>>>>> > > Pankaj >>>>>>> > > >>>>>>> > > Midori Harris wrote: >>>>>>> > >> These terms have never been ideal; we've known about the >>>>>>> problems with them >>>>>>> > >> literally for years. 'Structural integrity' is no more a >>>>>>> molecular function >>>>>>> > >> than the present names; it's a biological quality. >>>>>>> > >> >>>>>>> > >> m >>>>>>> > >> >>>>>>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>>> > >> >>>>>>> > >>> >>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>>>> > >>> 9&session_id=3810amigo1254420818 >>>>>>> > >>> >>>>>>> > >>> This term and some other sibling terms may require renaming of >>>>>>> the terms. >>>>>>> > >>> >>>>>>> > >>> As I understand, 'constituent' means a component of or part >>>>>>> of. >>>>>>> E.g. The >>>>>>> > >>> cell wall is composed of cellulose fiber, polysaccharides, and >>>>>>> proteins. >>>>>>> > >>> Means these components are in essence is_a structural >>>>>>> constituent of cell >>>>>>> > >>> wall and obviously these are not the function terms. >>>>>>> > >>> >>>>>>> > >>> The suggested function term could be 'structural integrity of >>>>>>> a >>>>>>> cell >>>>>>> > >>> wall'. Though it may as well be a process term. >>>>>>> > >>> >>>>>>> > > >>>>>>> > _______________________________________________ >>>>>>> > Go mailing list >>>>>>> > Go at geneontology.org >>>>>>> > http://fafner.stanford.edu/mailman/listinfo/go >>>>>>> _______________________________________________ >>>>>>> Go mailing list >>>>>>> Go at geneontology.org >>>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>>> >>>>>> -- >>>>>> Pankaj Jaiswal >>>>>> Assistant Professor >>>>>> Dept. of Botany and Plant Pathology >>>>>> 3082 Cordley Hall >>>>>> Oregon State University >>>>>> Corvallis, OR, 97331-2902, USA >>>>>> >>>>>> Ph.: +1-541-737-8471 >>>>>> Fax: +1-541-737-3573 >>>>>> Web: www.gramene.org >>>>>> www.plantontology.org >>>>>> >>>>>> _______________________________________________ >>>>>> Go mailing list >>>>>> Go at geneontology.org >>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>> >>>>> ===================================== >>>>> Jim Hu >>>>> Associate Professor >>>>> Dept. of Biochemistry and Biophysics >>>>> 2128 TAMU >>>>> Texas A&M Univ. >>>>> College Station, TX 77843-2128 >>>>> 979-862-4054 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> -- >>> 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 >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> > > -- > 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 Fri Oct 2 01:32:27 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 2 Oct 2009 09:32:27 +0100 (BST) Subject: [Go] AmiGO: binding In-Reply-To: <4AC504AC.5050102@informatics.jax.org> References: <4AC4F9BC.6090907@science.oregonstate.edu> <4AC504AC.5050102@informatics.jax.org> Message-ID: hi, On Thu, 1 Oct 2009, Harold Drabkin wrote: > Pankaj Jaiswal (OSU) wrote: >> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005488&session_id=3810amigo1254420818 >> >> The narrow synonym 'ligand' seems inappropriate. 'ligand' is used for "a >> substance (an atom or molecule or radical or ion) that forms a complex >> around a central atom" and it may require a physical/chemical >> bonding/binding. Therefore it is not used for 'binding' function. >> >> Pankaj >> > "ligand" is the that is bound; Thus a receptor binds (or has a function of > binding) a ligand. If the entities that form any one binary interaction are > both proteins, one can think of each of them being ligands of the other. > However, in most types of biological experiments, a ligand is usually a > non-protein entity. In any case, the term isn't really a synonym for the > function binding. I thought this was one of those things that was a function, > but then removed and made a synonym? Yes, that's what happened; maybe the scope should be 'related', but as I recall the rationale for 'narrow' was that a receptor could be bound either by a ligand or by something (e.g. another protein) not considered a ligand. Going back to Pankaj's original comment, and to expand on what Harold said, I'll just point out that GO is using 'ligand' in the biological sense of a molecule whose binding to a receptor initiates a signaling cascade; this is very common usage in the signal transduction field. In other words, GO is not using 'ligand' in the chemistry sense that invokes 'around a central atom'. Midori From val at sanger.ac.uk Fri Oct 2 02:10:06 2009 From: val at sanger.ac.uk (val at sanger.ac.uk) Date: Fri, 2 Oct 2009 10:10:06 +0100 (BST) Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC55CC7.30808@informatics.jax.org> References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> <4AC5304E.6080100@informatics.jax.org> <4AC55CC7.30808@informatics.jax.org> Message-ID: So, there are 2 issues here 1. Whether we need the term (or some equivaelnt way to capture this information): Many complexes have scaffold which contribute to the structural integrity If we were to break the process of "x complex assembly" down into its constituent function(ings) we may need a way to capture that some gene products have a function(ing) as a scaffold molecule onto which the other subunits assemble. This is frequently the case with WD proteins, and HEAT repeat proteins which have no catalytic activity but serve as a "platform" for the assembly of a protein complex. Similarly for the ribosome, some subunits are required for assembly and may be part of the "scaffold". We probably want to capture this information. For example the SIN component scaffold protein Cdc11 is a leucine rich repeat scaffold protein for the signaling molecules of the septation initiation network. It might be useful here to have a structural molecule annotation to clearly distinguish this component from the catalytic activities of the other molecules. This "functioning" would be part of the "x complex assembly". When this is clearly the function(ing) for this gene product it seems that we do need some way to describe it, rather than annotating with "molecular function(ing) ND" 2. Whether the ribosomal subunit annotations to the existing term are correct Part of the problem is that "structural molecule of the ribosome" has been use to provide a function annotation for all the ribosomal subunits of unknown function regardless of whether they have a role as a scaffold molecule during the assembly of the complex. Historically this term was used so that the ribosomal subunits did not get an "unknown function" annotation This does require a clean up. I often see in peoples GO analysis say their gene set is enriched for "structural molecule activity" when they are enriched for ribosomal proteins, which often get this annotation whether they are a structural molecule or not Val > Karen, > > I think this is a good way to think about this. If there are no gene > products that contribute to the ribosome like a brick contributes to a > chimney, play a role in its physical organization, then we ditch the > function 'structural constituent of