From jdeegan at ebi.ac.uk Thu Nov 1 03:05:51 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Thu, 01 Nov 2007 10:05:51 +0000 Subject: [go] offer of human GO annotations In-Reply-To: <1193848625.19079.33.camel@paul.gen.cam.ac.uk> References: <1193848625.19079.33.camel@paul.gen.cam.ac.uk> Message-ID: <4729A4FF.7080102@ebi.ac.uk> Hi Susan, Thanks, this is exactly the kind of information we are looking for. We will follow it up. Jen Susan Tweedie wrote: > This is probably most relevant to Emily but others may like to comment. > Also Jen's may like to include this in her 'feedback from conferences' > aspect of the outreach report. > > Kira Anthony from the PathwayInteractionDatabase - > http://pid.nci.nih.gov (a collaboration between th U.S. National Cancer > Institute and Nature Publishing Group) talked to several of us at the > biocurator meeting and expressed an interest in submitting their GO > annotations relating to signalling pathways. The data is basically all > human (in some cases they know there is evidence in other species but > I'm not sure if they record the annotation details for the other > species). > > One problem with submitting their data is that they use a mix of GO > evidence codes and their own codes. > > e.g. IOS (inferred from other species) i.e. no evidence in human; IAE > (inferred from array experiments) chIP on chip, protein arrays, chemical > compound arrays; IFC (inferred from functional complementation); RGE > (inferred from reporter gene expression). > > However, it looks like most of these would map onto GO codes. > > Another point to clarify is whether they track which evidence is > associated with which reference - this isn't obvious from the way they > present it on the web but I haven't had more than a cursory look. > > Kira's email is k.anthony at boston.nature.com. I said I would pass on her > offer to the consortium and we'd get back to her. > > Thanks, > > Susan > -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From edimmer at ebi.ac.uk Thu Nov 1 06:29:34 2007 From: edimmer at ebi.ac.uk (E Dimmer) Date: Thu, 01 Nov 2007 13:29:34 +0000 Subject: [go] offer of human GO annotations In-Reply-To: <4729A4FF.7080102@ebi.ac.uk> References: <1193848625.19079.33.camel@paul.gen.cam.ac.uk> <4729A4FF.7080102@ebi.ac.uk> Message-ID: <4729D4BE.6000806@ebi.ac.uk> Hi Susan, Good networking! :-) I'll contact Kira and later report back to Jen/GOC to let you know how its progressing. Thanks! Emily Jennifer Deegan (nee Clark) wrote: > Hi Susan, > > Thanks, this is exactly the kind of information we are looking for. We > will follow it up. > > Jen > > Susan Tweedie wrote: >> This is probably most relevant to Emily but others may like to comment. >> Also Jen's may like to include this in her 'feedback from conferences' >> aspect of the outreach report. >> >> Kira Anthony from the PathwayInteractionDatabase - >> http://pid.nci.nih.gov (a collaboration between th U.S. National Cancer >> Institute and Nature Publishing Group) talked to several of us at the >> biocurator meeting and expressed an interest in submitting their GO >> annotations relating to signalling pathways. The data is basically all >> human (in some cases they know there is evidence in other species but >> I'm not sure if they record the annotation details for the other >> species). >> >> One problem with submitting their data is that they use a mix of GO >> evidence codes and their own codes. >> e.g. IOS (inferred from other species) i.e. no evidence in human; IAE >> (inferred from array experiments) chIP on chip, protein arrays, chemical >> compound arrays; IFC (inferred from functional complementation); RGE >> (inferred from reporter gene expression). >> >> However, it looks like most of these would map onto GO codes. >> >> Another point to clarify is whether they track which evidence is >> associated with which reference - this isn't obvious from the way they >> present it on the web but I haven't had more than a cursory look. >> Kira's email is k.anthony at boston.nature.com. I said I would pass on her >> offer to the consortium and we'd get back to her. >> >> Thanks, >> >> Susan >> > -- ************************************ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ From edimmer at ebi.ac.uk Thu Nov 1 09:17:33 2007 From: edimmer at ebi.ac.uk (E Dimmer) Date: Thu, 01 Nov 2007 16:17:33 +0000 Subject: [go] Protein domain GO annotation Message-ID: <4729FC1D.6050102@ebi.ac.uk> Hi, Could I please ask people's opinion on the functional annotation of protein domains/regions to the GO? I have been contacted by a group who would like to annotate GO functions to identified disordered regions in proteins. The thought so far is that they would annotate to a 'disordered_region' SO term, along with sequence co-ordinates, and then also attach a GO term with a reference and evidence code. (I have spoken with Gabby Reeves from BioSapiens, who would be happy to add 'disordered_region' terms to the BioSapiens protein feature ontology section of SO). For an annotation example: protein LEF-1 (Q9QXN1) has a disordered region corresponding to residues 296 - 397. This domain has been found to act to bend DNA, as reported in a experiment in PMID: 7651541. In the normal course of GO annotation I would of course happily to annotate the whole protein (Q9QXN1) to the DNA bending term (DNA bending activity, GO:0008301), and while I might read about the discrete region in the protein that is responsible for this function I would not capture this data. However the IUP(Intrinsically Unstructured Protein) curators would include the aa residue information in their annotations and want to describe the individual functions that a protein's multiple domains might have. So I assume that for these kinds of annotations, where an equivalent GO term exists, a GOC annotation group could integrate this group's annotations and relate it up to the whole protein/gene product (and possibly being able to keep the SO term in the new cross-reference column 16? but not the aa residue location?). While the majority of the function terms that the IUP community are interested in applying to their domains do map quite straight-forwardly to GO terms, there are some new ones which would need to be requested. And some of these new terms seem to describe more domain-specific, intra-protein function. For example, for some of the function terms used in the DisProt database: flexible linker/spacer Provides separation and permits movement between adjacent domains entropic brisle A disordered region that creates a zone of exclusion by its entropic movement entropic spring Provides a restoring force resulting from randomization of bond torsion angles that become restricted upon stretching. (see: http://www.disprot.org/view_function_subclass.php) So, would GO be willing to add these types of terms? And how much of the IUP communities annotation data would GOC groups be happy to incorporate into their own annotation sets? Thanks, Emily -- ************************************ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ From hjd at informatics.jax.org Thu Nov 1 11:05:36 2007 From: hjd at informatics.jax.org (Harold Drabkin) Date: Thu, 01 Nov 2007 14:05:36 -0400 Subject: [go] Protein domain GO annotation In-Reply-To: <4729FC1D.6050102@ebi.ac.uk> References: <4729FC1D.6050102@ebi.ac.uk> Message-ID: <472A1570.3080802@informatics.jax.org> This sounds more like an interpro to GO translation table,. E Dimmer wrote: > Hi, > > Could I please ask people's opinion on the functional annotation of > protein domains/regions to the GO? > > I have been contacted by a group who would like to annotate GO > functions to identified disordered regions in proteins. > > The thought so far is that they would annotate to a > 'disordered_region' SO term, along with sequence co-ordinates, and > then also attach a GO term with a reference and evidence code. > (I have spoken with Gabby Reeves from BioSapiens, who would be happy > to add 'disordered_region' terms to the BioSapiens protein feature > ontology section of SO). > > For an annotation example: protein LEF-1 (Q9QXN1) has a disordered > region corresponding to residues 296 - 397. This domain has been found > to act to bend DNA, as reported in a experiment in PMID: 7651541. > In the normal course of GO annotation I would of course happily to > annotate the whole protein (Q9QXN1) to the DNA bending term (DNA > bending activity, GO:0008301), and while I might read about the > discrete region in the protein that is responsible for this function I > would not capture this data. > However the IUP(Intrinsically Unstructured Protein) curators would > include the aa residue information in their annotations and want to > describe the individual functions that a protein's multiple domains > might have. > > So I assume that for these kinds of annotations, where an equivalent > GO term exists, a GOC annotation group could integrate this group's > annotations and relate it up to the whole protein/gene product (and > possibly being able to keep the SO term in the new cross-reference > column 16? but not the aa residue location?). > > While the majority of the function terms that the IUP community are > interested in applying to their domains do map quite > straight-forwardly to GO terms, there are some new ones which would > need to be requested. And some of these new terms seem to describe > more domain-specific, intra-protein function. For example, for some of > the function terms used in the DisProt database: > > flexible linker/spacer > Provides separation and permits movement between adjacent domains > > entropic brisle > A disordered region that creates a zone of exclusion by its entropic > movement > > entropic spring > Provides a restoring force resulting from randomization of bond > torsion angles that become restricted upon stretching. > > (see: http://www.disprot.org/view_function_subclass.php) > > So, would GO be willing to add these types of terms? And how much of > the IUP communities annotation data would GOC groups be happy to > incorporate into their own annotation sets? > > Thanks, > Emily > > From adiehl at informatics.jax.org Thu Nov 1 11:27:05 2007 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Thu, 01 Nov 2007 18:27:05 +0000 Subject: [go] Protein domain GO annotation In-Reply-To: <472A1570.3080802@informatics.jax.org> References: <4729FC1D.6050102@ebi.ac.uk> <472A1570.3080802@informatics.jax.org> Message-ID: <472A1A79.104@informatics.jax.org> Emily, I am not entirely happy with the idea of adding "sub-molecular" functions for protein domains to the GO that refer functions that occur between parts of the same protein such as "entropic spring" as these would not map neatly to the whole protein were we to import IUP (Intrinsically Unstructured Protein) annotations into the GO. -- Alex Harold Drabkin wrote: > This sounds more like an interpro to GO translation table,. > > E Dimmer wrote: >> Hi, >> >> Could I please ask people's opinion on the functional annotation of >> protein domains/regions to the GO? >> >> I have been contacted by a group who would like to annotate GO >> functions to identified disordered regions in proteins. >> >> The thought so far is that they would annotate to a >> 'disordered_region' SO term, along with sequence co-ordinates, and >> then also attach a GO term with a reference and evidence code. >> (I have spoken with Gabby Reeves from BioSapiens, who would be happy >> to add 'disordered_region' terms to the BioSapiens protein feature >> ontology section of SO). >> >> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered >> region corresponding to residues 296 - 397. This domain has been >> found to act to bend DNA, as reported in a experiment in PMID: 7651541. >> In the normal course of GO annotation I would of course happily to >> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA >> bending activity, GO:0008301), and while I might read about the >> discrete region in the protein that is responsible for this function >> I would not capture this data. >> However the IUP(Intrinsically Unstructured Protein) curators would >> include the aa residue information in their annotations and want to >> describe the individual functions that a protein's multiple domains >> might have. >> >> So I assume that for these kinds of annotations, where an equivalent >> GO term exists, a GOC annotation group could integrate this group's >> annotations and relate it up to the whole protein/gene product (and >> possibly being able to keep the SO term in the new cross-reference >> column 16? but not the aa residue location?). >> >> While the majority of the function terms that the IUP community are >> interested in applying to their domains do map quite >> straight-forwardly to GO terms, there are some new ones which would >> need to be requested. And some of these new terms seem to describe >> more domain-specific, intra-protein function. For example, for some >> of the function terms used in the DisProt database: >> >> flexible linker/spacer >> Provides separation and permits movement between adjacent domains >> >> entropic brisle >> A disordered region that creates a zone of exclusion by its entropic >> movement >> >> entropic spring >> Provides a restoring force resulting from randomization of bond >> torsion angles that become restricted upon stretching. >> >> (see: http://www.disprot.org/view_function_subclass.php) >> >> So, would GO be willing to add these types of terms? And how much of >> the IUP communities annotation data would GOC groups be happy to >> incorporate into their own annotation sets? >> >> Thanks, >> Emily >> >> > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From jimhu at tamu.edu Thu Nov 1 11:39:15 2007 From: jimhu at tamu.edu (Jim Hu) Date: Thu, 1 Nov 2007 13:39:15 -0500 Subject: [go] Protein domain GO annotation In-Reply-To: <4729FC1D.6050102@ebi.ac.uk> References: <4729FC1D.6050102@ebi.ac.uk> Message-ID: Hi Emily, Here are my thoughts: On Nov 1, 2007, at 11:17 AM, E Dimmer wrote: > Hi, > > Could I please ask people's opinion on the functional annotation of > protein domains/regions to the GO? > > I have been contacted by a group who would like to annotate GO > functions to identified disordered regions in proteins. > > The thought so far is that they would annotate to a > 'disordered_region' SO term, along with sequence co-ordinates, and > then also attach a GO term with a reference and evidence code. > (I have spoken with Gabby Reeves from BioSapiens, who would be > happy to add 'disordered_region' terms to the BioSapiens protein > feature ontology section of SO). This clearly would need to go in all of SO, not just BioSapiens > > For an annotation example: protein LEF-1 (Q9QXN1) has a disordered > region corresponding to residues 296 - 397. This