From midori at ebi.ac.uk Mon Dec 3 07:12:07 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 3 Dec 2007 15:12:07 +0000 (GMT) Subject: [go] Ontology development - November highlights Message-ID: Dear GO, The most recent monthly report on ontology content, for November 2007, is now available at: http://gocwiki.geneontology.org/index.php/Nov2007_ontology_report Ontology development highlights from November: * The work on resolving inconsistencies in regulation terms is almost done. Cross-products and the 'regulates' relationship are not far off now (http://gocwiki.geneontology.org/index.php/Regulation_Main_Page). * Preparation for the content meeting on lung development is well under way. The meeting will be held on December 5th-6th; a file is available in go/scratch/ (http://wiki.geneontology.org/index.php/Lung_Development). * The update article for the January 2008 NAR Database Issue has been published online (full text: http://nar.oxfordjournals.org/cgi/content/full/gkm883v1). * Work on 'sensu' terms has resumed, and will be finished soon (main wiki page: http://gocwiki.geneontology.org/index.php/Sensu_Main_Page; outstanding items: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3). * There's been progress on the 'response to drug' revamp (http://gocwiki.geneontology.org/index.php/Response_to_drug). In December, in addition to the lung development meeting, we will continue to work on cross-products, including regulation and GO-Cell xps. 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. Have a great holiday season! Midori & David on behalf of GO's ontology developers From ma11 at gen.cam.ac.uk Wed Dec 5 01:42:47 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Wed, 5 Dec 2007 09:42:47 +0000 Subject: [go] Ontology development - November highlights In-Reply-To: References: Message-ID: Thankyou Midori. Michael On 3 Dec 2007, at 15:12, Midori Harris wrote: > Dear GO, > > The most recent monthly report on ontology content, for November > 2007, is now available at: > > http://gocwiki.geneontology.org/index.php/Nov2007_ontology_report > > Ontology development highlights from November: > > * The work on resolving inconsistencies in regulation terms is > almost done. Cross-products and the 'regulates' relationship are > not far off now (http://gocwiki.geneontology.org/index.php/ > Regulation_Main_Page). > > * Preparation for the content meeting on lung development is well > under way. The meeting will be held on December 5th-6th; a file is > available in go/scratch/ (http://wiki.geneontology.org/index.php/ > Lung_Development). > > * The update article for the January 2008 NAR Database Issue has > been published online (full text: http://nar.oxfordjournals.org/cgi/ > content/full/gkm883v1). > > * Work on 'sensu' terms has resumed, and will be finished soon > (main wiki page: http://gocwiki.geneontology.org/index.php/ > Sensu_Main_Page; outstanding items: http://gocwiki.geneontology.org/ > index.php/Meeting_Notes_3). > > * There's been progress on the 'response to drug' revamp (http:// > gocwiki.geneontology.org/index.php/Response_to_drug). > > In December, in addition to the lung development meeting, we will > continue to work on cross-products, including regulation and GO- > Cell xps. > > 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. > > Have a great holiday season! > > Midori & David > on behalf of GO's ontology developers From ma11 at gen.cam.ac.uk Wed Dec 5 08:03:05 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Wed, 5 Dec 2007 16:03:05 +0000 Subject: [go] Please send me conf call numbers asp Message-ID: <0288EE7B-18EF-467E-BA21-58B6B0A5BCEF@gen.cam.ac.uk> From jdeegan at ebi.ac.uk Thu Dec 6 05:47:37 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Thu, 06 Dec 2007 13:47:37 +0000 Subject: [go] advocacy and outreach monthly reports Message-ID: <4757FD79.6030304@ebi.ac.uk> Hi, I am about to write the reports on outreach and advocacy progress for December. If you done anything this month that involved educating users on how to use the GO, feeding back from users on how the GO could better support their needs, or supporting new groups that are interested in starting annotation, could you possible let me know about it? Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From jdeegan at ebi.ac.uk Thu Dec 6 05:49:28 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Thu, 06 Dec 2007 13:49:28 +0000 Subject: [go] advocacy and outreach monthly reports In-Reply-To: <4757FD79.6030304@ebi.ac.uk> References: <4757FD79.6030304@ebi.ac.uk> Message-ID: <4757FDE8.3080307@ebi.ac.uk> Hi again, I am getting ahead of myself. I meant the report for November. :-) Thanks, Jen Jennifer Deegan (nee Clark) wrote: > Hi, > > I am about to write the reports on outreach and advocacy progress for > December. If you done anything this month that involved educating users > on how to use the GO, feeding back from users on how the GO could better > support their needs, or supporting new groups that are interested in > starting annotation, could you possible let me know about it? > > Thanks, > > Jen > > > -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From val at sanger.ac.uk Thu Dec 6 06:25:49 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 06 Dec 2007 14:25:49 +0000 Subject: [go] Re: regulation of cell cycle vs. regulation of progression through cell cycle In-Reply-To: <474F0EF5.6090002@acoma.stanford.edu> References: <474F0EF5.6090002@acoma.stanford.edu> Message-ID: <4758066D.3050508@sanger.ac.uk> Hi Tanya, Sorry for the delay. At first glance, I think that what you propsed is OK. You are correct that the seperate terms were created to cope with the switching between mitotic and meiotic cell-cycles, but your solution of making these positive and negative regulatory terms respectively seems logically consistant. I think however, there is a more fundamental problem in this portion of the graph in that there is some confusion between the concurrent use of meiosis to describe 'meiotic division' and meiosis as a 'developmental stage' I'm not sure if the terms created to cope with the switching between mitotic and meiotic cell-cycles rather refer to a switch between developmental stage for example "entry into meiosis" for yeast would include response to pheromone, and conjugation etc, and gene products annotated to these terms would not necessarily be considered be a 'cell-cycle ' genes. current child terms of "meiosis" also include megasporogenesis (synonym megaspore development ) and these terms do not appear to be referring specifically to meiosis as a cell cycle process. This is essentially what I was trying to describe in SF 1831804 ] yeast meiotic development. Even some of the definitions of these terms seem to merge both concepts into a single term. It might make sense to tackle both issues at the same time. I'm not sure what the solution is.... Val Tanya Berardini wrote: > Dear GO Consortium, > > As part of the 'regulates' project, we have come across a set of terms > in the cell cycle portion of the graph that seem problematic. We are > writing because we know that a lot of previous work has gone into this > part of the graph and want to be sure that our plan makes sense. We have > two sets of terms similar to these: > > term: regulation of cell cycle (simple term) > def:A cell cycle process that modulates the rate, extent or mode of the > cell cycle. > > term: regulation of progression through cell cycle (progression term) > def: Any process that modulates the rate or extent of progression > through the cell cycle. > > Our question is how does 'regulation of progression through cell cycle' > differ from 'regulation of cell cycle'? > > Note that 'cell cycle' itself is defined