ribosome' or whatever other name we > choose for these kinds of terms. > > > > > Karen Christie wrote: >> sort of brainstorming here, just thinking trying to think through a >> possible way to distinguish between things we do and do not need to >> represent in Function... it may not work, but it seems interesting to >> try to think it through and share with the group to see if this is a >> useful way of thinking about this issue... >> >> Perhaps we should think about the idea of distinguishing between >> something that is a structural constitent of something that is itself >> considered for its structural role, vs a structural constituent of >> something that once assembled has a catalytic role. >> >> Actin is a constituent of a type of filament. While the filament is a >> dynamic structure, in terms of being assembled on one end and >> disassembled on the other, it is basically a structure that other gene >> products use to move things around, and more... Similarly, flagellin >> is a unit of something that is basically a structure, the flagellum. I >> realize the flagellum does have a larger role in terms of motility, >> but that's implemented through motor proteins rotating a long >> filament, which itself is basically structural. The cell wall is also >> largely structural. >> >> However, things like the spliceosome and the ribosome, while very >> large as complexes go, are not generally considered to be structural >> constitents of the cell. Both of these things have catalytic roles. It >> seems that we do need to represent the catalytic activity that is >> ascribed to the complex (we already do this for the spliceosome). But >> I don't think we need to represent being a member of a very large >> complex as a function. >> >> -Karen >> >> >> >> >> On Thu, 1 Oct 2009, David Hill wrote: >> >>> If we stick with the idea that all molecular functions are parts of >>> biological processes, then we must ask what is the function of a gene >>> product that has a role 'structural constituent of x' with respect to >>> a biological process. We have many processes that are 'x structural >>> organization'. In this sense, structural organization refers to the >>> physical shaping of a structure. >>> >>> I think we need to have a function for a gene product like actin. It >>> is like a brick. A brick contributes to the structural organization >>> of a building. We could describe the function of actin as 'molecular >>> function involved in microfilament structural organization'. We need >>> to decide whether the current 'structural' functions are worthy. Are >>> they providing a function that contributes to a meaningful physical >>> organization of a structure? >>> >>> For those of you who are old enough in GO, we had a similar argument >>> about an old molecular function called 'tRNA'. We renamed the term >>> 'triplet codon-amino acid adapter activity' and defined it with >>> respect to its role in a process: The codon binding activity of a >>> tRNA that positions an activated amino acid, mediating its insertion >>> at the correct point in the sequence of a nascent polypeptide chain >>> during protein synthesis.. >>> >>> David >>> >>> >>> >>> Chris Mungall wrote: >>>> >>>> On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: >>>> >>>>> - "constitution provision" is really awkward. >>>>> - I don't understand how functioning as a structural protein is an >>>>> action. >>>>> - why not just have structural component as a high level term to >>>>> distinguish from the implication that function is unknown if there >>>>> are no MF terms, but infer what it's a structural component of from >>>>> the CC terms? For Michelle's example, flagellin would get >>>>> >>>>> GO:0005198 ! structural molecule activity (function) >>>>> GO:0009420 ! bacterial-type flagellum filament (component) >>>> >>>> two annotations say less than a single annotation to the >>>> compositional term (either pre-composed in the ontology, or >>>> post-composed in the annotation using col16). >>>> >>>>> Jim >>>>> >>>>> On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: >>>>> >>>>>> We may agree with the annotations such as >>>>>> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >>>>>> >>>>>> Alternative suggestions for terms would be >>>>>> >>>>>> MF >>>>>> is_a structural constitution provision >>>>>> is_a cell wall structural constitution provision >>>>>> >>>>>> Pankaj >>>>>> >>>>>> Judith Blake wrote: >>>>>>> We need terms for these actions; we just need to find the right >>>>>>> term. These are functions (or as I?m learning to say, >>>>>>> functionings). Right now... ?structural constituent function >>>>>>> for the cell wall?... Or ?structural constituent of the cell >>>>>>> wall?. That would be the MF term, ya? >>>>>>> judy >>>>>>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>>>>>> wrote: >>>>>>> Hi, >>>>>>> I don't see how we can retire these. Proteins that form the >>>>>>> building blocks >>>>>>> of a structure have this as their "function". It is not an >>>>>>> "action", but it >>>>>>> is still a "function". >>>>>>> What is the function of a brick if not to form part of a wall? >>>>>>> What would be the function for proteins like flagellin if these >>>>>>> terms were >>>>>>> obsoleted? >>>>>>> Michelle >>>>>>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>>>>>> > I've wanted to for those aforementioned years. Let's see >>>>>>> what the >>>>>>> rest of >>>>>>> > the list says ... >>>>>>> > >>>>>>> > m >>>>>>> > >>>>>>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>>> > >>>>>>> > > Can we retire them. >>>>>>> > > >>>>>>> > > Pankaj >>>>>>> > > >>>>>>> > > Midori Harris wrote: >>>>>>> > >> These terms have never been ideal; we've known about the >>>>>>> problems with them >>>>>>> > >> literally for years. 'Structural integrity' is no more a >>>>>>> molecular function >>>>>>> > >> than the present names; it's a biological quality. >>>>>>> > >> >>>>>>> > >> m >>>>>>> > >> >>>>>>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>>> > >> >>>>>>> > >>> >>>>>>> >>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>>>> >>>>>>> > >>> 9&session_id=3810amigo1254420818 >>>>>>> > >>> >>>>>>> > >>> This term and some other sibling terms may require >>>>>>> renaming of >>>>>>> the terms. >>>>>>> > >>> >>>>>>> > >>> As I understand, 'constituent' means a component of or >>>>>>> part of. >>>>>>> E.g. The >>>>>>> > >>> cell wall is composed of cellulose fiber, >>>>>>> polysaccharides, and >>>>>>> proteins. >>>>>>> > >>> Means these components are in essence is_a structural >>>>>>> constituent of cell >>>>>>> > >>> wall and obviously these are not the function terms. >>>>>>> > >>> >>>>>>> > >>> The suggested function term could be 'structural >>>>>>> integrity of a >>>>>>> cell >>>>>>> > >>> wall'. Though it may as well be a process term. >>>>>>> > >>> >>>>>>> > > >>>>>>> > _______________________________________________ >>>>>>> > Go mailing list >>>>>>> > Go at geneontology.org >>>>>>> > http://fafner.stanford.edu/mailman/listinfo/go >>>>>>> _______________________________________________ >>>>>>> Go mailing list >>>>>>> Go at geneontology.org >>>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>>> >>>>>> -- >>>>>> Pankaj Jaiswal >>>>>> Assistant Professor >>>>>> Dept. of Botany and Plant Pathology >>>>>> 3082 Cordley Hall >>>>>> Oregon State University >>>>>> Corvallis, OR, 97331-2902, USA >>>>>> >>>>>> Ph.: +1-541-737-8471 >>>>>> Fax: +1-541-737-3573 >>>>>> Web: www.gramene.org >>>>>> www.plantontology.org >>>>>> >>>>>> _______________________________________________ >>>>>> Go mailing list >>>>>> Go at geneontology.org >>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>> >>>>> ===================================== >>>>> Jim Hu >>>>> Associate Professor >>>>> Dept. of Biochemistry and Biophysics >>>>> 2128 TAMU >>>>> Texas A&M Univ. >>>>> College Station, TX 77843-2128 >>>>> 979-862-4054 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> -- >>> 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 >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> > > -- > 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 > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From aji at ebi.ac.uk Fri Oct 2 03:29:08 2009 From: aji at ebi.ac.uk (Amelia Ireland) Date: Fri, 2 Oct 2009 11:29:08 +0100 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC505B6.6080206@science.oregonstate.edu> References: <4AC505B6.6080206@science.oregonstate.edu> Message-ID: <91297FDF-6698-45D9-AC56-2DD361864F8E@ebi.ac.uk> On Oct 1, 2009, at 8:40 PM, Pankaj Jaiswal (OSU) wrote: > > Gwinn Giglio, Michelle wrote: >> Hi, >> I don't see how we can retire these. Proteins that form the >> building blocks >> of a structure have this as their "function". It is not an >> "action", but it >> is still a "function". > > Is it necessary to assign a function? Can they live with only > process and component terms associated to gene products. I think we need to get away from this unwritten rule that everything HAS to have a process, function and a component annotation, or more specifically, that everything should have a function annotation. I believe that the heterogeneity of terms in the MF ontology has been caused by trying to create MF terms for "qualities" or "roles", rather than true functionings. -- Amelia Ireland GO Editorial Office http://www.berkeleybop.org || http://www.ebi.ac.uk Boycott Trader Joe's Red List seafood: http://traitorjoe.com From dph at informatics.jax.org Fri Oct 2 04:15:04 2009 From: dph at informatics.jax.org (David Hill) Date: Fri, 02 Oct 2009 07:15:04 -0400 Subject: [Go] AmiGO: binding In-Reply-To: References: <4AC4F9BC.6090907@science.oregonstate.edu> <4AC504AC.5050102@informatics.jax.org> Message-ID: <4AC5E0B8.2080605@informatics.jax.org> This is the way I remember it as well. Ligand originally meant 'receptor ligand'. Midori Harris wrote: > hi, > > On Thu, 1 Oct 2009, Harold Drabkin wrote: > >> Pankaj Jaiswal (OSU) wrote: >>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005488&session_id=3810amigo1254420818 >>> >>> The narrow synonym 'ligand' seems inappropriate. 'ligand' is used >>> for "a substance (an atom or molecule or radical or ion) that forms >>> a complex around a central atom" and it may require a >>> physical/chemical bonding/binding. Therefore it is not used for >>> 'binding' function. >>> >>> Pankaj >>> >> "ligand" is the that is bound; Thus a receptor binds (or has a >> function of binding) a ligand. If the entities that form any one >> binary interaction are both proteins, one can think of each of them >> being ligands of the other. However, in most types of biological >> experiments, a ligand is usually a non-protein entity. In any case, >> the term isn't really a synonym for the function binding. I thought >> this was one of those things that was a function, but then removed >> and made a synonym? > > Yes, that's what happened; maybe the scope should be 'related', but as > I recall the rationale for 'narrow' was that a receptor could be bound > either by a ligand or by something (e.g. another protein) not > considered a ligand. > > Going back to Pankaj's original comment, and to expand on what Harold > said, I'll just point out that GO is using 'ligand' in the biological > sense of a molecule whose binding to a receptor initiates a signaling > cascade; this is very common usage in the signal transduction field. > In other words, GO is not using 'ligand' in the chemistry sense that > invokes 'around a central atom'. > > Midori > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go -- 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 Judith.Blake at jax.org Fri Oct 2 04:56:26 2009 From: Judith.Blake at jax.org (Judith Blake) Date: Fri, 2 Oct 2009 07:56:26 -0400 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC55CC7.30808@informatics.jax.org> Message-ID: One test of that is whether the ribosome functions without the gene product present. j On 10/1/09 9:52 PM, "David Hill" wrote: Karen, I think this is a good way to think about this. If there are no gene products that contribute to the ribosome like a brick contributes to a chimney, play a role in its physical organization, then we ditch the function 'structural constituent of ribosome' or whatever other name we choose for these kinds of terms. Karen Christie wrote: > sort of brainstorming here, just thinking trying to think through a > possible way to distinguish between things we do and do not need to > represent in Function... it may not work, but it seems interesting to > try to think it through and share with the group to see if this is a > useful way of thinking about this issue... > > Perhaps we should think about the idea of distinguishing between > something that is a structural constitent of something that is itself > considered for its structural role, vs a structural constituent of > something that once assembled has a catalytic role. > > Actin is a constituent of a type of filament. While the filament is a > dynamic structure, in terms of being assembled on one end and > disassembled on the other, it is basically a structure that other gene > products use to move things around, and more... Similarly, flagellin > is a unit of something that is basically a structure, the flagellum. I > realize the flagellum does have a larger role in terms of motility, > but that's implemented through motor proteins rotating a long > filament, which itself is basically structural. The cell wall is also > largely structural. > > However, things like the spliceosome and the ribosome, while very > large as complexes go, are not generally considered to be structural > constitents of the cell. Both of these things have catalytic roles. It > seems that we do need to represent the catalytic activity that is > ascribed to the complex (we already do this for the spliceosome). But > I don't think we need to represent being a member of a very large > complex as a function. > > -Karen > > > > > On Thu, 1 Oct 2009, David Hill wrote: > >> If we stick with the idea that