domain has been > found to act to bend DNA, as reported in a experiment in PMID: > 7651541. > In the normal course of GO annotation I would of course happily to > annotate the whole protein (Q9QXN1) to the DNA bending term (DNA > bending activity, GO:0008301), and while I might read about the > discrete region in the protein that is responsible for this > function I would not capture this data. I don't think GO should capture the protein region coordinates directly, but it should be possible to find coordinates if they exist via something linked. > However the IUP(Intrinsically Unstructured Protein) curators would > include the aa residue information in their annotations and want to > describe the individual functions that a protein's multiple domains > might have. > > So I assume that for these kinds of annotations, where an > equivalent GO term exists, a GOC annotation group could integrate > this group's annotations and relate it up to the whole protein/gene > product (and possibly being able to keep the SO term in the new > cross-reference column 16? but not the aa residue location?). I don't recall how column 16 works, but wouldn't it point to a SO annotation for the protein that captures the residue locations. Isn't that also better from a normalization POV? i.e. if the gene model changes we have to change the GO annotation? > > While the majority of the function terms that the IUP community are > interested in applying to their domains do map quite straight- > forwardly to GO terms, there are some new ones which would need to > be requested. And some of these new terms seem to describe more > domain-specific, intra-protein function. For example, for some of > the function terms used in the DisProt database: > > flexible linker/spacer > Provides separation and permits movement between adjacent domains > > entropic brisle > A disordered region that creates a zone of exclusion by its > entropic movement > > entropic spring > Provides a restoring force resulting from randomization of bond > torsion angles that become restricted upon stretching. > > (see: http://www.disprot.org/view_function_subclass.php) > > So, would GO be willing to add these types of terms? And how much > of the IUP communities annotation data would GOC groups be happy to > incorporate into their own annotation sets? Consider the reductio - should GO annotate individual residues in an active site? I think not, even though there is a lot of information of that kind in the literature and people find it useful. So, I'd be opposed. Not for GO. Yes for SO or some other domain/feature ontology if SO is not quite appropriate. Jim > > Thanks, > Emily > > > -- > ************************************ > Emily Dimmer > GOA Coordinator > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD, U.K. > Tel: +44 1223 494654 > Fax: +44 1223 494468 > email: edimmer at ebi.ac.uk > ************************************ > ===================================== 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: http://fafner.stanford.edu/pipermail/go/attachments/20071101/a36833de/attachment.html From hitz at genome.Stanford.EDU Thu Nov 1 11:49:25 2007 From: hitz at genome.Stanford.EDU (Benjamin Hitz) Date: Thu, 1 Nov 2007 11:49:25 -0700 Subject: [go] Protein domain GO annotation In-Reply-To: <4729FC1D.6050102@ebi.ac.uk> References: <4729FC1D.6050102@ebi.ac.uk> Message-ID: <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> As resident protein structure expert, no. Not that what they are doing is wrong, or not important - but it's not a biological process/function/component of the gene (product) in question. What's next? We annotate alpha helices? Ben On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: > Hi, > > Could I please ask people's opinion on the functional annotation of > protein domains/regions to the GO? > > I have been contacted by a group who would like to annotate GO > functions to identified disordered regions in proteins. > > The thought so far is that they would annotate to a > 'disordered_region' SO term, along with sequence co-ordinates, and > then also attach a GO term with a reference and evidence code. > (I have spoken with Gabby Reeves from BioSapiens, who would be > happy to add 'disordered_region' terms to the BioSapiens protein > feature ontology section of SO). > > For an annotation example: protein LEF-1 (Q9QXN1) has a disordered > region corresponding to residues 296 - 397. This domain has been > found to act to bend DNA, as reported in a experiment in PMID: > 7651541. > In the normal course of GO annotation I would of course happily to > annotate the whole protein (Q9QXN1) to the DNA bending term (DNA > bending activity, GO:0008301), and while I might read about the > discrete region in the protein that is responsible for this > function I would not capture this data. > However the IUP(Intrinsically Unstructured Protein) curators would > include the aa residue information in their annotations and want to > describe the individual functions that a protein's multiple domains > might have. > > So I assume that for these kinds of annotations, where an > equivalent GO term exists, a GOC annotation group could integrate > this group's annotations and relate it up to the whole protein/gene > product (and possibly being able to keep the SO term in the new > cross-reference column 16? but not the aa residue location?). > > While the majority of the function terms that the IUP community are > interested in applying to their domains do map quite straight- > forwardly to GO terms, there are some new ones which would need to > be requested. And some of these new terms seem to describe more > domain-specific, intra-protein function. For example, for some of > the function terms used in the DisProt database: > > flexible linker/spacer > Provides separation and permits movement between adjacent domains > > entropic brisle > A disordered region that creates a zone of exclusion by its > entropic movement > > entropic spring > Provides a restoring force resulting from randomization of bond > torsion angles that become restricted upon stretching. > > (see: http://www.disprot.org/view_function_subclass.php) > > So, would GO be willing to add these types of terms? And how much > of the IUP communities annotation data would GOC groups be happy to > incorporate into their own annotation sets? > > Thanks, > Emily > > > -- > ************************************ > Emily Dimmer > GOA Coordinator > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD, U.K. > Tel: +44 1223 494654 > Fax: +44 1223 494468 > email: edimmer at ebi.ac.uk > ************************************ -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu From ma11 at gen.cam.ac.uk Thu Nov 1 13:03:09 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Thu, 1 Nov 2007 16:03:09 -0400 Subject: [go] Protein domain GO annotation In-Reply-To: <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> References: <4729FC1D.6050102@ebi.ac.uk> <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> Message-ID: <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> I agree with Ben, this is not for the GO. Michael On 1 Nov 2007, at 14:49, Benjamin Hitz wrote: > > As resident protein structure expert, no. > Not that what they are doing is wrong, or not important - but it's > not a biological process/function/component of the gene (product) > in question. > > What's next? We annotate alpha helices? > > Ben > > On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: > >> Hi, >> >> Could I please ask people's opinion on the functional annotation >> of protein domains/regions to the GO? >> >> I have been contacted by a group who would like to annotate GO >> functions to identified disordered regions in proteins. >> >> The thought so far is that they would annotate to a >> 'disordered_region' SO term, along with sequence co-ordinates, and >> then also attach a GO term with a reference and evidence code. >> (I have spoken with Gabby Reeves from BioSapiens, who would be >> happy to add 'disordered_region' terms to the BioSapiens protein >> feature ontology section of SO). >> >> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered >> region corresponding to residues 296 - 397. This domain has been >> found to act to bend DNA, as reported in a experiment in PMID: >> 7651541. >> In the normal course of GO annotation I would of course happily to >> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA >> bending activity, GO:0008301), and while I might read about the >> discrete region in the protein that is responsible for this >> function I would not capture this data. >> However the IUP(Intrinsically Unstructured Protein) curators would >> include the aa residue information in their annotations and want >> to describe the individual functions that a protein's multiple >> domains might have. >> >> So I assume that for these kinds of annotations, where an >> equivalent GO term exists, a GOC annotation group could integrate >> this group's annotations and relate it up to the whole protein/ >> gene product (and possibly being able to keep the SO term in the >> new cross-reference column 16? but not the aa residue location?). >> >> While the majority of the function terms that the IUP community >> are interested in applying to their domains do map quite straight- >> forwardly to GO terms, there are some new ones which would need to >> be requested. And some of these new terms seem to describe more >> domain-specific, intra-protein function. For example, for some of >> the function terms used in the DisProt database: >> >> flexible linker/spacer >> Provides separation and permits movement between adjacent domains >> >> entropic brisle >> A disordered region that creates a zone of exclusion by its >> entropic movement >> >> entropic spring >> Provides a restoring force resulting from randomization of bond >> torsion angles that become restricted upon stretching. >> >> (see: http://www.disprot.org/view_function_subclass.php) >> >> So, would GO be willing to add these types of terms? And how much >> of the IUP communities annotation data would GOC groups be happy >> to incorporate into their own annotation sets? >> >> Thanks, >> Emily >> >> >> -- >> ************************************ >> Emily Dimmer >> GOA Coordinator >> EMBL-EBI >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD, U.K. >> Tel: +44 1223 494654 >> Fax: +44 1223 494468 >> email: edimmer at ebi.ac.uk >> ************************************ > > -- > Ben Hitz > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO > Consortium > Stanford University ** hitz at genome.stanford.edu > > > From midori at ebi.ac.uk Fri Nov 2 02:11:45 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 2 Nov 2007 09:11:45 +0000 (GMT) Subject: [go] Ontology development - October highlights Message-ID: Dear GO, The most recent monthly report on ontology content, for October 2007, is now available at: http://gocwiki.geneontology.org/index.php/Oct2007_ontology_report The big news this month is that the changes resulting from the content meetings on cardiovascular physiology and muscle development have gone live. For more details, see the relevant wiki pages: http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/development http://wiki.geneontology.org/index.php/Muscle_Development Other highlights from October: * Lots of progress on regulation, with the aim of adding cross-products and using the 'regulates' relationship; (http://gocwiki.geneontology.org/index.php/Regulation_Main_Page). * There are plans afoot for a content meeting on lung development, to be held in December (http://wiki.geneontology.org/index.php/Lung_Development). * Updates to the wiki material on function-process links (http://gocwiki.geneontology.org/index.php/Function-Process_Links). * The update article for the January 2008 NAR Database Issue has been accepted, and should appear online soon. In November, work on the last few 'sensu' terms will resume (main wiki page: http://gocwiki.geneontology.org/index.php/Sensu_Main_Page; outstanding items: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3). 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. Midori & David on behalf of GO's ontology developers From edimmer at ebi.ac.uk Fri Nov 2 02:28:56 2007 From: edimmer at ebi.ac.uk (E Dimmer) Date: Fri, 02 Nov 2007 09:28:56 +0000 Subject: [go] Protein domain GO annotation In-Reply-To: <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> References: <4729FC1D.6050102@ebi.ac.uk> <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> Message-ID: <472AEDD8.7040607@ebi.ac.uk> However there are quite a number of GO function terms which occur on discrete portions of a protein sequence, for instance many of the child terms of 'binding' (GO:0005488) (protein, ATP, lipid, co-factor etc) and simple catalytic domains. I feel that there could be a mid-way point - there are GO terms that can be annotated to a specific region of a sequence where it is also appropriate for the function to be 'inherited' by the whole protein. But also there there are domain terms which are not appropriate for a whole protein - then these should go into another ontology, which could be a composite of GO terms and domain-specific terms. So while protein domain function annotators and and gene-product annotators will need to work from a different term set and add different parameters to their annotations, where a domain has been annotated to a GO term e.g. 