as "the progression of > ...phases and events ...", implying that regulation of the cell cycle > is regulation of progression through the cycle; the same holds for the > types of cell cycle (i.e. its is_a children). > > cell cycle: The progression of biochemical and morphological phases and > events that occur in a cell during successive cell replication or > nuclear replication events. Canonically, the cell cycle comprises the > replication and segregation of genetic material followed by the division > of the cell, but in endocycles or syncytial cells nuclear replication or > nuclear division may not be followed by cell division. > > If they are indeed describing the same processes, the 'regulation of %' > and 'regulation of progression of %' terms should be merged. If not, > then we need to create a bona-fide biological process called > 'progression through cell cycle' and we need to differentiate that from > 'cell cycle' with a really good definition. Currently the progression > terms are only used in conjunction with regulation. > > The way we represent these in the graph is also inconsistent. An example > follows: > > Case 1: No direct link between the 'regulation of progression through > cell cycle' term and 'cell cycle' term exists. > > regulation of cell cycle > --[i]regulation of progression through cell cycle > > > Case 2: Direct link between 'regulation of progression through meiotic > cell cycle' and 'meiotic cell cycle' exists. > > regulation of meiotic cell cycle > --[i]regulation of progression through meiotic cell cycle > > meiotic cell cycle > --[p]regulation of progression through meiotic cell cycle > > > We propose: > > 1) Merging the 'regulation of progression through' terms > with their simpler parents when they exist. > > 2) Renaming the 'regulation of progression through' terms to their > simpler forms when the simpler parents do not exist since the parent > non-regulates terms are already defined as the progression of... > > 3) Moving 'cell cycle switching, meiotic to mitotic cell cycle' to > become an is_a 'negative regulation of meiotic cell cycle' and an is_a > 'positive regulation of mitotic cell cycle'. > > 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' > to be an is_a 'positive regulation of meiotic cell cycle' and an is_a > 'negative regulation of mitotic cell cycle'. We think that the last two > terms were why 'regulation of cell cycle' and 'regulation of > progression through cell cycle' were originally created as distinct > terms. However, the movement of these as in 3 and 4 makes more logical > sense since the process they describe stops (negatively regulates) one > type of cell cycle and initiates (positively regulates) > another. > > Please comment if you think that these merges/renames are not ok. If > this is the case then we will need to make the missing 'progression' > terms or 'simpler terms' and will need help in differentiating the > 'progression' terms from their parents. > > > David & Tanya > > > > -- 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 eurie at genome.Stanford.EDU Thu Dec 6 10:30:21 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Thu, 6 Dec 2007 10:30:21 -0800 Subject: [go] Re: regulation of cell cycle vs. regulation of progression through cell cycle In-Reply-To: <4758066D.3050508@sanger.ac.uk> References: <474F0EF5.6090002@acoma.stanford.edu> <4758066D.3050508@sanger.ac.uk> Message-ID: I have a couple of questions - Are the "regulation of cell cycle" and "regulation of progression through cell cycle" going to be specific for just regulating the rate at which the progression through the cell cycle occurs? Then maybe they should be renamed "regulation of cell cycle phase" (cell cycle phase is GO:0022403)? Or do we need to keep the structure of the regulation terms to mimic how the cell cycle branch is organized? "regulation of cell cycle" - general grouping term for both molecular/ cellular events and temporal phasing -- "regulation of cell cycle processes" - grouping term for all the regulation of processes ---- "regulation of cell cycle phase" - specific for going through the temporal phases The mitotic - meiotic switch terms sound ok. As long as there are synonyms to find them - most folks in the field do refer to "entry into meiosis" but there are positive and negative regulators of the process. On Dec 6, 2007, at 6:25 AM, Valerie Wood wrote: > Hi Tanya, > > Sorry for the delay. > > At first glance, I think that what you propsed is OK. You are > correct that the seperate terms were created to cope with the > switching between mitotic and meiotic cell-cycles, but your > solution of making these positive and negative regulatory terms > respectively seems logically consistant. > > I think however, there is a more fundamental problem in this > portion of the graph in that there is some confusion between the > concurrent use of meiosis to describe 'meiotic division' and > meiosis as a 'developmental stage' > > I'm not sure if the terms created to cope with the switching > between mitotic and meiotic cell-cycles rather refer to a switch > between developmental stage > for example "entry into meiosis" for yeast would include response > to pheromone, and conjugation etc, and gene products annotated to > these terms would not necessarily be considered be a 'cell-cycle ' > genes. > > current child terms of "meiosis" also include > megasporogenesis (synonym megaspore development ) and these terms > do not appear to be referring specifically to meiosis as a cell > cycle process. > > This is essentially what I was trying to describe in > SF 1831804 ] yeast meiotic development. > > Even some of the definitions of these terms seem to merge both > concepts into a single term. > > It might make sense to tackle both issues at the same time. I'm not > sure what the solution is.... > > Val > > > > > Tanya Berardini wrote: > >> Dear GO Consortium, >> >> As part of the 'regulates' project, we have come across a set of >> terms >> in the cell cycle portion of the graph that seem problematic. We are >> writing because we know that a lot of previous work has gone into >> this >> part of the graph and want to be sure that our plan makes sense. >> We have >> two sets of terms similar to these: >> >> term: regulation of cell cycle (simple term) >> def:A cell cycle process that modulates the rate, extent or mode >> of the >> cell cycle. >> >> term: regulation of progression through cell cycle (progression term) >> def: Any process that modulates the rate or extent of progression >> through the cell cycle. >> >> Our question is how does 'regulation of progression through cell >> cycle' >> differ from 'regulation of cell cycle'? >> >> Note that 'cell cycle' itself is defined as "the progression >> of ...phases and events ...", implying that regulation of the cell >> cycle is regulation of progression through the cycle; the same >> holds for the types of cell cycle (i.e. its is_a children). >> >> cell cycle: The progression of biochemical and morphological >> phases and >> events that occur in a cell during successive cell replication or >> nuclear replication events. Canonically, the cell cycle comprises the >> replication and segregation of genetic material followed by the >> division >> of the cell, but in endocycles or syncytial cells nuclear >> replication or >> nuclear division may not be followed by cell division. >> >> If they are indeed describing the same processes, the 'regulation >> of %' >> and 'regulation of progression of %' terms should be merged. If not, >> then we need to create a bona-fide biological process called >> 'progression through cell cycle' and we need to differentiate that >> from >> 'cell cycle' with a