all molecular functions are parts of >> biological processes, then we must ask what is the function of a gene >> product that has a role 'structural constituent of x' with respect to >> a biological process. We have many processes that are 'x structural >> organization'. In this sense, structural organization refers to the >> physical shaping of a structure. >> >> I think we need to have a function for a gene product like actin. It >> is like a brick. A brick contributes to the structural organization >> of a building. We could describe the function of actin as 'molecular >> function involved in microfilament structural organization'. We need >> to decide whether the current 'structural' functions are worthy. Are >> they providing a function that contributes to a meaningful physical >> organization of a structure? >> >> For those of you who are old enough in GO, we had a similar argument >> about an old molecular function called 'tRNA'. We renamed the term >> 'triplet codon-amino acid adapter activity' and defined it with >> respect to its role in a process: The codon binding activity of a >> tRNA that positions an activated amino acid, mediating its insertion >> at the correct point in the sequence of a nascent polypeptide chain >> during protein synthesis.. >> >> David >> >> >> >> Chris Mungall wrote: >>> >>> On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: >>> >>>> - "constitution provision" is really awkward. >>>> - I don't understand how functioning as a structural protein is an >>>> action. >>>> - why not just have structural component as a high level term to >>>> distinguish from the implication that function is unknown if there >>>> are no MF terms, but infer what it's a structural component of from >>>> the CC terms? For Michelle's example, flagellin would get >>>> >>>> GO:0005198 ! structural molecule activity (function) >>>> GO:0009420 ! bacterial-type flagellum filament (component) >>> >>> two annotations say less than a single annotation to the >>> compositional term (either pre-composed in the ontology, or >>> post-composed in the annotation using col16). >>> >>>> Jim >>>> >>>> On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: >>>> >>>>> We may agree with the annotations such as >>>>> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >>>>> >>>>> Alternative suggestions for terms would be >>>>> >>>>> MF >>>>> is_a structural constitution provision >>>>> is_a cell wall structural constitution provision >>>>> >>>>> Pankaj >>>>> >>>>> Judith Blake wrote: >>>>>> We need terms for these actions; we just need to find the right >>>>>> term. These are functions (or as I'm learning to say, >>>>>> functionings). Right now... 'structural constituent function >>>>>> for the cell wall'... Or 'structural constituent of the cell >>>>>> wall'. That would be the MF term, ya? >>>>>> judy >>>>>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>>>>> wrote: >>>>>> Hi, >>>>>> I don't see how we can retire these. Proteins that form the >>>>>> building blocks >>>>>> of a structure have this as their "function". It is not an >>>>>> "action", but it >>>>>> is still a "function". >>>>>> What is the function of a brick if not to form part of a wall? >>>>>> What would be the function for proteins like flagellin if these >>>>>> terms were >>>>>> obsoleted? >>>>>> Michelle >>>>>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>>>>> > I've wanted to for those aforementioned years. Let's see >>>>>> what the >>>>>> rest of >>>>>> > the list says ... >>>>>> > >>>>>> > m >>>>>> > >>>>>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>> > >>>>>> > > Can we retire them. >>>>>> > > >>>>>> > > Pankaj >>>>>> > > >>>>>> > > Midori Harris wrote: >>>>>> > >> These terms have never been ideal; we've known about the >>>>>> problems with them >>>>>> > >> literally for years. 'Structural integrity' is no more a >>>>>> molecular function >>>>>> > >> than the present names; it's a biological quality. >>>>>> > >> >>>>>> > >> m >>>>>> > >> >>>>>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>> > >> >>>>>> > >>> >>>>>> >>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>>> >>>>>> > >>> 9&session_id=3810amigo1254420818 >>>>>> > >>> >>>>>> > >>> This term and some other sibling terms may require >>>>>> renaming of >>>>>> the terms. >>>>>> > >>> >>>>>> > >>> As I understand, 'constituent' means a component of or >>>>>> part of. >>>>>> E.g. The >>>>>> > >>> cell wall is composed of cellulose fiber, >>>>>> polysaccharides, and >>>>>> proteins. >>>>>> > >>> Means these components are in essence is_a structural >>>>>> constituent of cell >>>>>> > >>> wall and obviously these are not the function terms. >>>>>> > >>> >>>>>> > >>> The suggested function term could be 'structural >>>>>> integrity of a >>>>>> cell >>>>>> > >>> wall'. Though it may as well be a process term. >>>>>> > >>> >>>>>> > > >>>>>> > _______________________________________________ >>>>>> > Go mailing list >>>>>> > Go at geneontology.org >>>>>> > http://fafner.stanford.edu/mailman/listinfo/go >>>>>> _______________________________________________ >>>>>> Go mailing list >>>>>> Go at geneontology.org >>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>> >>>>> -- >>>>> Pankaj Jaiswal >>>>> Assistant Professor >>>>> Dept. of Botany and Plant Pathology >>>>> 3082 Cordley Hall >>>>> Oregon State University >>>>> Corvallis, OR, 97331-2902, USA >>>>> >>>>> Ph.: +1-541-737-8471 >>>>> Fax: +1-541-737-3573 >>>>> Web: www.gramene.org >>>>> www.plantontology.org >>>>> >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>>> ===================================== >>>> Jim Hu >>>> Associate Professor >>>> Dept. of Biochemistry and Biophysics >>>> 2128 TAMU >>>> Texas A&M Univ. >>>> College Station, TX 77843-2128 >>>> 979-862-4054 >>>> >>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> -- >> 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 >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> -- 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 _______________________________________________ Go mailing list Go at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdeegan at ebi.ac.uk Fri Oct 2 07:19:01 2009 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Fri, 02 Oct 2009 15:19:01 +0100 Subject: [Go] Outreeach and Advocacy report Message-ID: <4AC60BD5.7070809@ebi.ac.uk> Hi, Jane and I are writing the outreach and advocacy report for September now. If you have done anything to bring on new annotation groups, or to teach users about GO then we'd really appreciate if you could add your report directly to the wiki: http://wiki.geneontology.org/index.php/Outreach_September_2009_Report If you have given any GO talks, or produced GO posters or papers then it would be great if you could also post these at: http://wiki.geneontology.org/index.php/Publications%2C_Talks%2C_Posters_2007-2009 August was a very quiet month for outeach, but there is still time to add to the report if have not yet done so: http://wiki.geneontology.org/index.php/Outreach_August_2009_Report