'DNA binding' IDA , then we could consider including these into GO. Would this suggestion be more acceptable to GO folk? Emily Michael Ashburner wrote: > I agree with Ben, this is not for the GO. > Michael > > On 1 Nov 2007, at 14:49, Benjamin Hitz wrote: > >> >> As resident protein structure expert, no. >> Not that what they are doing is wrong, or not important - but it's >> not a biological process/function/component of the gene (product) in >> question. >> >> What's next? We annotate alpha helices? >> >> Ben >> >> On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: >> >>> Hi, >>> >>> Could I please ask people's opinion on the functional annotation of >>> protein domains/regions to the GO? >>> >>> I have been contacted by a group who would like to annotate GO >>> functions to identified disordered regions in proteins. >>> >>> The thought so far is that they would annotate to a >>> 'disordered_region' SO term, along with sequence co-ordinates, and >>> then also attach a GO term with a reference and evidence code. >>> (I have spoken with Gabby Reeves from BioSapiens, who would be happy >>> to add 'disordered_region' terms to the BioSapiens protein feature >>> ontology section of SO). >>> >>> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered >>> region corresponding to residues 296 - 397. This domain has been >>> found to act to bend DNA, as reported in a experiment in PMID: 7651541. >>> In the normal course of GO annotation I would of course happily to >>> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA >>> bending activity, GO:0008301), and while I might read about the >>> discrete region in the protein that is responsible for this function >>> I would not capture this data. >>> However the IUP(Intrinsically Unstructured Protein) curators would >>> include the aa residue information in their annotations and want to >>> describe the individual functions that a protein's multiple domains >>> might have. >>> >>> So I assume that for these kinds of annotations, where an equivalent >>> GO term exists, a GOC annotation group could integrate this group's >>> annotations and relate it up to the whole protein/gene product (and >>> possibly being able to keep the SO term in the new cross-reference >>> column 16? but not the aa residue location?). >>> >>> While the majority of the function terms that the IUP community are >>> interested in applying to their domains do map quite >>> straight-forwardly to GO terms, there are some new ones which would >>> need to be requested. And some of these new terms seem to describe >>> more domain-specific, intra-protein function. For example, for some >>> of the function terms used in the DisProt database: >>> >>> flexible linker/spacer >>> Provides separation and permits movement between adjacent domains >>> >>> entropic brisle >>> A disordered region that creates a zone of exclusion by its entropic >>> movement >>> >>> entropic spring >>> Provides a restoring force resulting from randomization of bond >>> torsion angles that become restricted upon stretching. >>> >>> (see: http://www.disprot.org/view_function_subclass.php) >>> >>> So, would GO be willing to add these types of terms? And how much of >>> the IUP communities annotation data would GOC groups be happy to >>> incorporate into their own annotation sets? >>> >>> Thanks, >>> Emily >>> >>> >>> --************************************ >>> Emily Dimmer >>> GOA Coordinator >>> EMBL-EBI >>> Wellcome Trust Genome Campus >>> Hinxton >>> Cambridge CB10 1SD, U.K. >>> Tel: +44 1223 494654 >>> Fax: +44 1223 494468 >>> email: edimmer at ebi.ac.uk >>> ************************************ >> >> -- >> Ben Hitz >> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >> Consortium >> Stanford University ** hitz at genome.stanford.edu >> >> >> -- ************************************ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ From val at sanger.ac.uk Fri Nov 2 04:33:15 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 02 Nov 2007 11:33:15 +0000 Subject: [go] Protein domain GO annotation In-Reply-To: <472AEDD8.7040607@ebi.ac.uk> References: <4729FC1D.6050102@ebi.ac.uk> <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> <472AEDD8.7040607@ebi.ac.uk> Message-ID: <472B0AFB.7080006@sanger.ac.uk> Hi Emily, I agree that when a function or process is known to be the role of a specific region of a protein, it is usful to capture this information. I often do this by recording the amino acid coordinates or the domain accession (if there is one) as a qualifier to the annotation, but at present do nothing further with this information. I was also hoping that this could somehow eventually be cross-referenced to a separate ontology in column 16 (i.e the protein feature region of SO). I have some extreme examples. In pombe there are a number of 'fusion proteins' which appear to be post translationally cleaved. For example the mitochondrial type I [2Fe-2S] ferredoxin Etp1/ cytochrome oxidase cofactor Cox15, fusion. As I don't know where the cleavage site is, and I annotate to the gene, the GO terms are all annotated to a single sequence. Clearly it will be useful to record the region which the process and function applies to in these cases. I agree also, that if a region or domain has clearly been ascribed a specific function or activity, then it is also useful to record this. Another For example, in obvious cases of mulitfunctional enzynmes like ura 1 http://pfam.sanger.ac.uk/protein?acc=Q09794 but also, more subtly if different regions of proteins have been identified to be important for different processes. This is all important data that should be captured by curators, even if it is not part of GO. Val E Dimmer wrote: > However there are quite a number of GO function terms which occur on > discrete portions of a protein sequence, for instance many of the > child terms of 'binding' (GO:0005488) (protein, ATP, lipid, co-factor > etc) and simple catalytic domains. > > I feel that there could be a mid-way point - there are GO terms that > can be annotated to a specific region of a sequence where it is also > appropriate for the function to be 'inherited' by the whole protein. > But also there there are domain terms which are not appropriate for a > whole protein - then these should go into another ontology, which > could be a composite of GO terms and domain-specific terms. > > So while protein domain function annotators and and gene-product > annotators will need to work from a different term set and add > different parameters to their annotations, where a domain has been > annotated to a GO term e.g. 'DNA binding' IDA , then we could consider > including these into GO. > > Would this suggestion be more acceptable to GO folk? > > Emily > > > Michael Ashburner wrote: > >> I agree with Ben, this is not for the GO. >> Michael >> >> On 1 Nov 2007, at 14:49, Benjamin Hitz wrote: >> >>> >>> As resident protein structure expert, no. >>> Not that what they are doing is wrong, or not important - but it's >>> not a biological process/function/component of the gene (product) in >>> question. >>> >>> What's next? We annotate alpha helices? >>> >>> Ben >>> >>> On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: >>> >>>> Hi, >>>> >>>> Could I please ask people's opinion on the functional annotation of >>>> protein domains/regions to the GO? >>>> >>>> I have been contacted by a group who would like to annotate GO >>>> functions to identified disordered regions in proteins. >>>> >>>> The thought so far is that they would annotate to a >>>> 'disordered_region' SO term, along with sequence co-ordinates, and >>>> then also attach a GO term with a reference and evidence code. >>>> (I have spoken with Gabby Reeves from BioSapiens, who would be >>>> happy to add 'disordered_region' terms to the BioSapiens protein >>>> feature ontology section of SO). >>>> >>>> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered >>>> region corresponding to residues 296 - 397. This domain has been >>>> found to act to bend DNA, as reported in a experiment in PMID: >>>> 7651541. >>>> In the normal course of GO annotation I would of course happily to >>>> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA >>>> bending activity, GO:0008301), and while I might read about the >>>> discrete region in the protein that is responsible for this >>>> function I would not capture this data. >>>> However the IUP(Intrinsically Unstructured Protein) curators would >>>> include the aa residue information in their annotations and want to >>>> describe the individual functions that a protein's multiple domains >>>> might have. >>>> >>>> So I assume that for these kinds of annotations, where an >>>> equivalent GO term exists, a GOC annotation group could integrate >>>> this group's annotations and relate it up to the whole protein/gene >>>> product (and possibly being able to keep the SO term in the new >>>> cross-reference column 16? but not the aa residue location?). >>>> >>>> While the majority of the function terms that the IUP community are >>>> interested in applying to their domains do map quite >>>> straight-forwardly to GO terms, there are some new ones which would >>>> need to be requested. And some of these new terms seem to describe >>>> more domain-specific, intra-protein function. For example, for some >>>> of the function terms used in the DisProt database: >>>> >>>> flexible linker/spacer >>>> Provides separation and permits movement between adjacent domains >>>> >>>> entropic brisle >>>> A disordered region that creates a zone of exclusion by its >>>> entropic movement >>>> >>>> entropic spring >>>> Provides a restoring force resulting from randomization of bond >>>> torsion angles that become restricted upon stretching. >>>> >>>> (see: http://www.disprot.org/view_function_subclass.php) >>>> >>>> So, would GO be willing to add these types of terms? And how much >>>> of the IUP communities annotation data would GOC groups be happy to >>>> incorporate into their own annotation sets? >>>> >>>> Thanks, >>>> Emily >>>> >>>> >>>> --************************************ >>>> Emily Dimmer >>>> GOA Coordinator >>>> EMBL-EBI >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD, U.K. >>>> Tel: +44 1223 494654 >>>> Fax: +44 1223 494468 >>>> email: edimmer at ebi.ac.uk >>>> ************************************ >>> >>> >>> -- >>> Ben Hitz >>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >>> Consortium >>> Stanford University ** hitz at genome.stanford.edu >>> >>> >>> > > -- 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 ma11 at gen.cam.ac.uk Fri Nov 2 05:36:18 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Fri, 2 Nov 2007 08:36:18 -0400 Subject: [go] Protein domain GO annotation In-Reply-To: <472AEDD8.7040607@ebi.ac.uk> References: <4729FC1D.6050102@ebi.ac.uk> <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> <472AEDD8.7040607@ebi.ac.uk> Message-ID: I am sorry, but I am still not convinced. GO terms are used by the GO to annotate gene products. I do not think that we, as the GO should use these to annotate the anatomy of a protein. Of course, of some other group want to do this then fine, but as Emily points out they will need more than the GO for that purpose. Michael On 2 Nov 2007, at 05:28, E Dimmer wrote: > However there are quite a number of GO function terms which occur > on discrete portions of a protein sequence, for instance many of > the child terms of 'binding' (GO:0005488) (protein, ATP, lipid, co- > factor etc) and simple catalytic domains. > > I feel that there could be a mid-way point - there are GO terms > that can be annotated to a specific region of a sequence where it > is also appropriate for the function to be 'inherited' by the whole > protein. > But also there there are domain terms which are not appropriate for > a whole protein - then these should go into another ontology, which > could be a composite of GO terms and domain-specific terms. > > So while protein domain function annotators and and gene-product > annotators will need to work from a different term set and add > different parameters to their annotations, where a domain has been > annotated to a GO term e.g. 'DNA binding' IDA , then we could > consider including these into GO. > > Would this suggestion be more acceptable to GO folk? > > Emily > > > Michael Ashburner wrote: >> I agree with Ben, this is not for the GO. >> Michael >> >> On 1 Nov 2007, at 14:49, Benjamin Hitz wrote: >> >>> >>> As resident protein structure expert, no. >>> Not that what they are doing is wrong, or not important - but >>> it's not a biological process/function/component of the gene >>> (product) in question. >>> >>> What's next? We annotate alpha helices? >>> >>> Ben >>> >>> On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: >>> >>>> Hi, >>>> >>>> Could I please ask people's opinion on the functional annotation >>>> of protein domains/regions to the GO? >>>> >>>> I have been contacted by a group who would like to annotate GO >>>> functions to identified disordered regions in proteins. >>>> >>>> The thought so far is that they would annotate to a >>>> 'disordered_region' SO term, along with sequence co-ordinates, >>>> and then also attach a GO term with a reference and evidence code. >>>> (I have spoken with Gabby Reeves from BioSapiens, who would be >>>> happy to add 'disordered_region' terms to the BioSapiens protein >>>> feature ontology section of SO). >>>> >>>> For an annotation example: protein LEF-1 (Q9QXN1) has a >>>> disordered region corresponding to residues 296 - 397. This >>>> domain has been found to act to bend DNA, as reported in a >>>> experiment in PMID: 7651541. >>>> In the normal course of GO annotation I would of course happily >>>> to annotate the whole protein (Q9QXN1) to the DNA bending term >>>> (DNA bending activity, GO:0008301), and while I might read about >>>> the discrete region in the protein that is responsible for this >>>> function I would not capture this data. >>>> However the IUP(Intrinsically Unstructured Protein) curators >>>> would include the aa residue information in their annotations >>>> and want to describe the individual functions that a protein's >>>> multiple domains might have. >>>> >>>> So I assume that for these kinds of annotations, where an >>>> equivalent GO term exists, a GOC annotation group could >>>> integrate this group's annotations and relate it up to the whole >>>> protein/gene product (and possibly being able to keep the SO >>>> term in the new cross-reference column 16? but not the aa >>>> residue location?). >>>> >>>> While the majority of the function terms that the IUP community >>>> are interested in applying to their domains do map quite >>>> straight-forwardly to GO terms, there are some new ones which >>>> would need to be requested. And some of these new terms seem to >>>> describe more domain-specific, intra-protein function. For >>>> example, for some of the function terms used in the DisProt >>>> database: >>>> >>>> flexible linker/spacer >>>> Provides separation and permits movement between adjacent domains >>>> >>>> entropic brisle >>>> A disordered region that creates a zone of exclusion by its >>>> entropic movement >>>> >>>> entropic spring >>>> Provides a restoring force resulting from randomization of bond >>>> torsion angles that become restricted upon stretching. >>>> >>>> (see: http://www.disprot.org/view_function_subclass.php) >>>> >>>> So, would GO be willing to add these types of terms? And how >>>> much of the IUP communities annotation data would GOC groups be >>>> happy to incorporate into their own annotation sets? >>>> >>>> Thanks, >>>> Emily >>>> >>>> >>>> --************************************ >>>> Emily Dimmer >>>> GOA Coordinator >>>> EMBL-EBI >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD, U.K. >>>> Tel: +44 1223 494654 >>>> Fax: +44 1223 494468 >>>> email: edimmer at ebi.ac.uk >>>> ************************************ >>> >>> -- >>> Ben Hitz >>> Senior Scientific Programmer ** Saccharomyces Genome Database ** >>> GO Consortium >>> Stanford University ** hitz at genome.stanford.edu >>> >>> >>> > > > -- > ************************************ > Emily Dimmer > GOA Coordinator > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD, U.K. > Tel: +44 1223 494654 > Fax: +44 1223 494468 > email: edimmer at ebi.ac.uk > ************************************ > From dph at informatics.jax.org Fri Nov 2 05:48:21 2007 From: dph at informatics.jax.org (David Hill) Date: Fri, 02 Nov 2007 08:48:21 -0400 Subject: [go] Protein domain GO annotation In-Reply-To: References: <4729FC1D.6050102@ebi.ac.uk> <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> <472AEDD8.7040607@ebi.ac.uk> Message-ID: <472B1C95.1080001@informatics.jax.org> Hi Everyone, I might as well weigh in as well. I think Michael hits the nail on the head: > GO terms are used by the GO to annotate gene products. Whenever we do anything with the GO it is always with the idea that we are using it for this purpose. The GO may suit other purposes, but our concern is that it is suitable for gene product annotation. That's what we do. David > > Michael > On 2 Nov 2007, at 05:28, E Dimmer wrote: > >> However there are quite a number of GO function terms which occur on >> discrete portions of a protein sequence, for instance many of the >> child terms of 'binding' (GO:0005488) (protein, ATP, lipid, >> co-factor etc) and simple catalytic domains. >> >> I feel that there could be a mid-way point - there are GO terms that >> can be annotated to a specific region of a sequence where it is also >> appropriate for the function to be 'inherited' by the whole protein. >> But also there there are domain terms which are not appropriate for a >> whole protein - then these should go into another ontology, which >> could be a composite of GO terms and domain-specific terms. >> >> So while protein domain function annotators and and gene-product >> annotators will need to work from a different term set and add >> different parameters to their annotations, where a domain has been >> annotated to a GO term e.g. 