really good definition. Currently the progression >> terms are only used in conjunction with regulation. >> >> The way we represent these in the graph is also inconsistent. An >> example >> follows: >> >> Case 1: No direct link between the 'regulation of progression through >> cell cycle' term and 'cell cycle' term exists. >> >> regulation of cell cycle >> --[i]regulation of progression through cell cycle >> >> >> Case 2: Direct link between 'regulation of progression through >> meiotic >> cell cycle' and 'meiotic cell cycle' exists. >> >> regulation of meiotic cell cycle >> --[i]regulation of progression through meiotic cell cycle >> >> meiotic cell cycle >> --[p]regulation of progression through meiotic cell cycle >> >> >> We propose: >> >> 1) Merging the 'regulation of progression through' terms >> with their simpler parents when they exist. >> >> 2) Renaming the 'regulation of progression through' terms to their >> simpler forms when the simpler parents do not exist since the parent >> non-regulates terms are already defined as the progression of... >> >> 3) Moving 'cell cycle switching, meiotic to mitotic cell cycle' to >> become an is_a 'negative regulation of meiotic cell cycle' and an >> is_a >> 'positive regulation of mitotic cell cycle'. >> >> 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' >> to be an is_a 'positive regulation of meiotic cell cycle' and an is_a >> 'negative regulation of mitotic cell cycle'. We think that the >> last two >> terms were why 'regulation of cell cycle' and 'regulation of >> progression through cell cycle' were originally created as >> distinct terms. However, the movement of these as in 3 and 4 makes >> more logical sense since the process they describe stops >> (negatively regulates) one type of cell cycle and initiates >> (positively regulates) >> another. >> From tberardi at acoma.Stanford.EDU Thu Dec 6 15:23:41 2007 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Thu, 06 Dec 2007 15:23:41 -0800 Subject: [go] Re: regulation of cell cycle vs. regulation of progression through cell cycle In-Reply-To: References: <474F0EF5.6090002@acoma.stanford.edu> <4758066D.3050508@sanger.ac.uk> Message-ID: <4758847D.8070706@acoma.stanford.edu> Hi Eurie and Val, Answers are interspersed below: Eurie Hong wrote: > I have a couple of questions - > > Are the "regulation of cell cycle" and "regulation of progression > through cell cycle" going to be specific for just regulating the rate at > which the progression through the cell cycle occurs? Not just the rate. The standard definition of 'regulation of xxx' is: Any process that modulates the frequency, rate or extent of process, [definition of process]. Since the cell cycle is defined as the progression... then the regulation of the cell cycle would be anything that modulates the frequency, rate or extent of the progression. Then maybe they > should be renamed "regulation of cell cycle phase" (cell cycle phase is > GO:0022403)? No, that would be a different term, because there are cell cycle phase terms in the ontology (see all children of 'cell cycle phase'). So the regulation of a cell cycle phase would describe the regulation of one of these, for example, 'regulation of interphase' (which doesn't yet exist). > > Or do we need to keep the structure of the regulation terms to mimic how > the cell cycle branch is organized? > > "regulation of cell cycle" - general grouping term for both > molecular/cellular events and temporal phasing > -- "regulation of cell cycle processes" - grouping term for all the > regulation of processes > ---- "regulation of cell cycle phase" - specific for going through the > temporal phases Yes. Our goal is to create regulates terms that don't conflict with the structure of the process ontology. Right now, we're not creating all of these terms but if and when they are needed, we should be able to insert them easily because the structure already exists. > The mitotic - meiotic switch terms sound ok. As long as there are > synonyms to find them - most folks in the field do refer to "entry into > meiosis" but there are positive and negative regulators of the process. Since we're not proposing changing the terms, synonyms or textual definitions but rather their locations in the graph, if there are synonyms that are missing, please let us know. Now, on to Val's comments. > On Dec 6, 2007, at 6:25 AM, Valerie Wood wrote: > >> At first glance, I think that what you propsed is OK. You are correct >> that the seperate terms were created to cope with the switching >> between mitotic and meiotic cell-cycles, but your solution of making >> these positive and negative regulatory terms respectively seems >> logically consistant. Great! We assume this means that our proposed changes 1-4 are ok. >> >> I think however, there is a more fundamental problem in this portion >> of the graph in that there is some confusion between the concurrent >> use of meiosis to describe 'meiotic division' and meiosis as a >> 'developmental stage' From its current placement in the graph, meiosis is a type of cell cycle phase. It is not restricted to simply meiotic division. >> I'm not sure if the terms created to cope with the switching between >> mitotic and meiotic cell-cycles rather refer to a switch between >> developmental stage >> for example "entry into meiosis" for yeast would include response to >> pheromone, and conjugation etc, and gene products annotated to these >> terms would not necessarily be considered be a 'cell-cycle ' genes. It seems that a problem here is that 'regulation of cell cycle' is_a 'cell cycle process.' If we remove this relationship, then 'regulation of cell cycle' will only have a regulates relationship with 'cell cycle' and will not be a cell cycle process. If we adopt our proposal and remove this relationship, genes annotated to the terms 'cell cycle switching, mitotic to meiotic cell cycle' and 'cell cycle switching, meiotic to mitotic cell cycle' will be involved in regulation of the cell cycle and will not necessarily be annotated to terms that are part_of or is_a children of 'cell cycle.' >> current child terms of "meiosis" also include >> megasporogenesis (synonym megaspore development ) and these terms do >> not appear to be referring specifically to meiosis as a cell cycle >> process. Megasporogenesis, despite the name, does not refer to the genesis of the megaspore but specifically to the meiosis of the diploid megasporocyte to give rise to four haploid megaspores. >> >> This is essentially what I was trying to describe in >> SF 1831804 ] yeast meiotic development. >> >> Even some of the definitions of these terms seem to merge both >> concepts into a single term. >> >> It might make sense to tackle both issues at the same time. I'm not >> sure what the solution is.... While a valid concern, this is not immediately relevant to our current project of cleaning up the ontology for implementation of the regulates relationship. We will address this issue at a later time. We are still waiting to hear back from Kimberly who is also looking at their annotations to these terms. If no other conflicts arise, we look forward to making the changes on Dec. 10th. Thank you both for your comments. Please let us know if we didn't address your issues satisfactorily. Tanya and David >> Val >> >> >> >> >> Tanya Berardini wrote: >> >>> Dear GO Consortium, >>> >>> As part of the 'regulates' project, we have come across a set of terms >>> in the cell cycle portion of the graph that seem problematic. We are >>> writing because we know that a lot of previous work has gone into this >>> part of the graph and want to be sure that our plan makes sense. We have >>> two sets of terms similar to