Best wishes, Jennifer Deegan GO Curator From r.lovering at ucl.ac.uk Fri Oct 2 09:03:28 2009 From: r.lovering at ucl.ac.uk (Ruth Lovering) Date: Fri, 2 Oct 2009 17:03:28 +0100 Subject: [Go] CV GO Annotation Initiative October Newsletter Message-ID: <6360C0FF-8468-4A8D-9841-20B6931DDA2E@ucl.ac.uk> Please find attached the most recent Cardiovascular GO Annotation Initiative Newsletter. Kind Regards Ruth h -------------- next part -------------- A non-text attachment was scrubbed... Name: CVGOAINewsOctober09.pdf Type: application/pdf Size: 231903 bytes Desc: not available URL: -------------- next part -------------- Ruth Lovering, PhD Gene Ontology Coordinator Cardiovascular Gene Ontology Annotation Initiative Centre for Cardiovascular Genetics Department of Medicine University College London Rayne Institute 5 University Street London WC1E 6JF Email: r.lovering at ucl.ac.uk Tel:44-20-7679-0930 URL: http://www.cardiovasculargeneontology.com From suzi at fruitfly.org Fri Oct 2 10:21:02 2009 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 2 Oct 2009 10:21:02 -0700 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC5304E.6080100@informatics.jax.org> References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> <4AC5304E.6080100@informatics.jax.org> Message-ID: <431C0213-0FE4-47D6-9351-40EF80246CC4@fruitfly.org> On Oct 1, 2009, at 3:42 PM, David Hill wrote: > If we stick with the idea that all molecular functions are parts of > biological processes, I don't believe that we did agree to this. As far as I know, we are still agreed that both function (a potential for functioning) and and structural constituents are incorporated into the MF branch because both are needed for our annotations. > then we must ask what is the function of a gene product that has a > role 'structural constituent of x' with respect to a biological > process. We have many processes that are 'x structural > organization'. In this sense, structural organization refers to the > physical shaping of a structure. > > I think we need to have a function for a gene product like actin. It > is like a brick. A brick contributes to the structural organization > of a building. We could describe the function of actin as 'molecular > function involved in microfilament structural organization'. We need > to decide whether the current 'structural' functions are worthy. > Are they providing a function that contributes to a meaningful > physical organization of a structure? > > For those of you who are old enough in GO, we had a similar argument > about an old molecular function called 'tRNA'. We renamed the term > 'triplet codon-amino acid adapter activity' and defined it with > respect to its role in a process: The codon binding activity of a > tRNA that positions an activated amino acid, mediating its insertion > at the correct point in the sequence of a nascent polypeptide chain > during protein synthesis.. > > David > > > > Chris Mungall wrote: >> >> On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: >> >>> - "constitution provision" is really awkward. >>> - I don't understand how functioning as a structural protein is an >>> action. >>> - why not just have structural component as a high level term to >>> distinguish from the implication that function is unknown if there >>> are no MF terms, but infer what it's a structural component of >>> from the CC terms? For Michelle's example, flagellin would get >>> >>> GO:0005198 ! structural molecule activity (function) >>> GO:0009420 ! bacterial-type flagellum filament (component) >> >> two annotations say less than a single annotation to the >> compositional term (either pre-composed in the ontology, or post- >> composed in the annotation using col16). >> >>> Jim >>> >>> On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: >>> >>>> We may agree with the annotations such as >>>> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >>>> >>>> Alternative suggestions for terms would be >>>> >>>> MF >>>> is_a structural constitution provision >>>> is_a cell wall structural constitution provision >>>> >>>> Pankaj >>>> >>>> Judith Blake wrote: >>>>> We need terms for these actions; we just need to find the right >>>>> term. These are functions (or as I?m learning to say, >>>>> functionings). Right now... ?structural constituent function >>>>> for the cell wall?... Or ?structural constituent of the cell >>>>> wall?. That would be the MF term, ya? >>>>> judy >>>>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>>> > wrote: >>>>> Hi, >>>>> I don't see how we can retire these. Proteins that form the >>>>> building blocks >>>>> of a structure have this as their "function". It is not an >>>>> "action", but it >>>>> is still a "function". >>>>> What is the function of a brick if not to form part of a wall? >>>>> What would be the function for proteins like flagellin if these >>>>> terms were >>>>> obsoleted? >>>>> Michelle >>>>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>>>> > I've wanted to for those aforementioned years. Let's see >>>>> what the >>>>> rest of >>>>> > the list says ... >>>>> > >>>>> > m >>>>> > >>>>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>> > >>>>> > > Can we retire them. >>>>> > > >>>>> > > Pankaj >>>>> > > >>>>> > > Midori Harris wrote: >>>>> > >> These terms have never been ideal; we've known about the >>>>> problems with them >>>>> > >> literally for years. 'Structural integrity' is no more a >>>>> molecular function >>>>> > >> than the present names; it's a biological quality. >>>>> > >> >>>>> > >> m >>>>> > >> >>>>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>> > >> >>>>> > >>> >>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>> > >>> 9&session_id=3810amigo1254420818 >>>>> > >>> >>>>> > >>> This term and some other sibling terms may require >>>>> renaming of >>>>> the terms. >>>>> > >>> >>>>> > >>> As I understand, 'constituent' means a component of or >>>>> part of. >>>>> E.g. The >>>>> > >>> cell wall is composed of cellulose fiber, >>>>> polysaccharides, and >>>>> proteins. >>>>> > >>> Means these components are in essence is_a structural >>>>> constituent of cell >>>>> > >>> wall and obviously these are not the function terms. >>>>> > >>> >>>>> > >>> The suggested function term could be 'structural >>>>> integrity of a >>>>> cell >>>>> > >>> wall'. Though it may as well be a process term. >>>>> > >>> >>>>> > > >>>>> > _______________________________________________ >>>>> > Go mailing list >>>>> > Go at geneontology.org >>>>> > http://fafner.stanford.edu/mailman/listinfo/go >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>>> -- >>>> Pankaj Jaiswal >>>> Assistant Professor >>>> Dept. of Botany and Plant Pathology >>>> 3082 Cordley Hall >>>> Oregon State University >>>> Corvallis, OR, 97331-2902, USA >>>> >>>> Ph.: +1-541-737-8471 >>>> Fax: +1-541-737-3573 >>>> Web: www.gramene.org >>>> www.plantontology.org >>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> ===================================== >>> Jim