'DNA binding' IDA , then we could >> consider including these into GO. >> >> Would this suggestion be more acceptable to GO folk? >> >> Emily >> >> >> Michael Ashburner wrote: >>> I agree with Ben, this is not for the GO. >>> Michael >>> >>> On 1 Nov 2007, at 14:49, Benjamin Hitz wrote: >>> >>>> >>>> As resident protein structure expert, no. >>>> Not that what they are doing is wrong, or not important - but it's >>>> not a biological process/function/component of the gene (product) >>>> in question. >>>> >>>> What's next? We annotate alpha helices? >>>> >>>> Ben >>>> >>>> On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: >>>> >>>>> Hi, >>>>> >>>>> Could I please ask people's opinion on the functional annotation >>>>> of protein domains/regions to the GO? >>>>> >>>>> I have been contacted by a group who would like to annotate GO >>>>> functions to identified disordered regions in proteins. >>>>> >>>>> The thought so far is that they would annotate to a >>>>> 'disordered_region' SO term, along with sequence co-ordinates, and >>>>> then also attach a GO term with a reference and evidence code. >>>>> (I have spoken with Gabby Reeves from BioSapiens, who would be >>>>> happy to add 'disordered_region' terms to the BioSapiens protein >>>>> feature ontology section of SO). >>>>> >>>>> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered >>>>> region corresponding to residues 296 - 397. This domain has been >>>>> found to act to bend DNA, as reported in a experiment in PMID: >>>>> 7651541. >>>>> In the normal course of GO annotation I would of course happily to >>>>> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA >>>>> bending activity, GO:0008301), and while I might read about the >>>>> discrete region in the protein that is responsible for this >>>>> function I would not capture this data. >>>>> However the IUP(Intrinsically Unstructured Protein) curators would >>>>> include the aa residue information in their annotations and want >>>>> to describe the individual functions that a protein's multiple >>>>> domains might have. >>>>> >>>>> So I assume that for these kinds of annotations, where an >>>>> equivalent GO term exists, a GOC annotation group could integrate >>>>> this group's annotations and relate it up to the whole >>>>> protein/gene product (and possibly being able to keep the SO term >>>>> in the new cross-reference column 16? but not the aa residue >>>>> location?). >>>>> >>>>> While the majority of the function terms that the IUP community >>>>> are interested in applying to their domains do map quite >>>>> straight-forwardly to GO terms, there are some new ones which >>>>> would need to be requested. And some of these new terms seem to >>>>> describe more domain-specific, intra-protein function. For >>>>> example, for some of the function terms used in the DisProt database: >>>>> >>>>> flexible linker/spacer >>>>> Provides separation and permits movement between adjacent domains >>>>> >>>>> entropic brisle >>>>> A disordered region that creates a zone of exclusion by its >>>>> entropic movement >>>>> >>>>> entropic spring >>>>> Provides a restoring force resulting from randomization of bond >>>>> torsion angles that become restricted upon stretching. >>>>> >>>>> (see: http://www.disprot.org/view_function_subclass.php) >>>>> >>>>> So, would GO be willing to add these types of terms? And how much >>>>> of the IUP communities annotation data would GOC groups be happy >>>>> to incorporate into their own annotation sets? >>>>> >>>>> Thanks, >>>>> Emily >>>>> >>>>> >>>>> --************************************ >>>>> Emily Dimmer >>>>> GOA Coordinator >>>>> EMBL-EBI >>>>> Wellcome Trust Genome Campus >>>>> Hinxton >>>>> Cambridge CB10 1SD, U.K. >>>>> Tel: +44 1223 494654 >>>>> Fax: +44 1223 494468 >>>>> email: edimmer at ebi.ac.uk >>>>> ************************************ >>>> >>>> --Ben Hitz >>>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >>>> Consortium >>>> Stanford University ** hitz at genome.stanford.edu >>>> >>>> >>>> >> >> >> --************************************ >> Emily Dimmer >> GOA Coordinator >> EMBL-EBI >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD, U.K. >> Tel: +44 1223 494654 >> Fax: +44 1223 494468 >> email: edimmer at ebi.ac.uk >> ************************************ >> > From hitz at genome.Stanford.EDU Fri Nov 2 08:31:48 2007 From: hitz at genome.Stanford.EDU (Ben Hitz) Date: Fri, 2 Nov 2007 08:31:48 -0700 Subject: [go] Protein domain GO annotation In-Reply-To: <472AEDD8.7040607@ebi.ac.uk> References: <4729FC1D.6050102@ebi.ac.uk> <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> <472AEDD8.7040607@ebi.ac.uk> Message-ID: <506868AF-09C2-418B-A9F6-C90D737488A4@genome.stanford.edu> The difference is whether or not the (sub) domain imparts the "quality" (i.e, MF) to the whole protein or not. An ATP binding domain imparts the function ATP binding to the protein that contains it. "Linker Region" does not impart anything to the whole. "Entropic Bristle", might I suppose depending on the definition. "Entropic Spring" really sounds like a function of the whole protein. So really there are two separate issues here: 1) whether or not we should annotate regions of protein ("domains") to distinct terms. 2) Whether or not we should add certain MF terms that are related to a protein domains "disorder". Interpro, in principal, already does the former. I can see a possible argument for the latter, but a curator would have to determine biological significance. (Assuming experimental evidence, yadda yadda) Ben On Nov 2, 2007, at 2:28 AM, E Dimmer wrote: > However there are quite a number of GO function terms which occur > on discrete portions of a protein sequence, for instance many of > the child terms of 'binding' (GO:0005488) (protein, ATP, lipid, co- > factor etc) and simple catalytic domains. > > I feel that there could be a mid-way point - there are GO terms > that can be annotated to a specific region of a sequence where it > is also appropriate for the function to be 'inherited' by the whole > protein. > But also there there are domain terms which are not appropriate for > a whole protein - then these should go into another ontology, which > could be a composite of GO terms and domain-specific terms. > > So while protein domain function annotators and and gene-product > annotators will need to work from a different term set and add > different parameters to their annotations, where a domain has been > annotated to a GO term e.g. 'DNA binding' IDA , then we could > consider including these into GO. > > Would this suggestion be more acceptable to GO folk? > > Emily > > > Michael Ashburner wrote: >> I agree with Ben, this is not for the GO. >> Michael >> >> On 1 Nov 2007, at 14:49, Benjamin Hitz wrote: >> >>> >>> As resident protein structure expert, no. >>> Not that what they are doing is wrong, or not important - but >>> it's not a biological process/function/component of the gene >>> (product) in question. >>> >>> What's next? We annotate alpha helices? >>> >>> Ben >>> >>> On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: >>> >>>> Hi, >>>> >>>> Could I please ask people's opinion on the functional annotation >>>> of protein domains/regions to the GO? >>>> >>>> I have been contacted by a group who would like to annotate GO >>>> functions to identified disordered regions in proteins. >>>> >>>> The thought so far is that they would annotate to a >>>> 'disordered_region' SO term, along with sequence co-ordinates, >>>> and then also attach a GO term with a reference and evidence code. >>>> (I have spoken with Gabby Reeves from BioSapiens, who would be >>>> happy to add 'disordered_region' terms to the BioSapiens protein >>>> feature ontology section of SO). >>>> >>>> For an annotation example: protein LEF-1 (Q9QXN1) has a >>>> disordered region corresponding to residues 296 - 397. This >>>> domain has been found to act to bend DNA, as reported in a >>>> experiment in PMID: 7651541. >>>> In the normal course of GO annotation I would of course happily >>>> to annotate the whole protein (Q9QXN1) to the DNA bending term >>>> (DNA bending activity, GO:0008301), and while I might read about >>>> the discrete region in the protein that is responsible for this >>>> function I would not capture this data. >>>> However the IUP(Intrinsically Unstructured Protein) curators >>>> would include the aa residue information in their annotations >>>> and want to describe the individual functions that a protein's >>>> multiple domains might have. >>>> >>>> So I assume that for these kinds of annotations, where an >>>> equivalent GO term exists, a GOC annotation group could >>>> integrate this group's annotations and relate it up to the whole >>>> protein/gene product (and possibly being able to keep the SO >>>> term in the new cross-reference column 16? but not the aa >>>> residue location?). >>>> >>>> While the majority of the function terms that the IUP community >>>> are interested in applying to their domains do map quite >>>> straight-forwardly to GO terms, there are some new ones which >>>> would need to be requested. And some of these new terms seem to >>>> describe more domain-specific, intra-protein function. For >>>> example, for some of the function terms used in the DisProt >>>> database: >>>> >>>> flexible linker/spacer >>>> Provides separation and permits movement between adjacent domains >>>> >>>> entropic brisle >>>> A disordered region that creates a zone of exclusion by its >>>> entropic movement >>>> >>>> entropic spring >>>> Provides a restoring force resulting from randomization of bond >>>> torsion angles that become restricted upon stretching. >>>> >>>> (see: http://www.disprot.org/view_function_subclass.php) >>>> >>>> So, would GO be willing to add these types of terms? And how >>>> much of the IUP communities annotation data would GOC groups be >>>> happy to incorporate into their own annotation sets? >>>> >>>> Thanks, >>>> Emily >>>> >>>> >>>> --************************************ >>>> Emily Dimmer >>>> GOA Coordinator >>>> EMBL-EBI >>>> Wellcome Trust Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD, U.K. >>>> Tel: +44 1223 494654 >>>> Fax: +44 1223 494468 >>>> email: edimmer at ebi.ac.uk >>>> ************************************ >>> >>> -- >>> Ben Hitz >>> Senior Scientific Programmer ** Saccharomyces Genome Database ** >>> GO Consortium >>> Stanford University ** hitz at genome.stanford.edu >>> >>> >>> > > > -- > ************************************ > Emily Dimmer > GOA Coordinator > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD, U.K. > Tel: +44 1223 494654 > Fax: +44 1223 494468 > email: edimmer at ebi.ac.uk > ************************************ -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu From hjd at informatics.jax.org Fri Nov 2 09:36:26 2007 From: hjd at informatics.jax.org (Harold Drabkin) Date: Fri, 02 Nov 2007 12:36:26 -0400 Subject: [go] Protein domain GO annotation In-Reply-To: <506868AF-09C2-418B-A9F6-C90D737488A4@genome.stanford.edu> References: <4729FC1D.6050102@ebi.ac.uk> <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> <472AEDD8.7040607@ebi.ac.uk> <506868AF-09C2-418B-A9F6-C90D737488A4@genome.stanford.edu> Message-ID: <472B520A.4080608@informatics.jax.org> I agree with Ben Really, this seems very close to InterPro. These are closer to "domains". We don't annotate domains, we annotate whole gene products. An ip2go translation table can be used as a first pass for an entire protein for function prediction. But we don't annotate the domain itself. suppose one could call the translation table a file that is essentially GO annotation to the domain; it's a curated "set" of domains. But it's not the same as annotating the entire gene product. hjd Ben Hitz wrote: > > The difference is whether or not the (sub) domain imparts the > "quality" (i.e, MF) to the whole protein or not. > An ATP binding domain imparts the function ATP binding to the protein > that contains it. > "Linker Region" does not impart anything to the whole. > "Entropic Bristle", might I suppose depending on the definition. > "Entropic Spring" really sounds like a function of the whole protein. > > So really there are two separate issues here: 1) whether or not we > should annotate regions of protein ("domains") to distinct terms. 