these: >>> >>> term: regulation of cell cycle (simple term) >>> def:A cell cycle process that modulates the rate, extent or mode of the >>> cell cycle. >>> >>> term: regulation of progression through cell cycle (progression term) >>> def: Any process that modulates the rate or extent of progression >>> through the cell cycle. >>> >>> Our question is how does 'regulation of progression through cell cycle' >>> differ from 'regulation of cell cycle'? >>> >>> Note that 'cell cycle' itself is defined as "the progression of >>> ...phases and events ...", implying that regulation of the cell cycle >>> is regulation of progression through the cycle; the same holds for >>> the types of cell cycle (i.e. its is_a children). >>> >>> cell cycle: The progression of biochemical and morphological phases and >>> events that occur in a cell during successive cell replication or >>> nuclear replication events. Canonically, the cell cycle comprises the >>> replication and segregation of genetic material followed by the division >>> of the cell, but in endocycles or syncytial cells nuclear replication or >>> nuclear division may not be followed by cell division. >>> >>> If they are indeed describing the same processes, the 'regulation of %' >>> and 'regulation of progression of %' terms should be merged. If not, >>> then we need to create a bona-fide biological process called >>> 'progression through cell cycle' and we need to differentiate that from >>> 'cell cycle' with a really good definition. Currently the progression >>> terms are only used in conjunction with regulation. >>> >>> The way we represent these in the graph is also inconsistent. An example >>> follows: >>> >>> Case 1: No direct link between the 'regulation of progression through >>> cell cycle' term and 'cell cycle' term exists. >>> >>> regulation of cell cycle >>> --[i]regulation of progression through cell cycle >>> >>> >>> Case 2: Direct link between 'regulation of progression through meiotic >>> cell cycle' and 'meiotic cell cycle' exists. >>> >>> regulation of meiotic cell cycle >>> --[i]regulation of progression through meiotic cell cycle >>> >>> meiotic cell cycle >>> --[p]regulation of progression through meiotic cell cycle >>> >>> >>> We propose: >>> >>> 1) Merging the 'regulation of progression through' terms >>> with their simpler parents when they exist. >>> >>> 2) Renaming the 'regulation of progression through' terms to their >>> simpler forms when the simpler parents do not exist since the parent >>> non-regulates terms are already defined as the progression of... >>> >>> 3) Moving 'cell cycle switching, meiotic to mitotic cell cycle' to >>> become an is_a 'negative regulation of meiotic cell cycle' and an is_a >>> 'positive regulation of mitotic cell cycle'. >>> >>> 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' >>> to be an is_a 'positive regulation of meiotic cell cycle' and an is_a >>> 'negative regulation of mitotic cell cycle'. We think that the last two >>> terms were why 'regulation of cell cycle' and 'regulation of >>> progression through cell cycle' were originally created as distinct >>> terms. However, the movement of these as in 3 and 4 makes more >>> logical sense since the process they describe stops (negatively >>> regulates) one type of cell cycle and initiates (positively regulates) >>> another. >>> -- ------------------------------------------------------------------------------------------ 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 vanauken at caltech.edu Thu Dec 6 16:06:54 2007 From: vanauken at caltech.edu (Kimberly Van Auken) Date: Thu, 06 Dec 2007 16:06:54 -0800 Subject: [go] Re: regulation of cell cycle vs. regulation of progression through cell cycle In-Reply-To: <4758847D.8070706@acoma.stanford.edu> References: <474F0EF5.6090002@acoma.stanford.edu> <4758066D.3050508@sanger.ac.uk> <4758847D.8070706@acoma.stanford.edu> Message-ID: <47588E9E.6060805@caltech.edu> Hi-- In the course of going through our annotations, I've come across cases that doesn't seem to work for change #4, if I understand it correctly. 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' to be an is_a 'positive regulation of meiotic cell cycle' and an is_a 'negative regulation of mitotic cell cycle'. We think that the last two terms were why 'regulation of cell cycle' and 'regulation of progression through cell cycle' were originally created as distinct terms. However, the movement of these as in 3 and 4 makes more logical sense since the process they describe stops (negatively regulates) one type of cell cycle and initiates (positively regulates) another. As an example, we have a gene, glp-1, that regulates the decision between mitosis and meiosis in the germ line. glp-1 could be annotated to 'germline cell cycle switching, mitotic to meiotic cell cycle', but its role in this process is as a positive regulator of the mitotic cell cycle and a negative regulator of the meiotic cell cycle. This is opposite to what is proposed above. One alternative is to make the cell cycle switching terms is_a children of regulation of mitotic cell cycle and regulation of meiotic cell cycle, but then we lose the directionality of the regulation. In that case we'd could additionally annotate to the respective positive and negative regulation terms that could also be is_a children of the regulation parent. Or, we could make positive and negative regulation terms for cell cycle switching to capture the appropriate directionality. glp-1 would then be annotated to negative regulation of germline cell cycle switching, mitotic to meiotic cell cycle. I would also then annotate glp-1 to positive regulation of cell proliferation, which is not related to the cell cycle terms in GO, I believe. --Kimberly Tanya Berardini wrote: > Hi Eurie and Val, > > Answers are interspersed below: > > Eurie Hong wrote: > >> I have a couple of questions - >> >> Are the "regulation of cell cycle" and "regulation of progression >> through cell cycle" going to be specific for just regulating the rate >> at which the progression through the cell cycle occurs? > > > Not just the rate. The standard definition of 'regulation of xxx' is: > > Any process that modulates the frequency, rate or extent of process, > [definition of process]. > > Since the cell cycle is defined as the progression... then the > regulation of the cell cycle would be anything that modulates the > frequency, rate or extent of the progression. > > Then maybe they > >> should be renamed "regulation of cell cycle phase" (cell cycle phase >> is GO:0022403)? > > > No, that would be a different term, because there are cell cycle phase > terms in the ontology (see all children of 'cell cycle phase'). So > the regulation of a cell cycle phase would describe the regulation of > one of these, for example, 'regulation of interphase' (which doesn't > yet exist). > >> >> Or do we need to keep the structure of the regulation terms to mimic >> how the cell cycle branch is organized? >> >> "regulation of cell cycle" - general grouping term for both >> molecular/cellular events and temporal phasing >> -- "regulation of cell cycle processes" - grouping term for all the >> regulation of processes >> ---- "regulation of cell cycle phase" - specific for going through >> the temporal phases > > > Yes. Our goal is to create regulates terms that don't conflict with > the structure of the process ontology. Right now, we're not creating > all of these terms but if and when they are needed, we should be able > to insert them easily because the structure already exists. > >> The mitotic - meiotic switch terms sound ok. As long as there are >> synonyms to find them - most folks in the field do refer to "entry >> into