Hu >>> Associate Professor >>> Dept. of Biochemistry and Biophysics >>> 2128 TAMU >>> Texas A&M Univ. >>> College Station, TX 77843-2128 >>> 979-862-4054 >>> >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > -- > 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 > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From suzi at fruitfly.org Fri Oct 2 10:23:10 2009 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 2 Oct 2009 10:23:10 -0700 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> <4AC5304E.6080100@informatics.jax.org> Message-ID: On Oct 1, 2009, at 4:13 PM, Karen Christie wrote: > sort of brainstorming here, just thinking trying to think through a > possible way to distinguish between things we do and do not need to > represent in Function... it may not work, but it seems interesting > to try to think it through and share with the group to see if this > is a useful way of thinking about this issue... > > Perhaps we should think about the idea of distinguishing between > something that is a structural constitent of something that is > itself considered for its structural role, vs a structural > constituent of something that once assembled has a catalytic role. This is an interesting idea. It would certainly help to clarify things. l like it. > > Actin is a constituent of a type of filament. While the filament is > a dynamic structure, in terms of being assembled on one end and > disassembled on the other, it is basically a structure that other > gene products use to move things around, and more... Similarly, > flagellin is a unit of something that is basically a structure, the > flagellum. I realize the flagellum does have a larger role in terms > of motility, but that's implemented through motor proteins rotating > a long filament, which itself is basically structural. The cell wall > is also largely structural. > > However, things like the spliceosome and the ribosome, while very > large as complexes go, are not generally considered to be structural > constitents of the cell. Both of these things have catalytic roles. > It seems that we do need to represent the catalytic activity that is > ascribed to the complex (we already do this for the spliceosome). > But I don't think we need to represent being a member of a very > large complex as a function. > > -Karen > > > > > On Thu, 1 Oct 2009, David Hill wrote: > >> If we stick with the idea that all molecular functions are parts of >> biological processes, then we must ask what is the function of a >> gene product that has a role 'structural constituent of x' with >> respect to a biological process. We have many processes that are 'x >> structural organization'. In this sense, structural organization >> refers to the physical shaping of a structure. >> >> I think we need to have a function for a gene product like actin. >> It is like a brick. A brick contributes to the structural >> organization of a building. We could describe the function of actin >> as 'molecular function involved in microfilament structural >> organization'. We need to decide whether the current 'structural' >> functions are worthy. Are they providing a function that >> contributes to a meaningful physical organization of a structure? >> >> For those of you who are old enough in GO, we had a similar >> argument about an old molecular function called 'tRNA'. We renamed >> the term 'triplet codon-amino acid adapter activity' and defined it >> with respect to its role in a process: The codon binding activity >> of a tRNA that positions an activated amino acid, mediating its >> insertion at the correct point in the sequence of a nascent >> polypeptide chain during protein synthesis.. >> >> David >> >> >> >> Chris Mungall wrote: >>> On Oct 1, 2009, at 9:49 PM, Jim Hu wrote: >>>> - "constitution provision" is really awkward. >>>> - I don't understand how functioning as a structural protein is >>>> an action. >>>> - why not just have structural component as a high level term to >>>> distinguish from the implication that function is unknown if >>>> there are no MF terms, but infer what it's a structural component >>>> of from the CC terms? For Michelle's example, flagellin would get >>>> GO:0005198 ! structural molecule activity (function) >>>> GO:0009420 ! bacterial-type flagellum filament (component) >>> two annotations say less than a single annotation to the >>> compositional term (either pre-composed in the ontology, or post- >>> composed in the annotation using col16). >>>> Jim >>>> On Oct 1, 2009, at 3:23 PM, Pankaj Jaiswal (OSU) wrote: >>>>> We may agree with the annotations such as >>>>> http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=TIGR_CMR:BA_1706 >>>>> Alternative suggestions for terms would be >>>>> MF >>>>> is_a structural constitution provision >>>>> is_a cell wall structural constitution provision >>>>> Pankaj >>>>> Judith Blake wrote: >>>>>> We need terms for these actions; we just need to find the right >>>>>> term. These are functions (or as I?m learning to say, >>>>>> functionings). Right now... ?structural constituent function >>>>>> for the cell wall?... Or ?structural constituent of the cell >>>>>> wall?. That would be the MF term, ya? >>>>>> judy >>>>>> On 10/1/09 3:20 PM, "Gwinn Giglio, Michelle" >>>>> > wrote: >>>>>> Hi, >>>>>> I don't see how we can retire these. Proteins that form the >>>>>> building blocks >>>>>> of a structure have this as their "function". It is not an >>>>>> "action", but it >>>>>> is still a "function". >>>>>> What is the function of a brick if not to form part of a wall? >>>>>> What would be the function for proteins like flagellin if these >>>>>> terms were >>>>>> obsoleted? >>>>>> Michelle >>>>>> On 10/1/09 2:53 PM, "Midori Harris" wrote: >>>>>> > I've wanted to for those aforementioned years. Let's see >>>>>> what the >>>>>> rest of >>>>>> > the list says ... >>>>>> > >>>>>> > m >>>>>> > >>>>>> > On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>> > >>>>>> > > Can we retire them. >>>>>> > > >>>>>> > > Pankaj >>>>>> > > >>>>>> > > Midori Harris wrote: >>>>>> > >> These terms have never been ideal; we've known about the >>>>>> problems with them >>>>>> > >> literally for years. 