2) > Whether or not we should add certain MF terms that are related to a > protein domains "disorder". > > Interpro, in principal, already does the former. I can see a possible > argument for the latter, but a curator would have to determine > biological significance. (Assuming experimental evidence, yadda yadda) > > Ben > On Nov 2, 2007, at 2:28 AM, E Dimmer wrote: > >> However there are quite a number of GO function terms which occur on >> discrete portions of a protein sequence, for instance many of the >> child terms of 'binding' (GO:0005488) (protein, ATP, lipid, >> co-factor etc) and simple catalytic domains. >> >> I feel that there could be a mid-way point - there are GO terms that >> can be annotated to a specific region of a sequence where it is also >> appropriate for the function to be 'inherited' by the whole protein. >> But also there there are domain terms which are not appropriate for a >> whole protein - then these should go into another ontology, which >> could be a composite of GO terms and domain-specific terms. >> >> So while protein domain function annotators and and gene-product >> annotators will need to work from a different term set and add >> different parameters to their annotations, where a domain has been >> annotated to a GO term e.g. 'DNA binding' IDA , then we could >> consider including these into GO. >> >> Would this suggestion be more acceptable to GO folk? >> >> Emily >> >> >> Michael Ashburner wrote: >>> I agree with Ben, this is not for the GO. >>> Michael >>> >>> On 1 Nov 2007, at 14:49, Benjamin Hitz wrote: >>> >>>> >>>> As resident protein structure expert, no. >>>> Not that what they are doing is wrong, or not important - but it's >>>> not a biological process/function/component of the gene (product) >>>> in question. >>>> >>>> What's next? We annotate alpha helices? >>>> >>>> Ben >>>> >>>> On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: >>>> >>>>> Hi, >>>>> >>>>> Could I please ask people's opinion on the functional annotation >>>>> of protein domains/regions to the GO? >>>>> >>>>> I have been contacted by a group who would like to annotate GO >>>>> functions to identified disordered regions in proteins. >>>>> >>>>> The thought so far is that they would annotate to a >>>>> 'disordered_region' SO term, along with sequence co-ordinates, and >>>>> then also attach a GO term with a reference and evidence code. >>>>> (I have spoken with Gabby Reeves from BioSapiens, who would be >>>>> happy to add 'disordered_region' terms to the BioSapiens protein >>>>> feature ontology section of SO). >>>>> >>>>> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered >>>>> region corresponding to residues 296 - 397. This domain has been >>>>> found to act to bend DNA, as reported in a experiment in PMID: >>>>> 7651541. >>>>> In the normal course of GO annotation I would of course happily to >>>>> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA >>>>> bending activity, GO:0008301), and while I might read about the >>>>> discrete region in the protein that is responsible for this >>>>> function I would not capture this data. >>>>> However the IUP(Intrinsically Unstructured Protein) curators would >>>>> include the aa residue information in their annotations and want >>>>> to describe the individual functions that a protein's multiple >>>>> domains might have. >>>>> >>>>> So I assume that for these kinds of annotations, where an >>>>> equivalent GO term exists, a GOC annotation group could integrate >>>>> this group's annotations and relate it up to the whole >>>>> protein/gene product (and possibly being able to keep the SO term >>>>> in the new cross-reference column 16? but not the aa residue >>>>> location?). >>>>> >>>>> While the majority of the function terms that the IUP community >>>>> are interested in applying to their domains do map quite >>>>> straight-forwardly to GO terms, there are some new ones which >>>>> would need to be requested. And some of these new terms seem to >>>>> describe more domain-specific, intra-protein function. For >>>>> example, for some of the function terms used in the DisProt database: >>>>> >>>>> flexible linker/spacer >>>>> Provides separation and permits movement between adjacent domains >>>>> >>>>> entropic brisle >>>>> A disordered region that creates a zone of exclusion by its >>>>> entropic movement >>>>> >>>>> entropic spring >>>>> Provides a restoring force resulting from randomization of bond >>>>> torsion angles that become restricted upon stretching. >>>>> >>>>> (see: http://www.disprot.org/view_function_subclass.php) >>>>> >>>>> So, would GO be willing to add these types of terms? And how much >>>>> of the IUP communities annotation data would GOC groups be happy >>>>> to incorporate into their own annotation sets? >>>>> >>>>> Thanks, >>>>> Emily >>>>> >>>>> >>>>> --************************************ >>>>> Emily Dimmer >>>>> GOA Coordinator >>>>> EMBL-EBI >>>>> Wellcome Trust Genome Campus >>>>> Hinxton >>>>> Cambridge CB10 1SD, U.K. >>>>> Tel: +44 1223 494654 >>>>> Fax: +44 1223 494468 >>>>> email: edimmer at ebi.ac.uk >>>>> ************************************ >>>> >>>> -- >>>> Ben Hitz >>>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >>>> Consortium >>>> Stanford University ** hitz at genome.stanford.edu >>>> >>>> >>>> >> >> >> -- >> ************************************ >> Emily Dimmer >> GOA Coordinator >> EMBL-EBI >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD, U.K. >> Tel: +44 1223 494654 >> Fax: +44 1223 494468 >> email: edimmer at ebi.ac.uk >> ************************************ > > -- > Ben Hitz > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO > Consortium > Stanford University ** hitz at genome.stanford.edu > > > From edimmer at ebi.ac.uk Fri Nov 2 09:37:16 2007 From: edimmer at ebi.ac.uk (E Dimmer) Date: Fri, 02 Nov 2007 16:37:16 +0000 Subject: [go] Protein domain GO annotation In-Reply-To: <506868AF-09C2-418B-A9F6-C90D737488A4@genome.stanford.edu> References: <4729FC1D.6050102@ebi.ac.uk> <73AEC744-1356-4ABE-8514-B5045EDA7FDA@genome.stanford.edu> <835B32EF-DC7F-4DDD-B396-51681EAEDD74@gen.cam.ac.uk> <472AEDD8.7040607@ebi.ac.uk> <506868AF-09C2-418B-A9F6-C90D737488A4@genome.stanford.edu> Message-ID: <472B523C.3070809@ebi.ac.uk> Hi, I realize I'm getting nowhere fast with this suggestion(!), but I thought it would be important to clarify how InterPro2GO works - as it produces a large number of GO annotations and there appears to be misunderstanding as to how these are created. 1. taking a InterPro domain, an InterPro curator looks at all the proteins which contain this domain in UniProtKB, and will only continue if there is an adequate number Swiss-Prot entries in this group of proteins which have useful manual annotation. 2. the curator looks at the existing annotations to these proteins and then asks the question - can all these proteins be safely annotated to the same term in GO? Therefore from what is known of the uncurated UniProtKB entries that are included in this set, is it likely that this mapping will be correct for them also? InterPro curators then proceed conservatively with the mapping (which is why there are often some high-level GO terms used). So, InterPro curators annotate at the level of the whole protein. While InterPro2GO mappings may often hint as to what kind of contribution a domain might have, it is not correct to assume this - e.g. if two domains always appear together in a protein, then both may be mapped to the same set of GO terms. Emily Ben Hitz wrote: > > The difference is whether or not the (sub) domain imparts the > "quality" (i.e, MF) to the whole protein or not. > An ATP binding domain imparts the function ATP binding to the protein > that contains it. > "Linker Region" does not impart anything to the whole. > "Entropic Bristle", might I suppose depending on the definition. > "Entropic Spring" really sounds like a function of the whole protein. > > So really there are two separate issues here: 1) whether or not we > should annotate regions of protein ("domains") to distinct terms. 2) > Whether or not we should add certain MF terms that are related to a > protein domains "disorder". > > Interpro, in principal, already does the former. I can see a possible > argument for the latter, but a curator would have to determine > biological significance. (Assuming experimental evidence, yadda yadda) > > Ben > On Nov 2, 2007, at 2:28 AM, E Dimmer wrote: > >> However there are quite a number of GO function terms which occur on >> discrete portions of a protein sequence, for instance many of the >> child terms of 'binding' (GO:0005488) (protein, ATP, lipid, >> co-factor etc) and simple catalytic domains. >> >> I feel that there could be a mid-way point - there are GO terms that >> can be annotated to a specific region of a sequence where it is also >> appropriate for the function to be 'inherited' by the whole protein. >> But also there there are domain terms which are not appropriate for a >> whole protein - then these should go into another ontology, which >> could be a composite of GO terms and domain-specific terms. >> >> So while protein domain function annotators and and gene-product >> annotators will need to work from a different term set and add >> different parameters to their annotations, where a domain has been >> annotated to a GO term e.g. 'DNA binding' IDA , then we could >> consider including these into GO. >> >> Would this suggestion be more acceptable to GO folk? >> >> Emily >> >> >> Michael Ashburner wrote: >>> I agree with Ben, this is not for the GO. >>> Michael >>> >>> On 1 Nov 2007, at 14:49, Benjamin Hitz wrote: >>> >>>> >>>> As resident protein structure expert, no. >>>> Not that what they are doing is wrong, or not important - but it's >>>> not a biological process/function/component of the gene (product) >>>> in question. >>>> >>>> What's next? We annotate alpha helices? >>>> >>>> Ben >>>> >>>> On Nov 1, 2007, at 9:17 AM, E Dimmer wrote: >>>> >>>>> Hi, >>>>> >>>>> Could I please ask people's opinion on the functional annotation >>>>> of protein domains/regions to the GO? >>>>> >>>>> I have been contacted by a group who would like to annotate GO >>>>> functions to identified disordered regions in proteins. >>>>> >>>>> The thought so far is that they would annotate to a >>>>> 'disordered_region' SO term, along with sequence co-ordinates, and >>>>> then also attach a GO term with a reference and evidence code. >>>>> (I have spoken with Gabby Reeves from BioSapiens, who would be >>>>> happy to add 'disordered_region' terms to the BioSapiens protein >>>>> feature ontology section of SO). >>>>> >>>>> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered >>>>> region corresponding to residues 296 - 397. This domain has been >>>>> found to act to bend DNA, as reported in a experiment in PMID: >>>>> 7651541. >>>>> In the normal course of GO annotation I would of course happily to >>>>> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA >>>>> bending activity, GO:0008301), and while I might read about the >>>>> discrete region in the protein that is responsible for this >>>>> function I would not capture this data. >>>>> However the IUP(Intrinsically Unstructured Protein) curators would >>>>> include the aa residue information in their annotations and want >>>>> to describe the individual functions that a protein's multiple >>>>> domains might have. >>>>> >>>>> So I assume that for these kinds of annotations, where an >>>>> equivalent GO term exists, a GOC annotation group could integrate >>>>> this group's annotations and relate it up to the whole >>>>> protein/gene product (and possibly being able to keep the SO term >>>>> in the new cross-reference column 16? but not the aa residue >>>>> location?). >>>>> >>>>> While the majority of the function terms that the IUP community >>>>> are interested in applying to their domains do map quite >>>>> straight-forwardly to GO terms, there are some new ones which >>>>> would need to be requested. And some of these new terms seem to >>>>> describe more domain-specific, intra-protein function. For >>>>> example, for some of the function terms used in the DisProt database: >>>>> >>>>> flexible linker/spacer >>>>> Provides separation and permits movement between adjacent domains >>>>> >>>>> entropic brisle >>>>> A disordered region that creates a zone of exclusion by its >>>>> entropic movement >>>>> >>>>> entropic spring >>>>> Provides a restoring force resulting from randomization of bond >>>>> torsion angles that become restricted upon stretching. >>>>> >>>>> (see: http://www.disprot.org/view_function_subclass.php) >>>>> >>>>> So, would GO be willing to add these types of terms? And how much >>>>> of the IUP communities annotation data would GOC groups be happy >>>>> to incorporate into their own annotation sets? >>>>> >>>>> Thanks, >>>>> Emily >>>>> >>>>> >>>>> --************************************ >>>>> Emily Dimmer >>>>> GOA Coordinator >>>>> EMBL-EBI >>>>> Wellcome Trust Genome Campus >>>>> Hinxton >>>>> Cambridge CB10 1SD, U.K. >>>>> Tel: +44 1223 494654 >>>>> Fax: +44 1223 494468 >>>>> email: edimmer at ebi.ac.uk >>>>> ************************************ >>>> >>>> --Ben Hitz >>>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >>>> Consortium >>>> Stanford University ** hitz at genome.stanford.edu >>>> >>>> >>>> >> >> >> --************************************ >> Emily Dimmer >> GOA Coordinator >> EMBL-EBI >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD, U.K. >> Tel: +44 1223 494654 >> Fax: +44 1223 494468 >> email: edimmer at ebi.ac.uk >> ************************************ > > -- > Ben Hitz > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO > Consortium > Stanford University ** hitz at genome.stanford.edu > > -- ************************************ Emily Dimmer GOA Coordinator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ From stacia at genome.Stanford.EDU Fri Nov 2 09:46:28 2007 From: stacia at genome.Stanford.EDU (Stacia Engel) Date: Fri, 2 Nov 2007 09:46:28 -0700 Subject: [go] upcoming meetings for newsletter? Message-ID: <54BA489A-57FA-48B2-A1A4-FA586291D362@genome.stanford.edu> Hi, Does anyone have some upcoming meetings that they would like to list in this month's issue of the GO Newsletter? We don't have any so far. Thanks, Stacia & The Newsletter Team From tberardi at acoma.Stanford.EDU Fri Nov 2 09:50:47 2007 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Fri, 02 Nov 2007 09:50:47 -0700 Subject: [go] upcoming meetings for newsletter? Message-ID: <472B5567.6070107@acoma.stanford.edu> Hi Stacia, How about PAG in January? http://www.intl-pag.org/ Also, I think the ASCB is in Dec. Lemme check. Yep. http://www.ascb.org/meetings/ I'm pretty sure we'll have some GO presence at PAG, not too sure about ASCB. Tanya Stacia Engel wrote: > Hi, > Does anyone have some upcoming meetings that they would like to list in > this month's issue of the GO Newsletter? > We don't have any so far. > > Thanks, > Stacia & The Newsletter Team > -- ------------------------------------------------------------------------------------------ Tanya Berardini, Ph.D. tberardi at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 325 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------------------ -- ------------------------------------------------------------------------------------------ Tanya Berardini, Ph.D. tberardi at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 