meiosis" but there are positive and negative regulators of the >> process. > > > Since we're not proposing changing the terms, synonyms or textual > definitions but rather their locations in the graph, if there are > synonyms that are missing, please let us know. > > Now, on to Val's comments. > > >> On Dec 6, 2007, at 6:25 AM, Valerie Wood wrote: >> > >>> At first glance, I think that what you propsed is OK. You are >>> correct that the seperate terms were created to cope with the >>> switching between mitotic and meiotic cell-cycles, but your solution >>> of making these positive and negative regulatory terms respectively >>> seems logically consistant. >> > > Great! We assume this means that our proposed changes 1-4 are ok. > >>> >>> I think however, there is a more fundamental problem in this portion >>> of the graph in that there is some confusion between the concurrent >>> use of meiosis to describe 'meiotic division' and meiosis as a >>> 'developmental stage' >> > > From its current placement in the graph, meiosis is a type of cell > cycle phase. It is not restricted to simply meiotic division. > >>> I'm not sure if the terms created to cope with the switching between >>> mitotic and meiotic cell-cycles rather refer to a switch between >>> developmental stage >>> for example "entry into meiosis" for yeast would include response to >>> pheromone, and conjugation etc, and gene products annotated to these >>> terms would not necessarily be considered be a 'cell-cycle ' genes. >> > > It seems that a problem here is that 'regulation of cell cycle' is_a > 'cell cycle process.' If we remove this relationship, then > 'regulation of cell cycle' will only have a regulates relationship > with 'cell cycle' and will not be a cell cycle process. > > If we adopt our proposal and remove this relationship, genes annotated > to the terms 'cell cycle switching, mitotic to meiotic cell cycle' and > 'cell cycle switching, meiotic to mitotic cell cycle' will be involved > in regulation of the cell cycle and will not necessarily be annotated > to terms that are part_of or is_a children of 'cell cycle.' > >>> current child terms of "meiosis" also include >>> megasporogenesis (synonym megaspore development ) and these terms do >>> not appear to be referring specifically to meiosis as a cell cycle >>> process. >> > > Megasporogenesis, despite the name, does not refer to the genesis of > the megaspore but specifically to the meiosis of the diploid > megasporocyte to give rise to four haploid megaspores. > >>> >>> This is essentially what I was trying to describe in >>> SF 1831804 ] yeast meiotic development. >>> >>> Even some of the definitions of these terms seem to merge both >>> concepts into a single term. >>> >>> It might make sense to tackle both issues at the same time. I'm not >>> sure what the solution is.... >> > > While a valid concern, this is not immediately relevant to our current > project of cleaning up the ontology for implementation of the > regulates relationship. We will address this issue at a later time. > > We are still waiting to hear back from Kimberly who is also looking at > their annotations to these terms. If no other conflicts arise, we > look forward to making the changes on Dec. 10th. > > Thank you both for your comments. Please let us know if we didn't > address your issues satisfactorily. > > Tanya and David > >>> Val >>> >>> >>> >>> >>> Tanya Berardini wrote: >>> >>>> Dear GO Consortium, >>>> >>>> As part of the 'regulates' project, we have come across a set of terms >>>> in the cell cycle portion of the graph that seem problematic. We are >>>> writing because we know that a lot of previous work has gone into this >>>> part of the graph and want to be sure that our plan makes sense. We >>>> have >>>> two sets of terms similar to these: >>>> >>>> term: regulation of cell cycle (simple term) >>>> def:A cell cycle process that modulates the rate, extent or mode of >>>> the >>>> cell cycle. >>>> >>>> term: regulation of progression through cell cycle (progression term) >>>> def: Any process that modulates the rate or extent of progression >>>> through the cell cycle. >>>> >>>> Our question is how does 'regulation of progression through cell >>>> cycle' >>>> differ from 'regulation of cell cycle'? >>>> >>>> Note that 'cell cycle' itself is defined as "the progression of >>>> ...phases and events ...", implying that regulation of the cell >>>> cycle is regulation of progression through the cycle; the same >>>> holds for the types of cell cycle (i.e. its is_a children). >>>> >>>> cell cycle: The progression of biochemical and morphological phases >>>> and >>>> events that occur in a cell during successive cell replication or >>>> nuclear replication events. Canonically, the cell cycle comprises the >>>> replication and segregation of genetic material followed by the >>>> division >>>> of the cell, but in endocycles or syncytial cells nuclear >>>> replication or >>>> nuclear division may not be followed by cell division. >>>> >>>> If they are indeed describing the same processes, the 'regulation >>>> of %' >>>> and 'regulation of progression of %' terms should be merged. If not, >>>> then we need to create a bona-fide biological process called >>>> 'progression through cell cycle' and we need to differentiate that >>>> from >>>> 'cell cycle' with a really good definition. Currently the progression >>>> terms are only used in conjunction with regulation. >>>> >>>> The way we represent these in the graph is also inconsistent. An >>>> example >>>> follows: >>>> >>>> Case 1: No direct link between the 'regulation of progression through >>>> cell cycle' term and 'cell cycle' term exists. >>>> >>>> regulation of cell cycle >>>> --[i]regulation of progression through cell cycle >>>> >>>> >>>> Case 2: Direct link between 'regulation of progression through meiotic >>>> cell cycle' and 'meiotic cell cycle' exists. >>>> >>>> regulation of meiotic cell cycle >>>> --[i]regulation of progression through meiotic cell cycle >>>> >>>> meiotic cell cycle >>>> --[p]regulation of progression through meiotic cell cycle >>>> >>>> >>>> We propose: >>>> >>>> 1) Merging the 'regulation of progression through' terms >>>> with their simpler parents when they exist. >>>> >>>> 2) Renaming the 'regulation of progression through' terms to their >>>> simpler forms when the simpler parents do not exist since the parent >>>> non-regulates terms are already defined as the progression of... >>>> >>>> 3) Moving 'cell cycle switching, meiotic to mitotic cell cycle' to >>>> become an is_a 'negative regulation of meiotic cell cycle' and an is_a >>>> 'positive regulation of mitotic cell cycle'. >>>> >>>> 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' >>>> to be an is_a 'positive regulation of meiotic cell cycle' and an is_a >>>> 'negative regulation of mitotic cell cycle'. We think that the last >>>> two >>>> terms were why 'regulation of cell cycle' and 'regulation of >>>> progression through cell cycle' were originally created as distinct >>>> terms. However, the movement of these as in 3 and 4 makes more >>>> logical sense since the process they describe stops (negatively >>>> regulates) one type of cell cycle and initiates (positively regulates) >>>> another. >>>> > From val at sanger.ac.uk Mon Dec 10 03:08:40 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Mon, 10 Dec 2007 11:08:40 +0000 Subject: [go] Re: regulation of cell cycle vs. regulation of progression through cell cycle In-Reply-To: <47588E9E.6060805@caltech.edu> References: <474F0EF5.6090002@acoma.stanford.edu> <4758066D.3050508@sanger.ac.uk> <4758847D.8070706@acoma.stanford.edu> <47588E9E.6060805@caltech.edu> Message-ID: <475D1E38.70006@sanger.ac.uk> Hi