'Structural integrity' is no more a >>>>>> molecular function >>>>>> > >> than the present names; it's a biological quality. >>>>>> > >> >>>>>> > >> m >>>>>> > >> >>>>>> > >> On Thu, 1 Oct 2009, Pankaj Jaiswal (OSU) wrote: >>>>>> > >> >>>>>> > >>> >>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:000519 >>>>>> > >>> 9&session_id=3810amigo1254420818 >>>>>> > >>> >>>>>> > >>> This term and some other sibling terms may require >>>>>> renaming of >>>>>> the terms. >>>>>> > >>> >>>>>> > >>> As I understand, 'constituent' means a component of or >>>>>> part of. >>>>>> E.g. The >>>>>> > >>> cell wall is composed of cellulose fiber, >>>>>> polysaccharides, and >>>>>> proteins. >>>>>> > >>> Means these components are in essence is_a structural >>>>>> constituent of cell >>>>>> > >>> wall and obviously these are not the function terms. >>>>>> > >>> >>>>>> > >>> The suggested function term could be 'structural >>>>>> integrity of a >>>>>> cell >>>>>> > >>> wall'. Though it may as well be a process term. >>>>>> > >>> >>>>>> > > >>>>>> > _______________________________________________ >>>>>> > Go mailing list >>>>>> > Go at geneontology.org >>>>>> > http://fafner.stanford.edu/mailman/listinfo/go >>>>>> _______________________________________________ >>>>>> Go mailing list >>>>>> Go at geneontology.org >>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>> -- >>>>> Pankaj Jaiswal >>>>> Assistant Professor >>>>> Dept. of Botany and Plant Pathology >>>>> 3082 Cordley Hall >>>>> Oregon State University >>>>> Corvallis, OR, 97331-2902, USA >>>>> Ph.: +1-541-737-8471 >>>>> Fax: +1-541-737-3573 >>>>> Web: www.gramene.org >>>>> www.plantontology.org >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> ===================================== >>>> Jim Hu >>>> Associate Professor >>>> Dept. of Biochemistry and Biophysics >>>> 2128 TAMU >>>> Texas A&M Univ. >>>> College Station, TX 77843-2128 >>>> 979-862-4054 >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> -- >> 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 >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From suzi at fruitfly.org Fri Oct 2 10:26:05 2009 From: suzi at fruitfly.org (Suzanna Lewis) Date: Fri, 2 Oct 2009 10:26:05 -0700 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <91297FDF-6698-45D9-AC56-2DD361864F8E@ebi.ac.uk> References: <4AC505B6.6080206@science.oregonstate.edu> <91297FDF-6698-45D9-AC56-2DD361864F8E@ebi.ac.uk> Message-ID: <30068D8C-C6AC-4A95-AAC9-CD011584E076@fruitfly.org> MF has always been heterogeneous (i.e. included more than potential- for-functioning in processes). But as Karen pointed out, this needs to be clarified/improved. -S On Oct 2, 2009, at 3:29 AM, Amelia Ireland wrote: > On Oct 1, 2009, at 8:40 PM, Pankaj Jaiswal (OSU) wrote: >> >> Gwinn Giglio, Michelle wrote: >>> Hi, >>> I don't see how we can retire these. Proteins that form the >>> building blocks >>> of a structure have this as their "function". It is not an >>> "action", but it >>> is still a "function". >> >> Is it necessary to assign a function? Can they live with only >> process and component terms associated to gene products. > > > I think we need to get away from this unwritten rule that everything > HAS to have a process, function and a component annotation, or more > specifically, that everything should have a function annotation. I > believe that the heterogeneity of terms in the MF ontology has been > caused by trying to create MF terms for "qualities" or "roles", > rather than true functionings. > > -- > Amelia Ireland > GO Editorial Office > http://www.berkeleybop.org || http://www.ebi.ac.uk > Boycott Trader Joe's Red List seafood: http://traitorjoe.com > > > > > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From midori at ebi.ac.uk Fri Oct 2 11:00:49 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 2 Oct 2009 18:00:49 UT Subject: [Go] SourceForge Update Message-ID: <200910021800.n92I0ne8013808@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 aji at ebi.ac.uk Mon Oct 5 04:18:12 2009 From: aji at ebi.ac.uk (Amelia Ireland) Date: Mon, 5 Oct 2009 12:18:12 +0100 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <4AC644C7.2000709@northwestern.edu> References: <4AC505B6.6080206@science.oregonstate.edu> <91297FDF-6698-45D9-AC56-2DD361864F8E@ebi.ac.uk> <4AC644C7.2000709@northwestern.edu> Message-ID: On Oct 2, 2009, at 7:21 PM, Pascale Gaudet wrote: > define 'unwritten'... : "Curators are encouraged to annotate to > terms from all three ontologies, using no data liberally if > necessary. " > http://geneontology.org/GO.annotation.conventions.shtml?all#unknown Aha! Thank you for pointing that out. I have just revised that section of the documentation to link to the GO evidence code guide, as the latter covers ND and its recommended use more thoroughly. Cheers, Amelia. -- Amelia Ireland GO Editorial Office http://www.berkeleybop.org || http://www.ebi.ac.uk Boycott Trader Joe's Red List seafood: http://traitorjoe.com From aji at ebi.ac.uk Mon Oct 5 08:18:32 2009 From: aji at ebi.ac.uk (Amelia Ireland) Date: Mon, 5 Oct 2009 16:18:32 +0100 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <431C0213-0FE4-47D6-9351-40EF80246CC4@fruitfly.org> References: <4AC50FCC.50400@science.oregonstate.edu> <51BBB457-A736-4FFC-8111-18784EEB7759@tamu.edu> <4AC5304E.6080100@informatics.jax.org> <431C0213-0FE4-47D6-9351-40EF80246CC4@fruitfly.org> Message-ID: <13EB2049-FE26-41B6-8E3E-06206F309435@ebi.ac.uk> On Oct 2, 2009, at 6:21 PM, Suzanna Lewis wrote: > On Oct 1, 2009, at 3:42 PM, David Hill wrote: > >> If we stick with the idea that all molecular functions are parts of >> biological processes, > > I don't believe that we did agree to this. As far as I know, we are > still agreed that both function (a potential for functioning) and > and structural constituents are incorporated into the MF branch > because both are needed for our annotations. At some point, I think we need to do a cost-benefit analysis of some of these problematic terms (the 'structural constituent' terms have come under scrutiny in the past) and decide whether the potential benefit of having a mixture of terms in MF is worth the cost they incur (in terms of ontological integrity, user confusion, time spent discussing them, etc.). Could these structural constituent terms not be put into component, or would they be considered a gene product-specific term? -- Amelia Ireland GO Editorial Office http://www.berkeleybop.org || http://www.ebi.ac.uk Boycott Trader Joe's Red List seafood: http://traitorjoe.com From midori at ebi.ac.uk Mon Oct 5 08:47:32 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 5 Oct 2009 16:47:32 +0100 (BST) Subject: [Go] Ontology development - September highlights Message-ID: Dear GO, The most recent monthly report on ontology content, for September 2009, is now available at: http://wiki.geneontology.org/index.php/Sep2009_ontology_report Ontology development highlights from September: We reported on and discussed several topics at the GO Consortium meeting in Cambridge (Sept. 23-25). See the meeting agenda and minutes on the wiki, as well as the topic-specific links below. Agenda: http://wiki.geneontology.org/index.php/Cambridge_GO_Consortium_Meeting Minutes: http://wiki.geneontology.org/index.php/GOC_Meeting_Minutes_September_2009 * Addition of part_of links between the MF and BP ontologies continues. See http://wiki.geneontology.org/index.php/Function-Process_Links for background. * Ontology quality control work (http://wiki.geneontology.org/index.php/Ontology_Quality_Control). * Addition of cross-product definitions to gene_ontology_write.obo and gene_ontology_ext.obo (see http://wiki.geneontology.org/index.php/CJM_EBI_Visit_June_2009#Status_overview_and_release_plan; for background see see http://wiki.geneontology.org/index.php/Category:Cross_Products and