325 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------------------ From vpetri at mcw.edu Fri Nov 2 10:07:02 2007 From: vpetri at mcw.edu (Petri, Victoria) Date: Fri, 2 Nov 2007 12:07:02 -0500 Subject: [go] upcoming meetings for newsletter? In-Reply-To: <54BA489A-57FA-48B2-A1A4-FA586291D362@genome.stanford.edu> References: <54BA489A-57FA-48B2-A1A4-FA586291D362@genome.stanford.edu> Message-ID: <1448A38A42714048B9C53E473E13CCF0010A60BF@davis.hmgc.mcw.edu> Hi Stacia, At the Rat Genomics and Models - December 6-9, Cold Spring Harbor Laboratory - will have a big presence and there will definitely be GO (probably in more than one poster as for sure one will be on the portals and another on the GVieewer tool). http://meetings.cshl.edu/meetings/rodent07.shtml Victoria Victoria Petri, Ph.D. Research Scientist Rat Genome Database (http://rgd.mcw.edu) Bioinformatics Program Human and Molecular Genetics Center Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI 53226 (414) 456-7507 Fax (414) 456-6595 vpetri at mcw.edu vpetri at mail.brc.mcw.edu -----Original Message----- From: owner-go at genome.stanford.edu [mailto:owner-go at genome.stanford.edu] On Behalf Of Stacia Engel Sent: Friday, November 02, 2007 11:46 AM To: GO LIST Subject: [go] upcoming meetings for newsletter? Hi, Does anyone have some upcoming meetings that they would like to list in this month's issue of the GO Newsletter? We don't have any so far. Thanks, Stacia & The Newsletter Team From suzi at berkeleybop.org Sun Nov 4 07:08:57 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 4 Nov 2007 10:08:57 -0500 Subject: [go] recombination and toxin in GO In-Reply-To: <89AE0930-7DEE-48D3-B731-6130052D876E@gen.cam.ac.uk> References: <962963.99958.qm@web26713.mail.ukl.yahoo.com> <89AE0930-7DEE-48D3-B731-6130052D876E@gen.cam.ac.uk> Message-ID: Hi all, Just checking in. Did these terms make it into the request queue/ tracker. Any progress or change in status to report? -S On Jul 10, 2007, at 5:15 AM, Michael Ashburner wrote: > Ariane > > Thanks, I understand that. I think the thing to to do is let Karen > and the GO office work on these terms and then > we will see just how much of PhiGO will be covered. > > Best - Michael > > > On 6 Jul 2007, at 15:37, Ariane Pourbaix wrote: > >> Dear Michael, >> The reason for assembling that list of phage and recombination >> terms is essentially that we need a robust and structured system >> to annotate the protein families in our ACLAME database. We hope >> that people using ACLAME will then be 'tempted' to use the same >> ontology. After the meeting we had last September in Hinxton I >> knew just enough to try following the GO schema of processes, >> components and functions. I looked at the virus related terms that >> are in GO and found things like 'capsomer', so I felt comfortable >> introducing the other components of the phage capsid? >> I thought it would be good to have as many of these terms in GO as >> possible. If some don' fit we'll just keep them in PhiGO. One >> point that isn't completely clear to me yet is whether we'll >> better keep PhiGO as it is, even if most of it gets integrated in GO. >> As Jane mentioned, I think it would be interesting to build a list >> of generic terms for viruses. This I suppose should also be done >> for mobile genetic elements (not easy either). >> In my suggestions for some reorganisation of the terms related to >> recombination, I'm afraid some may provoke some discussion if not >> disagreement? in any case I thin it is urgent to get something >> done there because the confusion between the different types of >> integrases, transposases etc. is increasing in recent annotations. >> Clear and correct definitions are obviously required. I'm not sure >> mine are perfect tough, but they are not wrong! >> I'm sure we'll progress on this? though on my side it may a bit >> slow since I'm away from the lab and with interrupted internet >> connection until the end of august! >> I hope this clarifies things a least a little! Best regards. Ariane. >> >> >> Michael Ashburner a ?crit :Ariane >> >> This looks like very productive work ! >> >> I am not clear as to the long-term objective, at least wrt to the >> relationship >> between this and the GO. I can see that most (if not all) of the >> terms under the >> 'phage function' and 'phage process' nodes could well be - and >> should be - incorporated into >> the GO. The same goes for the terms under the 3 'recombination' >> nodes. >> >> The 'phage component' terms would be harder. I wonder if what you >> could aim for is >> essentially a 'phage anatomy' ontology, analagous to those for >> cellular organisms ? >> >> Chris M: Could you have a look at this work ? The obo file is at: >> http://aclame.ulb.ac.be/Classification/PhiGO/PhiGO_live.obo >> >> There is a way using OBO-EDIT 1.2 where you can build an ontology >> for use within a domain (e.g. phage) >> by picking and choosing from several other ontologies. I am not >> sure exactly how this is done but >> I am sure Chris can advise. >> >> Best wishes - Michael >> >> >> Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers >> Yahoo! Mail > From suzi at berkeleybop.org Sun Nov 4 07:17:04 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 4 Nov 2007 10:17:04 -0500 Subject: [go] Invite to a discussion at PSB In-Reply-To: <4727B590.2040402@acoma.stanford.edu> References: <579CCDF5-466E-4706-BC94-7024DA5A961E@uchsc.edu> <4727939D.8030605@acoma.stanford.edu> <4727B590.2040402@acoma.stanford.edu> Message-ID: <2B19355D-9334-48DD-BCC0-376BD1D89AC0@berkeleybop.org> Could do. It is directly before PAG, so if anyone is coming from the beyond that west coast you might consider coming a few days earlier and traveling to san diego via palo alto. -S On Oct 30, 2007, at 6:52 PM, Sue Rhee wrote: > Yes, I can. > > GO people: Please let me know if you are interested in coming to > this mini-workshop (probably a few hours) sometime during Jan 9-11, > 2008 at Carnegie. > > Sue > > Larry Hunter wrote: >> >> On Oct 30, 2007, at 2:27 PM, Sue Rhee wrote: >> >>> I would be interested in this workshop but won't be able to go to >>> the meeting. Is there a way for you and/or your folks to stop by >>> Stanford on your way to/from the meeting? I think there are quite >>> a few GO folks in the SF bay area and I can provide the space for >>> the meeting at Carnegie (which is on Stanford campus). >> >> You all are a tough & jaded bunch! Usually offering a trip to >> Hawaii in January gets a more positive response :-). >> >> I do hope that at least one GO associated person can come in >> person (and I will subsidize a trip). Is there really no one >> interested and able? Speak up, please.... There will be several >> folks from other ontology building communities (e.g. Ida Sim from >> the clinical trial ontology) at the PSB meeting, so I will convene >> something regardless. >> >> I am planning to stop in the SF Bay area for a day or two when I >> return (somewhere in the neighborhood of Jan 9-11), so we can do a >> session there. Sue, can you look into who is available, when >> and find us a place? >> >> Some sort of e-meeting technology is also a possibility, although >> I will probably want to do that from Colorado rather than try to >> make it work on the road. >> >> Larry > > -- > Sue Rhee > Staff Scientist > Carnegie Institution, Department of Plant Biology > 260 Panama Street, Stanford, CA 94305 > Email: (650) 325-1521 x251 > Fax: (650) 325-6857 > > From midori at ebi.ac.uk Mon Nov 5 02:31:53 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 5 Nov 2007 10:31:53 +0000 (GMT) Subject: [go] Your article has been published in Nucleic Acids Research (fwd) Message-ID: Yay, and thanks again! ---------- Forwarded message ---------- Date: Sun, 4 Nov 2007 20:22:48 -0800 From: narese-tfl at highwire.stanford.edu To: midori at ebi.ac.uk Cc: narese at oxfordjournals.org Subject: Your article has been published in Nucleic Acids Research Oxford Journals Dear Author I am pleased to inform you that Oxford Journals has published your article in Nucleic Acids Research. 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Oxford Journals, Oxford University Press Information for authors From midori at ebi.ac.uk Mon Nov 5 02:34:08 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 5 Nov 2007 10:34:08 +0000 (GMT) Subject: [go] recombination and toxin in GO In-Reply-To: References: <962963.99958.qm@web26713.mail.ukl.yahoo.com> <89AE0930-7DEE-48D3-B731-6130052D876E@gen.cam.ac.uk> Message-ID: Hi, Some are in the tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=1742920&group_id=36855&atid=440764 We've been waiting to hear back from Ariane; I put some questions in the tracker item, but she was very busy over the summer. Much of the rest will probably end up waiting for Jane to come back, because she knows this stuff rather better than the rest of the GO editors. m On Sun, 4 Nov 2007, Suzanna Lewis wrote: > Hi all, > > Just checking in. Did these terms make it into the request queue/tracker. Any > progress or change in status to report? > > -S > > On Jul 10, 2007, at 5:15 AM, Michael Ashburner wrote: > >> Ariane >> >> Thanks, I understand that. I think the thing to to do is let Karen and the >> GO office work on these terms and then >> we will see just how much of PhiGO will be covered. >> >> Best - Michael >> >> >> On 6 Jul 2007, at 15:37, Ariane Pourbaix wrote: >> >>> Dear Michael, >>> The reason for assembling that list of phage and recombination terms is >>> essentially that we need a robust and structured system to annotate the >>> protein families in our ACLAME database. We hope that people using ACLAME >>> will then be 'tempted' to use the same ontology. After the meeting we had >>> last September in Hinxton I knew just enough to try following the GO >>> schema of processes, components and functions. I looked at the virus >>> related terms that are in GO and found things like 'capsomer', so I felt >>> comfortable introducing the other components of the phage capsid? >>> I thought it would be good to have as many of these terms in GO as >>> possible. If some don' fit we'll just keep them in PhiGO. One point that >>> isn't completely clear to me yet is whether we'll better keep PhiGO as it >>> is, even if most of it gets integrated in GO. >>> As Jane mentioned, I think it would be interesting to build a list of >>> generic terms for viruses. This I suppose should also be done for mobile >>> genetic elements (not easy either). >>> In my suggestions for some reorganisation of the terms related to >>> recombination, I'm afraid some may provoke some discussion if not >>> disagreement? in any case I thin it is urgent to get something done there >>> because the confusion between the different types of integrases, >>> transposases etc. is increasing in recent annotations. Clear and correct >>> definitions are obviously required. I'm not sure mine are perfect tough, >>> but they are not wrong! >>> I'm sure we'll progress on this? though on my side it may a bit slow since >>> I'm away from the lab and with interrupted internet connection until the >>> end of august! >>> I hope this clarifies things a least a little! Best regards. Ariane. >>> >>> >>> Michael Ashburner a ?crit :Ariane >>> >>> This looks like very productive work ! >>> >>> I am not clear as to the long-term objective, at least wrt to the >>> relationship >>> between this and the GO. I can see that most (if not all) of the terms >>> under the >>> 'phage function' and 'phage process' nodes could well be - and should be - >>> incorporated into >>> the GO. The same goes for the terms under the 3 'recombination' nodes. >>> >>> The 'phage component' terms would be harder. I wonder if what you could >>> aim for is >>> essentially a 'phage anatomy' ontology, analagous to those for cellular >>> organisms ? >>> >>> Chris M: Could you have a look at this work ? The obo file is at: >>> http://aclame.ulb.ac.be/Classification/PhiGO/PhiGO_live.obo >>> >>> There is a way using OBO-EDIT 1.2 where you can build an ontology for use >>> within a domain (e.g. phage) >>> by picking and choosing from several other ontologies. I am not sure >>> exactly how this is done but >>> I am sure Chris can advise. >>> >>> Best wishes - Michael >>> >>> >>> Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! >>> Mail >> > > From Larry.Hunter at UCHSC.edu Mon Nov 5 10:27:31 2007 From: Larry.Hunter at UCHSC.edu (Larry Hunter) Date: Mon, 5 Nov 2007 11:27:31 -0700 Subject: [go] Invite to a discussion at PSB In-Reply-To: <2B19355D-9334-48DD-BCC0-376BD1D89AC0@berkeleybop.org> References: <579CCDF5-466E-4706-BC94-7024DA5A961E@uchsc.edu> <4727939D.8030605@acoma.stanford.edu> <4727B590.2040402@acoma.stanford.edu> <2B19355D-9334-48DD-BCC0-376BD1D89AC0@berkeleybop.org> Message-ID: <6AB113C2-9766-43DF-8FB5-A92A4582AD22@UCHSC.edu> >> >> GO people: Please let me know if you are interested in coming to >> this mini-workshop (probably a few hours) sometime during Jan >> 9-11, 2008 at Carnegie. Go folks, I'd like to have this meeting on Jan 11 in the morning. I have a flight booked out of SFO at 4pm; if we want the possibility of a longer meeting, I could book a meeting room at the SFO red carpet club so we could go until about 3. Let me know. Should we consider e-meeting in other interested folks to this session? [Reminder: the purpose is to show a very preliminary demo of our NLP- based ontology quality metrics, and get input on what we should be trying to measure and how.] Larry From jblake at informatics.jax.org Mon Nov 5 11:13:35 2007 From: jblake at informatics.jax.org (Judith Blake) Date: Mon, 05 Nov 2007 14:13:35 -0500 Subject: ontology metrics: was...Re: [go] Invite to a discussion at PSB In-Reply-To: <6AB113C2-9766-43DF-8FB5-A92A4582AD22@UCHSC.edu> References: <579CCDF5-466E-4706-BC94-7024DA5A961E@uchsc.edu> <4727939D.8030605@acoma.stanford.edu> <4727B590.2040402@acoma.stanford.edu> <2B19355D-9334-48DD-BCC0-376BD1D89AC0@berkeleybop.org> <6AB113C2-9766-43DF-8FB5-A92A4582AD22@UCHSC.edu> Message-ID: <472F6B5F.4020100@informatics.jax.org> Hi Larry, I think a longer meeting might be more useful. One goal would be to investigate the intersection between GO tools and your NLP approaches. Chris Mungall and Mike Bada are in communication already I think. It could be very productive to have a little space/time to make assure each other that the developments are complementary rather tahn competing, and that they can be aligned to each other. In addition, it would be important to have either David or Midori attend as they are responsible for implementing any updates indicated by QC output. I would like to attend via e-meeting of some sort. Probably best would be to set up WebX from SFO conference room with skype...or something similar. Judy Larry Hunter