Tanya,David, I was thinking about this some more and I think we did need the 2 terms regulation of cell cycle and regulation of progression through cell cycle. where regulation of cell cycle included regulation of the 'mode' of cell cycle and the regulators for switching between types of cycle. Regulation of progression only includes the events after 'cell cycle' start (i.e after commitment to the type of cell cycle) and only includes the cyclical events and canonical cell cycle regulators and checkpoints. Otherwise there is no process term that can be used to retreive these cell cycle regulators. Val Kimberly Van Auken wrote: > Hi-- > > In the course of going through our annotations, I've come across cases > that doesn't seem to work for change #4, if I understand > it correctly. > > 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' to be > an is_a 'positive regulation of meiotic cell cycle' and an is_a > 'negative regulation of mitotic cell cycle'. We think that the last > two terms were why 'regulation of cell cycle' and 'regulation of > progression through cell cycle' were originally created as distinct > terms. However, the movement of these as in 3 and 4 makes more logical > sense since the process they describe stops (negatively regulates) one > type of cell cycle and initiates (positively regulates) > another. > > As an example, we have a gene, glp-1, that regulates the decision > between mitosis and meiosis in the germ line. glp-1 could be > annotated to 'germline cell cycle switching, mitotic to meiotic cell > cycle', but its role in this process is as a positive regulator of > the mitotic cell cycle and a negative regulator of the meiotic cell > cycle. This is opposite to what is proposed above. > > One alternative is to make the cell cycle switching terms is_a > children of regulation of mitotic cell cycle and regulation of > meiotic cell cycle, but then we lose the directionality of the > regulation. In that case we'd could additionally annotate to the > respective positive and negative regulation terms that could also be > is_a children of the regulation parent. Or, we could > make positive and negative regulation terms for cell cycle switching > to capture the appropriate directionality. glp-1 would then > be annotated to negative regulation of germline cell cycle switching, > mitotic to meiotic cell cycle. I would also then annotate > glp-1 to positive regulation of cell proliferation, which is not > related to the cell cycle terms in GO, I believe. > > --Kimberly > > > Tanya Berardini wrote: > >> Hi Eurie and Val, >> >> Answers are interspersed below: >> >> Eurie Hong wrote: >> >>> I have a couple of questions - >>> >>> Are the "regulation of cell cycle" and "regulation of progression >>> through cell cycle" going to be specific for just regulating the >>> rate at which the progression through the cell cycle occurs? >> >> >> >> Not just the rate. The standard definition of 'regulation of xxx' is: >> >> Any process that modulates the frequency, rate or extent of process, >> [definition of process]. >> >> Since the cell cycle is defined as the progression... then the >> regulation of the cell cycle would be anything that modulates the >> frequency, rate or extent of the progression. >> >> Then maybe they >> >>> should be renamed "regulation of cell cycle phase" (cell cycle phase >>> is GO:0022403)? >> >> >> >> No, that would be a different term, because there are cell cycle >> phase terms in the ontology (see all children of 'cell cycle >> phase'). So the regulation of a cell cycle phase would describe the >> regulation of one of these, for example, 'regulation of interphase' >> (which doesn't yet exist). >> >>> >>> Or do we need to keep the structure of the regulation terms to mimic >>> how the cell cycle branch is organized? >>> >>> "regulation of cell cycle" - general grouping term for both >>> molecular/cellular events and temporal phasing >>> -- "regulation of cell cycle processes" - grouping term for all the >>> regulation of processes >>> ---- "regulation of cell cycle phase" - specific for going through >>> the temporal phases >> >> >> >> Yes. Our goal is to create regulates terms that don't conflict with >> the structure of the process ontology. Right now, we're not creating >> all of these terms but if and when they are needed, we should be able >> to insert them easily because the structure already exists. >> >>> The mitotic - meiotic switch terms sound ok. As long as there are >>> synonyms to find them - most folks in the field do refer to "entry >>> into meiosis" but there are positive and negative regulators of the >>> process. >> >> >> >> Since we're not proposing changing the terms, synonyms or textual >> definitions but rather their locations in the graph, if there are >> synonyms that are missing, please let us know. >> >> Now, on to Val's comments. >> >> >>> On Dec 6, 2007, at 6:25 AM, Valerie Wood wrote: >>> >> >>>> At first glance, I think that what you propsed is OK. You are >>>> correct that the seperate terms were created to cope with the >>>> switching between mitotic and meiotic cell-cycles, but your >>>> solution of making these positive and negative regulatory terms >>>> respectively seems logically consistant. >>> >>> >> >> Great! We assume this means that our proposed changes 1-4 are ok. >> >>>> >>>> I think however, there is a more fundamental problem in this >>>> portion of the graph in that there is some confusion between the >>>> concurrent use of meiosis to describe 'meiotic division' and >>>> meiosis as a 'developmental stage' >>> >>> >> >> From its current placement in the graph, meiosis is a type of cell >> cycle phase. It is not restricted to simply meiotic division. >> >>>> I'm not sure if the terms created to cope with the switching >>>> between mitotic and meiotic cell-cycles rather refer to a switch >>>> between developmental stage >>>> for example "entry into meiosis" for yeast would include response >>>> to pheromone, and conjugation etc, and gene products annotated to >>>> these terms would not necessarily be considered be a 'cell-cycle ' >>>> genes. >>> >>> >> >> It seems that a problem here is that 'regulation of cell cycle' is_a >> 'cell cycle process.' If we remove this relationship, then >> 'regulation of cell cycle' will only have a regulates relationship >> with 'cell cycle' and will not be a cell cycle process. >> >> If we adopt our proposal and remove this relationship, genes >> annotated to the terms 'cell cycle switching, mitotic to meiotic cell >> cycle' and 'cell cycle switching, meiotic to mitotic cell cycle' will >> be involved in regulation of the cell cycle and will not necessarily >> be annotated to terms that are part_of or is_a children of 'cell cycle.' >> >>>> current child terms of "meiosis" also include >>>> megasporogenesis (synonym megaspore development ) and these terms >>>> do not appear to be referring specifically to meiosis as a cell >>>> cycle process. >>> >>> >> >> Megasporogenesis, despite the name, does not refer to the genesis of >> the megaspore but specifically to the meiosis of the diploid >> megasporocyte to give rise to four haploid megaspores. >> >>>> >>>> This is essentially what I was trying to describe in >>>> SF 1831804 ] yeast meiotic development. >>>> >>>> Even some of the definitions of these terms seem to merge both >>>> concepts into a single term. >>>> >>>> It might make sense to tackle both issues at the same time. I'm not >>>> sure what the solution is.... >>> >>> >> >> While a valid concern, this is not immediately relevant to our >> current project of cleaning up the ontology for implementation of the >> regulates relationship. We will address this issue at a