http://wiki.geneontology.org/index.php/Editors_cross-product_implementation_plan, plus individual pages in the Cross_Products category) * Work on signal transduction terms (http://wiki.geneontology.org/index.php/Signaling, especially http://wiki.geneontology.org/index.php/Signaling_Meeting_Minutes_July_2009#3rd_August_2009). * Work on taxon triggers (http://wiki.geneontology.org/index.php/Taxon-GO_Implementation_April_2009_onwards#5th_August_2009 and http://wiki.geneontology.org/index.php/Taxon-GO_Implementation_August_28th_2009_onwards). We are also still working on: * Kidney development terms (http://wiki.geneontology.org/index.php/Kidney_Development) * The overhaul of virus-related terms (http://wiki.geneontology.org/index.php/Virus_terms). As usual, details of small- and medium-scale changes are available in the SourceForge Curator Requests tracker. Please contact us if you want to help out with ontology work in a particular area, or if you have any comments or questions about what's going on. Ontology Development wiki: http://wiki.geneontology.org/index.php/Ontology_Development SourceForge Curator Requests tracker: https://sourceforge.net/tracker/?group_id=36855&atid=440764 Midori & David on behalf of GO's ontology developers From jaiswalp at science.oregonstate.edu Tue Oct 6 08:37:53 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Tue, 06 Oct 2009 08:37:53 -0700 Subject: [Go] AmiGO: structural constituent of cell wall In-Reply-To: <30068D8C-C6AC-4A95-AAC9-CD011584E076@fruitfly.org> References: <4AC505B6.6080206@science.oregonstate.edu> <91297FDF-6698-45D9-AC56-2DD361864F8E@ebi.ac.uk> <30068D8C-C6AC-4A95-AAC9-CD011584E076@fruitfly.org> Message-ID: <4ACB6451.2030900@science.oregonstate.edu> Do we have a resolution and/or action items with reference to this thread? Pankaj Suzanna Lewis wrote: > MF has always been heterogeneous (i.e. included more than > potential-for-functioning in processes). But as Karen pointed out, this > needs to be clarified/improved. > > -S > > On Oct 2, 2009, at 3:29 AM, Amelia Ireland wrote: > >> On Oct 1, 2009, at 8:40 PM, Pankaj Jaiswal (OSU) wrote: >>> >>> Gwinn Giglio, Michelle wrote: >>>> Hi, >>>> I don't see how we can retire these. Proteins that form the >>>> building blocks >>>> of a structure have this as their "function". It is not an >>>> "action", but it >>>> is still a "function". >>> >>> Is it necessary to assign a function? Can they live with only process >>> and component terms associated to gene products. >> >> >> I think we need to get away from this unwritten rule that everything >> HAS to have a process, function and a component annotation, or more >> specifically, that everything should have a function annotation. I >> believe that the heterogeneity of terms in the MF ontology has been >> caused by trying to create MF terms for "qualities" or "roles", rather >> than true functionings. >> >> -- >> Amelia Ireland >> GO Editorial Office >> http://www.berkeleybop.org || http://www.ebi.ac.uk >> Boycott Trader Joe's Red List seafood: http://traitorjoe.com >> >> >> >> >> From dhowe at zfin.org Mon Oct 19 10:44:19 2009 From: dhowe at zfin.org (Doug Howe) Date: Mon, 19 Oct 2009 10:44:19 -0700 Subject: [Go] graph path tab delimited file Message-ID: Are the files here being updated?: http://www.geneontology.org/scratch/transitive_closure/ Can they be kept current with the ontology? Our developers are interested in using the tab-delimited transitive closure as described on the Transitive_closure wiki page: http://wiki.geneontology.org/index.php/Transitive_closure -Doug From cjm at berkeleybop.org Mon Oct 19 11:15:40 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Mon, 19 Oct 2009 11:15:40 -0700 Subject: [Go] graph path tab delimited file In-Reply-To: References: Message-ID: <6F19EC5E-B778-4593-98A6-840DCA7C59A4@berkeleybop.org> On Oct 19, 2009, at 10:44 AM, Doug Howe wrote: > Are the files here being updated?: > http://www.geneontology.org/scratch/transitive_closure/ No, these were for demonstration purposes. > Can they be kept current with the ontology? Our developers are > interested in using the tab-delimited transitive closure as > described on the Transitive_closure wiki page: > > http://wiki.geneontology.org/index.php/Transitive_closure This will be available in the GO database very soon, and a tab delimited file can be extracted via Goose. You can also get the deductive closure for any obo ontology (including your own ZFA) from here: http://www.berkeleybop.org/ontologies/ (it's the file with suffix .linkfile) These files are generated via obo2obo, which is part of the standard OBO-Edit2.0 distribution. It's portable and easy to install. > -Doug > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From cherry at stanford.edu Mon Oct 26 10:55:20 2009 From: cherry at stanford.edu (Mike Cherry) Date: Mon, 26 Oct 2009 10:55:20 -0700 Subject: [Go] Stanford GOC meeting March 30th - April 1st Message-ID: The dates for the next GOC meeting have been set. Please mark your calendars and plan to arrive March 29th and depart after noon on April 1st. A preliminary meeting logistics page is available. http://wiki.geneontology.org/index.php/ 2010_Stanford_Meeting_Logistics -Mike From midori at ebi.ac.uk Thu Oct 29 08:06:58 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 29 Oct 2009 15:06:58 +0000 (GMT) Subject: [Go] Alert: proposal to obsolete two biological process terms that impacts existing annotations Message-ID: Dear GO, The proposal has been made to obsolete error-prone DNA repair ; GO:0045020 error-free DNA repair ; GO:0045021 Annotations to these terms exist as listed below: gene_association.goa_uniprot.gz GO ID IEA non-IEA total GO:0045020 70 0 70 gene_association.jcvi_Psyringae_phaseolicola.gz GO ID IEA non-IEA total GO:0045020 0 1 1 gene_association.GeneDB_Spombe.gz GO ID IEA non-IEA total GO:0045021 0 2 2 gene_association.sgd.gz GO ID IEA non-IEA total GO:0045021 0 4 4 The reason for obsoleting these terms is that they have been superseded by more specific terms. We have also decided not to retain them as grouping terms, because neither 'error-free' nor 'error-prone' corresponds to a mechanism. Terms that will be suggested for transferring annotations: GO:0045020: error-prone translesion synthesis ; GO:0042276 GO:0045021 error-free postreplication DNA repair ; GO:0042275 error-free translesion synthesis ; GO:0070987 These terms are not in any GO slim maintained in the GO .obo files, and are not used in any external mappings. Both are in the prokaryotic GO subset. SourceForge link: https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1691618&group_id=36855 Comment period ends on November 13, 2009. *** Unless objections are received by November 13, we will assume that you agree to this change. *** Thanks, Midori From midori at ebi.ac.uk Fri Oct 30 10:54:23 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 30 Oct 2009 17:54:23 +0000 (GMT) Subject: [Go] paper on benchmark GO datasets Message-ID: http://www.ncbi.nlm.nih.gov/pubmed/19811632