wrote: >>> >>> GO people: Please let me know if you are interested in coming to >>> this mini-workshop (probably a few hours) sometime during Jan 9-11, >>> 2008 at Carnegie. > > Go folks, > > I'd like to have this meeting on Jan 11 in the morning. I have a > flight booked out of SFO at 4pm; if we want the possibility of a > longer meeting, I could book a meeting room at the SFO red carpet club > so we could go until about 3. Let me know. > > Should we consider e-meeting in other interested folks to this session? > > [Reminder: the purpose is to show a very preliminary demo of our > NLP-based ontology quality metrics, and get input on what we should be > trying to measure and how.] > > Larry From rhee at acoma.Stanford.EDU Mon Nov 5 11:24:11 2007 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 05 Nov 2007 11:24:11 -0800 Subject: ontology metrics: was...Re: [go] Invite to a discussion at PSB In-Reply-To: <472F6B5F.4020100@informatics.jax.org> References: <579CCDF5-466E-4706-BC94-7024DA5A961E@uchsc.edu> <4727939D.8030605@acoma.stanford.edu> <4727B590.2040402@acoma.stanford.edu> <2B19355D-9334-48DD-BCC0-376BD1D89AC0@berkeleybop.org> <6AB113C2-9766-43DF-8FB5-A92A4582AD22@UCHSC.edu> <472F6B5F.4020100@informatics.jax.org> Message-ID: <472F6DDB.5000600@acoma.stanford.edu> Hi: We can set up a WebX with skype or a speaker phone (and a 800 number to dial in) at Carnegie. I was thinking of a meeting from 9-12 followed by lunch but if people want to go until 3 pm, that should not be a problem. Perhaps someone other than me should take charge of the agenda? Sue Judith Blake wrote: > Hi Larry, > > I think a longer meeting might be more useful. One goal would be to > investigate the intersection between GO tools and your NLP > approaches. Chris Mungall and Mike Bada are in communication already > I think. It could be very productive to have a little space/time to > make assure each other that the developments are complementary rather > tahn competing, and that they can be aligned to each other. In > addition, it would be important to have either David or Midori attend > as they are responsible for implementing any updates indicated by QC > output. > > I would like to attend via e-meeting of some sort. Probably best > would be to set up WebX from SFO conference room with skype...or > something similar. > > Judy > > Larry Hunter wrote: >>>> >>>> GO people: Please let me know if you are interested in coming to >>>> this mini-workshop (probably a few hours) sometime during Jan 9-11, >>>> 2008 at Carnegie. >> >> Go folks, >> >> I'd like to have this meeting on Jan 11 in the morning. I have a >> flight booked out of SFO at 4pm; if we want the possibility of a >> longer meeting, I could book a meeting room at the SFO red carpet >> club so we could go until about 3. Let me know. >> >> Should we consider e-meeting in other interested folks to this session? >> >> [Reminder: the purpose is to show a very preliminary demo of our >> NLP-based ontology quality metrics, and get input on what we should >> be trying to measure and how.] >> >> Larry > -- Sue Rhee Staff Scientist Carnegie Institution, Department of Plant Biology 260 Panama Street, Stanford, CA 94305 Email: (650) 325-1521 x251 Fax: (650) 325-6857 From Larry.Hunter at UCHSC.edu Mon Nov 5 11:28:45 2007 From: Larry.Hunter at UCHSC.edu (Larry Hunter) Date: Mon, 5 Nov 2007 12:28:45 -0700 Subject: ontology metrics: was...Re: [go] Invite to a discussion at PSB In-Reply-To: <472F6B5F.4020100@informatics.jax.org> References: <579CCDF5-466E-4706-BC94-7024DA5A961E@uchsc.edu> <4727939D.8030605@acoma.stanford.edu> <4727B590.2040402@acoma.stanford.edu> <2B19355D-9334-48DD-BCC0-376BD1D89AC0@berkeleybop.org> <6AB113C2-9766-43DF-8FB5-A92A4582AD22@UCHSC.edu> <472F6B5F.4020100@informatics.jax.org> Message-ID: On Nov 5, 2007, at 12:13 PM, Judith Blake wrote: > I think a longer meeting might be more useful. I just changed my flight to 2:25pm based on Sue's schedule, but I can probably change it back again if people want a more than 4 hour meeting (if we do it at the SFO red carpet club, I could stay until about 1:30 with the flight I have). I do need to get this settled in the next few hours, though. > One goal would be to investigate the intersection between GO tools > and your NLP approaches. For this meeting, I'd like to stay focused on the 'quality metrics' application, rather than open it to all GO / NLP issues (e.g. cross- products, using the GO as NLP output, etc.) > Chris Mungall and Mike Bada are in communication already I think. > It could be very productive to have a little space/time to make > assure each other that the developments are complementary rather > tahn competing, and that they can be aligned to each other. I think everyone agrees that we are working complementarily, and I believe Mike & Chris have sliced up the cross-product work to ensure there isn't duplicated effort. I agree it might make sense to have a separate (e-?)meeting trying to coordinate / consolidate the tools used for the (semi-) automation of the cross-products, but that's not my agenda for Jan 11. And I don't believe Mike will be with me in California (perhaps he can attend electronically, but that's pretty early for him...) > In addition, it would be important to have either David or Midori > attend as they are responsible for implementing any updates > indicated by QC output. Yes, yes, yes! Are either of you planning to be in CA on Jan 11? Their input is particularly important. > I would like to attend via e-meeting of some sort. Probably best > would be to set up WebX from SFO conference room with skype...or > something similar. I'm a little nervous about trying to make this work on the road, but I'm game. I'll have a skype-ready macbook pro with me, and will buy internet access with the meeting room. I've never tried to set up a webx meeting -- Sue, can you help me with that? Larry From Larry.Hunter at UCHSC.edu Mon Nov 5 11:36:35 2007 From: Larry.Hunter at UCHSC.edu (Larry Hunter) Date: Mon, 5 Nov 2007 12:36:35 -0700 Subject: ontology metrics: was...Re: [go] Invite to a discussion at PSB In-Reply-To: <472F6DDB.5000600@acoma.stanford.edu> References: <579CCDF5-466E-4706-BC94-7024DA5A961E@uchsc.edu> <4727939D.8030605@acoma.stanford.edu> <4727B590.2040402@acoma.stanford.edu> <2B19355D-9334-48DD-BCC0-376BD1D89AC0@berkeleybop.org> <6AB113C2-9766-43DF-8FB5-A92A4582AD22@UCHSC.edu> <472F6B5F.4020100@informatics.jax.org> <472F6DDB.5000600@acoma.stanford.edu> Message-ID: <46C89434-A200-42F8-8B0C-D838002DECBF@uchsc.edu> On Nov 5, 2007, at 12:24 PM, Sue Rhee wrote: > Hi: We can set up a WebX with skype or a speaker phone (and a 800 > number to dial in) at Carnegie. I was thinking of a meeting from > 9-12 followed by lunch but if people want to go until 3 pm, that > should not be a problem. Unless there is huge demand for more time, I suggest we do 9-12 at Carnegie. I can then grab a cab to the airport and catch my 2:25 flight. if at the end people want more time, we can schedule an e- meeting followup. > Perhaps someone other than me should take charge of the agenda? The agenda will be simple: I want to start with an introduction (maybe 30-45 minutes) of what we are trying to achieve, some preliminary results and our near term development plan. The rest of the time will be getting feedback (e.g. what you like /dislike in the preliminary versions) and improving our development plan. The overall direction of where we are going is partially sketched in the attached white paper we prepared for the NIST ontology metrics meeting last month, and also partly sketched in our NCBO- collaboration grant, which I will excerpt and send around the relevant parts of before Jan 11. Larry -------------- next part -------------- A non-text attachment was scrubbed... Name: Ontology quality metrics white paper.doc Type: application/octet-stream Size: 64512 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20071105/bec13796/attachment.obj -------------- next part -------------- From suzi at berkeleybop.org Mon Nov 5 11:45:59 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Mon, 5 Nov 2007 14:45:59 -0500 Subject: ontology metrics: was...Re: [go] Invite to a discussion at PSB In-Reply-To: <472F6DDB.5000600@acoma.stanford.edu> References: <579CCDF5-466E-4706-BC94-7024DA5A961E@uchsc.edu> <4727939D.8030605@acoma.stanford.edu> <4727B590.2040402@acoma.stanford.edu> <2B19355D-9334-48DD-BCC0-376BD1D89AC0@berkeleybop.org> <6AB113C2-9766-43DF-8FB5-A92A4582AD22@UCHSC.edu> <472F6B5F.4020100@informatics.jax.org> <472F6DDB.5000600@acoma.stanford.edu> Message-ID: <17CD0D9A-93F1-409A-954E-20F8B6110B6C@berkeleybop.org> Sounds good. And as I mentioned before, this is directly before PAG, so there is a possibility for folks who are attending PAG to piggy-back the these two meetings together. -S On Nov 5, 2007, at 2:24 PM, Sue Rhee wrote: > Hi: We can set up a WebX with skype or a speaker phone (and a 800 > number to dial in) at Carnegie. I was thinking of a meeting from > 9-12 followed by lunch but if people want to go until 3 pm, that > should not be a problem. Perhaps someone other than me should take > charge of the agenda? > > Sue > > Judith Blake wrote: >> Hi Larry, >> >> I think a longer meeting might be more useful. One goal would be >> to investigate the intersection between GO tools and your NLP >> approaches. Chris Mungall and Mike Bada are in communication >> already I think. It could be very productive to have a little >> space/time to make assure each other that the developments are >> complementary rather tahn competing, and that they can be aligned >> to each other. In addition, it would be important to have either >> David or Midori attend as they are responsible for implementing >> any updates indicated by QC output. >> >> I would like to attend via e-meeting of some sort. Probably best >> would be to set up WebX from SFO conference room with skype...or >> something similar. >> >> Judy >> >> Larry Hunter wrote: >>>>> >>>>> GO people: Please let me know if you are interested in coming >>>>> to this mini-workshop (probably a few hours) sometime during >>>>> Jan 9-11, 2008 at Carnegie. >>> >>> Go folks, >>> >>> I'd like to have this meeting on Jan 11 in the morning. I have a >>> flight booked out of SFO at 4pm; if we want the possibility of a >>> longer meeting, I could book a meeting room at the SFO red carpet >>> club so we could go until about 3. Let me know. >>> >>> Should we consider e-meeting in other interested folks to this >>> session? >>> >>> [Reminder: the purpose is to show a very preliminary demo of our >>> NLP-based ontology quality metrics, and get input on what we >>> should be trying to measure and how.] >>> >>> Larry >> > > -- > Sue Rhee > Staff Scientist > Carnegie Institution, Department of Plant Biology > 260 Panama Street, Stanford, CA 94305 > Email: (650) 325-1521 x251 > Fax: (650) 325-6857 > > From rhee at acoma.Stanford.EDU Mon Nov 5 12:57:19 2007 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 05 Nov 2007 12:57:19 -0800 Subject: [go] wild goose chase Message-ID: <472F83AF.8030604@acoma.stanford.edu> I've been trying to do a couple of SQLs using Goose and it's timing out. Can someone please run the following SQL for me please? SELECT evidence.code, count(distinct association.id) AS evidence__association_count FROM association, evidence where evidence.association_id = association.id GROUP BY evidence.code Thanks, Sue -- Sue Rhee Staff Scientist Carnegie Institution, Department of Plant Biology 260 Panama Street, Stanford, CA 94305 Email: (650) 325-1521 x251 Fax: (650) 325-6857 From sjcarbon at berkeleybop.org Mon Nov 5 13:14:36 2007 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Mon, 05 Nov 2007 13:14:36 -0800 Subject: [go] wild goose chase In-Reply-To: <472F83AF.8030604@acoma.stanford.edu> References: <472F83AF.8030604@acoma.stanford.edu> Message-ID: <1194297276.6358.77.camel@accordion> I believe that this is the query that you want--since every bit of evidence is going to belong to an association, there is no need for a join. It also runs fairly quickly (30s): SELECT evidence.code, count(*) AS evidence_count FROM evidence GROUP BY evidence.code; Cheers, -Seth On Mon, 2007-11-05 at 12:57 -0800, Sue Rhee wrote: > I've been trying to do a couple of SQLs using Goose and it's timing out. > Can someone please run the following SQL for me please? > > SELECT evidence.code, count(distinct association.id) AS > evidence__association_count FROM association, evidence where > evidence.association_id = association.id GROUP BY evidence.code > > Thanks, > Sue > > From cjm at fruitfly.org Mon Nov 5 13:34:24 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Mon, 5 Nov 2007 13:34:24 -0800 Subject: [go] wild goose chase In-Reply-To: <1194297276.6358.77.camel@accordion> References: <472F83AF.8030604@acoma.stanford.edu> <1194297276.6358.77.camel@accordion> Message-ID: <1F9238CF-C313-408B-9BF1-23D94A7B3EE2@fruitfly.org> IC 5167 IDA 71050 IEA 15687382 IEP 4598 IGC 4 IGI 8311 IMP 61549 IPI 17043 ISS 196643 NAS 25656 ND 132192 NR 1185 RCA 103792 TAS 44564 This is the 2007-10 release database If goose times out you can always try switching mirror from EBI/ Berkeley. On Nov 5, 2007, at 1:14 PM, Seth Carbon wrote: > I believe that this is the query that you want--since every bit of > evidence is going to belong to an association, there is no need for a > join. It also runs fairly quickly (30s): > > > SELECT evidence.code, count(*) AS evidence_count > FROM evidence > GROUP BY evidence.code; > > > Cheers, > > -Seth > > > On Mon, 2007-11-05 at 12:57 -0800, Sue Rhee wrote: >> I've been trying to do a couple of SQLs using Goose and it's >> timing out. >> Can someone please run the following SQL for me please? >> >> SELECT evidence.code, count(distinct association.id) AS >> evidence__association_count FROM association, evidence where >> evidence.association_id = association.id GROUP BY evidence.code >> >> Thanks, >> Sue >> >> > From cherry at stanford.edu Mon Nov 5 15:14:32 2007 From: cherry at stanford.edu (Mike Cherry) Date: Mon, 5 Nov 2007 15:14:32 -0800 Subject: [go] Re: GO website down? In-Reply-To: <472F9B75.5070908@acoma.stanford.edu> References: <472F9B75.5070908@acoma.stanford.edu> Message-ID: The medical school lost access for 45 minutes or so. We are back now. -Mike On Nov 5, 2007, at 2:38 PM, Tanya Berardini wrote: > Sadly, this appears to be the case. Is it scheduled maintenance? I > was hunting around for that email but can't seem to locate it. > > Thanks, > > Tanya From rama at genome.Stanford.EDU Mon Nov 5 16:04:07 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Mon, 5 Nov 2007 16:04:07 -0800 Subject: [go] Evidence code documentation Message-ID: Hi All, The much anticipated evidence code documentation 'update' is ready for prime time. The evidence code committee has