later time. >> >> We are still waiting to hear back from Kimberly who is also looking >> at their annotations to these terms. If no other conflicts arise, we >> look forward to making the changes on Dec. 10th. >> >> Thank you both for your comments. Please let us know if we didn't >> address your issues satisfactorily. >> >> Tanya and David >> >>>> Val >>>> >>>> >>>> >>>> >>>> Tanya Berardini wrote: >>>> >>>>> Dear GO Consortium, >>>>> >>>>> As part of the 'regulates' project, we have come across a set of >>>>> terms >>>>> in the cell cycle portion of the graph that seem problematic. We are >>>>> writing because we know that a lot of previous work has gone into >>>>> this >>>>> part of the graph and want to be sure that our plan makes sense. >>>>> We have >>>>> two sets of terms similar to these: >>>>> >>>>> term: regulation of cell cycle (simple term) >>>>> def:A cell cycle process that modulates the rate, extent or mode >>>>> of the >>>>> cell cycle. >>>>> >>>>> term: regulation of progression through cell cycle (progression term) >>>>> def: Any process that modulates the rate or extent of progression >>>>> through the cell cycle. >>>>> >>>>> Our question is how does 'regulation of progression through cell >>>>> cycle' >>>>> differ from 'regulation of cell cycle'? >>>>> >>>>> Note that 'cell cycle' itself is defined as "the progression of >>>>> ...phases and events ...", implying that regulation of the cell >>>>> cycle is regulation of progression through the cycle; the same >>>>> holds for the types of cell cycle (i.e. its is_a children). >>>>> >>>>> cell cycle: The progression of biochemical and morphological >>>>> phases and >>>>> events that occur in a cell during successive cell replication or >>>>> nuclear replication events. Canonically, the cell cycle comprises the >>>>> replication and segregation of genetic material followed by the >>>>> division >>>>> of the cell, but in endocycles or syncytial cells nuclear >>>>> replication or >>>>> nuclear division may not be followed by cell division. >>>>> >>>>> If they are indeed describing the same processes, the 'regulation >>>>> of %' >>>>> and 'regulation of progression of %' terms should be merged. If not, >>>>> then we need to create a bona-fide biological process called >>>>> 'progression through cell cycle' and we need to differentiate that >>>>> from >>>>> 'cell cycle' with a really good definition. Currently the progression >>>>> terms are only used in conjunction with regulation. >>>>> >>>>> The way we represent these in the graph is also inconsistent. An >>>>> example >>>>> follows: >>>>> >>>>> Case 1: No direct link between the 'regulation of progression through >>>>> cell cycle' term and 'cell cycle' term exists. >>>>> >>>>> regulation of cell cycle >>>>> --[i]regulation of progression through cell cycle >>>>> >>>>> >>>>> Case 2: Direct link between 'regulation of progression through >>>>> meiotic >>>>> cell cycle' and 'meiotic cell cycle' exists. >>>>> >>>>> regulation of meiotic cell cycle >>>>> --[i]regulation of progression through meiotic cell cycle >>>>> >>>>> meiotic cell cycle >>>>> --[p]regulation of progression through meiotic cell cycle >>>>> >>>>> >>>>> We propose: >>>>> >>>>> 1) Merging the 'regulation of progression through' terms >>>>> with their simpler parents when they exist. >>>>> >>>>> 2) Renaming the 'regulation of progression through' terms to their >>>>> simpler forms when the simpler parents do not exist since the parent >>>>> non-regulates terms are already defined as the progression of... >>>>> >>>>> 3) Moving 'cell cycle switching, meiotic to mitotic cell cycle' to >>>>> become an is_a 'negative regulation of meiotic cell cycle' and an >>>>> is_a >>>>> 'positive regulation of mitotic cell cycle'. >>>>> >>>>> 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' >>>>> to be an is_a 'positive regulation of meiotic cell cycle' and an is_a >>>>> 'negative regulation of mitotic cell cycle'. We think that the >>>>> last two >>>>> terms were why 'regulation of cell cycle' and 'regulation of >>>>> progression through cell cycle' were originally created as >>>>> distinct terms. However, the movement of these as in 3 and 4 makes >>>>> more logical sense since the process they describe stops >>>>> (negatively regulates) one type of cell cycle and initiates >>>>> (positively regulates) >>>>> another. >>>>> >> > > > > -- 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 dph at informatics.jax.org Mon Dec 10 06:15:14 2007 From: dph at informatics.jax.org (David Hill) Date: Mon, 10 Dec 2007 09:15:14 -0500 Subject: [go] Re: regulation of cell cycle vs. regulation of progression through cell cycle In-Reply-To: <475D1E38.70006@sanger.ac.uk> References: <474F0EF5.6090002@acoma.stanford.edu> <4758066D.3050508@sanger.ac.uk> <4758847D.8070706@acoma.stanford.edu> <47588E9E.6060805@caltech.edu> <475D1E38.70006@sanger.ac.uk> Message-ID: <475D49F2.7030000@informatics.jax.org> Hi Val, From the current structure of the graph it seems like we will need a term 'regulation of cell cycle phase', which Eurie hinted at in her original comments. The problem with 'regulation of progression' and just 'regulation' is that they mean exactly the same thing since the cycle itself is defined as a progression. Also remember, once the regulates relationship is in place, the regulation terms will not necessarily be is_a or part_of the parents themselves. We are going to have a look at the regulation of the modes of the cell cycle this afternoon. Kimberly had some really good points about these terms with respect to how it happens in worms and gene products do not necessarily act in the ways that they would first seem. David > > Kimberly Van Auken wrote: > >> Hi-- >> >> In the course of going through our annotations, I've come across >> cases that doesn't seem to work for change #4, if I understand >> it correctly. >> >> 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' to be >> an is_a 'positive regulation of meiotic cell cycle' and an is_a >> 'negative regulation of mitotic cell cycle'. We think that the last >> two terms were why 'regulation of cell cycle' and 'regulation of >> progression through cell cycle' were originally created as distinct >> terms. However, the movement of these as in 3 and 4 makes more >> logical sense since the process they describe stops (negatively >> regulates) one type of cell cycle and initiates (positively regulates) >> another. >> >> As an example, we have a gene, glp-1, that regulates the decision >> between mitosis and meiosis in the germ line. glp-1 could be >> annotated to 'germline cell cycle switching, mitotic to meiotic cell >> cycle', but its role in this process is as a positive regulator of >> the mitotic cell cycle and a negative regulator of the meiotic cell >> cycle. This is opposite to what is proposed above. >> >> One alternative is to make the cell cycle switching terms is_a >> children of regulation of mitotic cell cycle and regulation of >> meiotic cell cycle, but then we lose the directionality of the >> regulation. In that case we'd could additionally annotate to the >> respective positive and negative regulation terms that could also be >> is_a children of the regulation parent. Or, we could >> make positive and negative regulation terms for cell cycle switching >> to capture the appropriate directionality. glp-1 would then >> be annotated to negative regulation of germline cell cycle switching, >> mitotic to meiotic cell cycle. I would also then annotate >> glp-1 to positive regulation of cell proliferation, which is not >> related to the cell cycle terms in GO, I believe. >> >> --Kimberly >> >> >> Tanya Berardini wrote: >> >>> Hi Eurie and Val, >>> >>> Answers are interspersed