worked very hard over the last 10 months or so to update the documentation on *existing* evidence codes so that it reflects our current practice and is accurate. http://www-dev.yeastgenome.org/draftGO/go/www/GO.evidence.new.shtml The evidence code ontology, the new ISS proposal and the EXP evidence code that were discussed at the Princeton Meeting are *not* part of this update. Highlights in this version- 1) We have introduced a 'Last Updated' date to reflect when each evidence code was updated. Since ISS is going to be changed soon, we decided to update it when that proposal is ready. For now, ISS gets an 'Under Review' tag and will continue to display the existing documentation 2) On the top, the evidence codes are listed/grouped based on how they are assigned This document was put together after lot of deliberation and discussion and is in fairly good shape. We don't anticipate any serious issues with the content. However, we would appreciate if you can review this document and let us know *only* if you see obvious omissions or gaping holes in any part of the document. Typos, formatting, style, layout issues are always welcome. Comments by November 8th, 2007. Evidence Code Committee From cherry at stanford.edu Tue Nov 6 12:25:30 2007 From: cherry at stanford.edu (Mike Cherry) Date: Tue, 6 Nov 2007 12:25:30 -0800 Subject: [go] sorry we were down, again -- up now Message-ID: <982142F7-FD79-456E-8BF3-A7E8636B1D2C@stanford.edu> We had an electrical problem yesterday that brought us down, after the network outage that was a separate event. Checks this morning by the electrical staff indicated that a main breaker switch needed to be replaced. That has now been done and we are up. We hope to be up for a while this time. -Mike From pgaudet at northwestern.edu Fri Nov 9 12:20:55 2007 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Fri, 09 Nov 2007 15:20:55 -0500 Subject: [go] Nov 7 managers call - minutes available Message-ID: <4734C127.1040108@northwestern.edu> Hi all, The minutes from this week's GO Managers conference call are now on the internal wiki: http://gocwiki.geneontology.org/index.php/Managers_7Nov07 If you would like a particular issue to be discussed at the next managers' call, please contact the relevant manager(s): Reference Genomes: Pascale Annotation Outreach, User Advocacy: Jennifer (Jen is filling in for Jane until Feb. 2008) Content Development: Midori and David Software: Chris For general management and budget issues, contact the GO PIs . Thanks, Pascale From rama at genome.Stanford.EDU Mon Nov 12 11:54:53 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Mon, 12 Nov 2007 11:54:53 -0800 Subject: [go] Evidence Code documentation live now Message-ID: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> Hi All, The evidence code documentation update is now live. http://www.geneontology.org/GO.evidence.shtml Thank you all for your comments and help. Cheers, Rama From rhee at acoma.Stanford.EDU Mon Nov 12 11:58:45 2007 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 12 Nov 2007 11:58:45 -0800 Subject: [go] Evidence Code documentation live now In-Reply-To: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> References: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> Message-ID: <4738B075.8060909@acoma.stanford.edu> Thank YOU to all those involved in this. This is VERY helpful. Sue Rama Balakrishnan wrote: > Hi All, > > The evidence code documentation update is now live. > http://www.geneontology.org/GO.evidence.shtml > > Thank you all for your comments and help. > > Cheers, > > Rama -- Sue Rhee Staff Scientist Carnegie Institution, Department of Plant Biology 260 Panama Street, Stanford, CA 94305 Email: (650) 325-1521 x251 Fax: (650) 325-6857 From ma11 at gen.cam.ac.uk Mon Nov 12 12:59:12 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Mon, 12 Nov 2007 15:59:12 -0500 Subject: [go] Evidence Code documentation live now In-Reply-To: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> References: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> Message-ID: <93E7DF0F-F111-423A-80C3-D77AE0F893DE@gen.cam.ac.uk> Indeed, a great job ! Michael On 12 Nov 2007, at 14:54, Rama Balakrishnan wrote: > Hi All, > > The evidence code documentation update is now live. > http://www.geneontology.org/GO.evidence.shtml > > Thank you all for your comments and help. > > Cheers, > > Rama > From suzi at berkeleybop.org Mon Nov 12 14:53:30 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Mon, 12 Nov 2007 14:53:30 -0800 Subject: [go] Evidence Code documentation live now In-Reply-To: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> References: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> Message-ID: <3FAB36BB-58F8-4B6A-B92B-6C706262DD66@berkeleybop.org> Absolutely fabulous. The end (or at the very least a more than decent way station) of a long road, congrats to everyone. On Nov 12, 2007, at 11:54 AM, Rama Balakrishnan wrote: > Hi All, > > The evidence code documentation update is now live. > http://www.geneontology.org/GO.evidence.shtml > > Thank you all for your comments and help. > > Cheers, > > Rama > > From rama at genome.Stanford.EDU Tue Nov 13 10:31:29 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Tue, 13 Nov 2007 10:31:29 -0800 Subject: [go] Evidence Code documentation live now In-Reply-To: <3FAB36BB-58F8-4B6A-B92B-6C706262DD66@berkeleybop.org> References: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> <3FAB36BB-58F8-4B6A-B92B-6C706262DD66@berkeleybop.org> Message-ID: I would like to add that this document is not set on stone. I am sure there is room for refinement and improvement. If you have suggestions for improvement please don't hesitate to send them to the evidence code mailing list (evidence at genome.stanford.edu) and/or the GO mailing list. rama On Nov 12, 2007, at 2:53 PM, Suzanna Lewis wrote: > Absolutely fabulous. > > The end (or at the very least a more than decent way station) of a > long road, congrats to everyone. > > > On Nov 12, 2007, at 11:54 AM, Rama Balakrishnan wrote: > >> Hi All, >> >> The evidence code documentation update is now live. >> http://www.geneontology.org/GO.evidence.shtml >> >> Thank you all for your comments and help. >> >> Cheers, >> >> Rama >> >> From jblake at informatics.jax.org Wed Nov 14 06:14:33 2007 From: jblake at informatics.jax.org (Judith Blake) Date: Wed, 14 Nov 2007 09:14:33 -0500 Subject: [go] Evidence Code documentation live now In-Reply-To: References: <30ED7605-512C-4053-9734-FDCB6CA7A9C0@genome.stanford.edu> <3FAB36BB-58F8-4B6A-B92B-6C706262DD66@berkeleybop.org> Message-ID: <473B02C9.9090307@informatics.jax.org> Hi all contributors to this documenation, I thank you all for your intense work on this. I especially like the examples since they help greatly to clarify when and when not you might consider using a particular evidence code. One of the great things, as Rama notes below, is that this is now our 'working document' and the agreed upon place to start from in the future should changes come under discussion. excellent work judy Rama Balakrishnan wrote: > I would like to add that this document is not set on stone. I am sure > there is room for refinement and improvement. If you have suggestions > for improvement please don't hesitate to send them to the evidence > code mailing list (evidence at genome.stanford.edu) and/or the GO mailing > list. > > rama > > > On Nov 12, 2007, at 2:53 PM, Suzanna Lewis wrote: > >> Absolutely fabulous. >> >> The end (or at the very least a more than decent way station) of a >> long road, congrats to everyone. >> >> >> On Nov 12, 2007, at 11:54 AM, Rama Balakrishnan wrote: >> >>> Hi All, >>> >>> The evidence code documentation update is now live. >>> http://www.geneontology.org/GO.evidence.shtml >>> >>> Thank you all for your comments and help. >>> >>> Cheers, >>> >>> Rama >>> >>> > From stacia at genome.Stanford.EDU Wed Nov 14 13:30:03 2007 From: stacia at genome.Stanford.EDU (Stacia Engel) Date: Wed, 14 Nov 2007 13:30:03 -0800 Subject: [go] please proof November07 newsletter Message-ID: <66CD9453-B79C-44F2-B4AE-2915EC67978F@genome.stanford.edu> Hi, Thanks everyone for input on the November 2007 issue of the GO newsletter. We have a version that is ready for proofing by GOC members. Please have a look and let us know if we have any errors, typos, etc. We'd like to send it out by week's end. Thanks, Stacia & the Newsletter Team pdf - http://www.yeastgenome.org/~stacia/GOnewsletterNovember07.pdf html - http://www.geneontology.org/test-html.shtml From rama at genome.Stanford.EDU Wed Nov 14 13:53:13 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Wed, 14 Nov 2007 13:53:13 -0800 Subject: [go] please proof November07 newsletter In-Reply-To: <66CD9453-B79C-44F2-B4AE-2915EC67978F@genome.stanford.edu> References: <66CD9453-B79C-44F2-B4AE-2915EC67978F@genome.stanford.edu> Message-ID: Newsletter looks very good. Nice job. I have couple of suggestions (take or leave)- Section on Cardiovascular Physiology.. ------------------------------------- 1) Change first sentence to- Two large-scale addition *of GO terms* were made in October 2007... Was the addition to all 3 ontologies or only F and P? If latter, may be we can even say- Two large-scale addition of GO terms to the Molecular function and Biological process ontolgies were made... 2) Change the sentence about using AmiGO to: To see the blood pressure regulation...use the AmiGO Advanced Search; **type mtg_cardio or mtg_muscle in the text box on the top and select 'All fields' in the 'Search Type' section.** Section on spsl2go ---------------------------- Last sentence of first para-should it be 'coded' in (IEA coded)? can it be changed to '...electronic GO annotation (using IEA evidence code) in our latest...' Thats all. Thanks, Rama On Nov 14, 2007, at 1:30 PM, Stacia Engel wrote: > Hi, > > Thanks everyone for input on the November 2007 issue of the GO > newsletter. We have a version that is ready for proofing by GOC > members. Please have a look and let us know if we have any errors, > typos, etc. We'd like to send it out by week's end. > > Thanks, > Stacia & the Newsletter Team > > pdf - > http://www.yeastgenome.org/~stacia/GOnewsletterNovember07.pdf > > html - > http://www.geneontology.org/test-html.shtml > > From dph at informatics.jax.org Wed Nov 14 13:57:59 2007 From: dph at informatics.jax.org (David Hill) Date: Wed, 14 Nov 2007 16:57:59 -0500 Subject: [go] please proof November07 newsletter In-Reply-To: References: <66CD9453-B79C-44F2-B4AE-2915EC67978F@genome.stanford.edu> Message-ID: <473B6F67.1020600@informatics.jax.org> Hi Rama, The cardio and muscle terms were only added to process. David Rama Balakrishnan wrote: > Newsletter looks very good. Nice job. > > I have couple of suggestions (take or leave)- > > > Section on Cardiovascular Physiology.. > ------------------------------------- > 1) Change first sentence to- > > Two large-scale addition *of GO terms* were made in October 2007... > > Was the addition to all 3 ontologies or only F and P? If latter, may > be we can even say- > > Two large-scale addition of GO terms to the Molecular function and > Biological process ontolgies were made... > > 2) Change the sentence about using AmiGO to: > > To see the blood pressure regulation...use the AmiGO Advanced Search; > **type mtg_cardio or mtg_muscle in the text box on the top and select > 'All fields' in the 'Search Type' section.** > > Section on spsl2go > ---------------------------- > Last sentence of first para-should it be 'coded' in (IEA coded)? can > it be changed to '...electronic GO annotation (using IEA evidence > code) in our latest...' > > Thats all. > > Thanks, > > Rama > > On Nov 14, 2007, at 1:30 PM, Stacia Engel wrote: > >> Hi, >> >> Thanks everyone for input on the November 2007 issue of the GO >> newsletter. We have a version that is ready for proofing by GOC >> members. Please have a look and let us know if we have any errors, >> typos, etc. We'd like to send it out by week's end. >> >> Thanks, >> Stacia & the Newsletter Team >> >> pdf - >> http://www.yeastgenome.org/~stacia/GOnewsletterNovember07.pdf >> >> html - >> http://www.geneontology.org/test-html.shtml >> >> > From rama at genome.Stanford.EDU Wed Nov 14 14:00:39 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Wed, 14 Nov 2007 14:00:39 -0800 Subject: [go] please proof November07 newsletter In-Reply-To: <473B6F67.1020600@informatics.jax.org> References: <66CD9453-B79C-44F2-B4AE-2915EC67978F@genome.stanford.edu> <473B6F67.1020600@informatics.jax.org> Message-ID: <2D74C80E-D9B6-4941-AB66-0633D2519993@genome.stanford.edu> Thanks David. In that case, may be the sentence can be changed to just- Two large-scale addition of GO terms to the Biological process ontology was made..... Rama On Nov 14, 2007, at 1:57 PM, David Hill wrote: > Hi Rama, > > The cardio and muscle terms were only added to process. > > David > > Rama Balakrishnan wrote: >> Newsletter looks very good. Nice job. >> >> I have couple of suggestions (take or leave)- >> >> >> Section on Cardiovascular Physiology.. >> ------------------------------------- >> 1) Change first sentence to- >> >> Two large-scale addition *of GO terms* were made in October 2007... >> >> Was the addition to all 3 ontologies or only F and P? If latter, >> may be we can even say- >> >>>> Two large-scale addition of GO terms to the Molecular function >>>> and Biological process ontolgies were made... >> >> >> 2) Change the sentence about using AmiGO to: >> >> To see the blood pressure regulation...use the AmiGO Advanced >> Search; **type mtg_cardio or mtg_muscle in the text box on the top >> and select 'All fields' in the 'Search Type' section.** >> >> Section on spsl2go >> ---------------------------- >> Last sentence of first para-should it be 'coded' in (IEA coded)? >> can it be changed to '...electronic GO annotation (using IEA >> evidence code) in our latest...' >> >> Thats all. >> >> Thanks, >> >> Rama >> >> On Nov 14, 2007, at 1:30 PM, Stacia Engel wrote: >> >>> Hi, >>> >>> Thanks everyone for input on the November 2007 issue of the GO >>> newsletter. We have a version that is ready for proofing by GOC >>> members. Please have a look and let us know if we have any >>> errors, typos, etc. We'd like to send it out by week's end. >>> >>> Thanks, >>> Stacia & the Newsletter Team >>> >>> pdf - >>> http://www.yeastgenome.org/~stacia/GOnewsletterNovember07.pdf >>> >>> html - >>> http://www.geneontology.org/test-html.shtml >>> >>> >> From vanauken at caltech.edu Wed Nov 14 14:13:22 2007 From: vanauken at caltech.edu (Kimberly Van Auken) Date: Wed, 14 Nov 2007 14:13:22 -0800 Subject: [go] please proof November07 newsletter In-Reply-To: <66CD9453-B79C-44F2-B4AE-2915EC67978F@genome.stanford.edu> References: <66CD9453-B79C-44F2-B4AE-2915EC67978F@genome.stanford.edu> Mess