below: >>> >>> Eurie Hong wrote: >>> >>>> I have a couple of questions - >>>> >>>> Are the "regulation of cell cycle" and "regulation of progression >>>> through cell cycle" going to be specific for just regulating the >>>> rate at which the progression through the cell cycle occurs? >>> >>> >>> >>> Not just the rate. The standard definition of 'regulation of xxx' is: >>> >>> Any process that modulates the frequency, rate or extent of process, >>> [definition of process]. >>> >>> Since the cell cycle is defined as the progression... then the >>> regulation of the cell cycle would be anything that modulates the >>> frequency, rate or extent of the progression. >>> >>> Then maybe they >>> >>>> should be renamed "regulation of cell cycle phase" (cell cycle >>>> phase is GO:0022403)? >>> >>> >>> >>> No, that would be a different term, because there are cell cycle >>> phase terms in the ontology (see all children of 'cell cycle >>> phase'). So the regulation of a cell cycle phase would describe the >>> regulation of one of these, for example, 'regulation of interphase' >>> (which doesn't yet exist). >>> >>>> >>>> Or do we need to keep the structure of the regulation terms to >>>> mimic how the cell cycle branch is organized? >>>> >>>> "regulation of cell cycle" - general grouping term for both >>>> molecular/cellular events and temporal phasing >>>> -- "regulation of cell cycle processes" - grouping term for all the >>>> regulation of processes >>>> ---- "regulation of cell cycle phase" - specific for going through >>>> the temporal phases >>> >>> >>> >>> Yes. Our goal is to create regulates terms that don't conflict with >>> the structure of the process ontology. Right now, we're not >>> creating all of these terms but if and when they are needed, we >>> should be able to insert them easily because the structure already >>> exists. >>> >>>> The mitotic - meiotic switch terms sound ok. As long as there are >>>> synonyms to find them - most folks in the field do refer to "entry >>>> into meiosis" but there are positive and negative regulators of the >>>> process. >>> >>> >>> >>> Since we're not proposing changing the terms, synonyms or textual >>> definitions but rather their locations in the graph, if there are >>> synonyms that are missing, please let us know. >>> >>> Now, on to Val's comments. >>> >>> >>>> On Dec 6, 2007, at 6:25 AM, Valerie Wood wrote: >>>> >>> >>>>> At first glance, I think that what you propsed is OK. You are >>>>> correct that the seperate terms were created to cope with the >>>>> switching between mitotic and meiotic cell-cycles, but your >>>>> solution of making these positive and negative regulatory terms >>>>> respectively seems logically consistant. >>>> >>>> >>> >>> Great! We assume this means that our proposed changes 1-4 are ok. >>> >>>>> >>>>> I think however, there is a more fundamental problem in this >>>>> portion of the graph in that there is some confusion between the >>>>> concurrent use of meiosis to describe 'meiotic division' and >>>>> meiosis as a 'developmental stage' >>>> >>>> >>> >>> From its current placement in the graph, meiosis is a type of cell >>> cycle phase. It is not restricted to simply meiotic division. >>> >>>>> I'm not sure if the terms created to cope with the switching >>>>> between mitotic and meiotic cell-cycles rather refer to a switch >>>>> between developmental stage >>>>> for example "entry into meiosis" for yeast would include response >>>>> to pheromone, and conjugation etc, and gene products annotated to >>>>> these terms would not necessarily be considered be a 'cell-cycle ' >>>>> genes. >>>> >>>> >>> >>> It seems that a problem here is that 'regulation of cell cycle' is_a >>> 'cell cycle process.' If we remove this relationship, then >>> 'regulation of cell cycle' will only have a regulates relationship >>> with 'cell cycle' and will not be a cell cycle process. >>> >>> If we adopt our proposal and remove this relationship, genes >>> annotated to the terms 'cell cycle switching, mitotic to meiotic >>> cell cycle' and 'cell cycle switching, meiotic to mitotic cell >>> cycle' will be involved in regulation of the cell cycle and will not >>> necessarily be annotated to terms that are part_of or is_a children >>> of 'cell cycle.' >>> >>>>> current child terms of "meiosis" also include >>>>> megasporogenesis (synonym megaspore development ) and these terms >>>>> do not appear to be referring specifically to meiosis as a cell >>>>> cycle process. >>>> >>>> >>> >>> Megasporogenesis, despite the name, does not refer to the genesis of >>> the megaspore but specifically to the meiosis of the diploid >>> megasporocyte to give rise to four haploid megaspores. >>> >>>>> >>>>> This is essentially what I was trying to describe in >>>>> SF 1831804 ] yeast meiotic development. >>>>> >>>>> Even some of the definitions of these terms seem to merge both >>>>> concepts into a single term. >>>>> >>>>> It might make sense to tackle both issues at the same time. I'm >>>>> not sure what the solution is.... >>>> >>>> >>> >>> While a valid concern, this is not immediately relevant to our >>> current project of cleaning up the ontology for implementation of >>> the regulates relationship. We will address this issue at a later >>> time. >>> >>> We are still waiting to hear back from Kimberly who is also looking >>> at their annotations to these terms. If no other conflicts arise, >>> we look forward to making the changes on Dec. 10th. >>> >>> Thank you both for your comments. Please let us know if we didn't >>> address your issues satisfactorily. >>> >>> Tanya and David >>> >>>>> Val >>>>> >>>>> >>>>> >>>>> >>>>> Tanya Berardini wrote: >>>>> >>>>>> Dear GO Consortium, >>>>>> >>>>>> As part of the 'regulates' project, we have come across a set of >>>>>> terms >>>>>> in the cell cycle portion of the graph that seem problematic. We are >>>>>> writing because we know that a lot of previous work has gone into >>>>>> this >>>>>> part of the graph and want to be sure that our plan makes sense. >>>>>> We have >>>>>> two sets of terms similar to these: >>>>>> >>>>>> term: regulation of cell cycle (simple term) >>>>>> def:A cell cycle process that modulates the rate, extent or mode >>>>>> of the >>>>>> cell cycle. >>>>>> >>>>>> term: regulation of progression through cell cycle (progression >>>>>> term) >>>>>> def: Any process that modulates the rate or extent of progression >>>>>> through the cell cycle. >>>>>> >>>>>> Our question is how does 'regulation of progression through cell >>>>>> cycle' >>>>>> differ from 'regulation of cell cycle'? >>>>>> >>>>>> Note that 'cell cycle' itself is defined as "the progression of >>>>>> ...phases and events ...", implying that regulation of the cell >>>>>> cycle is regulation of progression through the cycle; the same >>>>>> holds for the types of cell cycle (i.e. its is_a children). >>>>>> >>>>>> cell cycle: The progression of biochemical and morphological >>>>>> phases and >>>>>> events that occur in a cell during successive cell replication or >>>>>> nuclear replication events. Canonically, the cell cycle comprises >>>>>> the >>>>>> replication and segregation of genetic material followed by the >>>>>> division >>>>>> of the cell, but in endocycles or syncytial cells nuclear >>>>>> replication or >>>>>> nuclear division may not be followed by cell division. >>>>>> >>>>>> If they are indeed describing the same processes, the 'regulation >>>>>> of %' >>>>>> and 'regulation of progression of %' terms should be merged. If not, >>>>>> then we need to create a bona-fide biological process called >>>>>> 'progression through cell cycle' and we need to differentiate >>>>>> that from >>>>>> 'cell cycle' with a really good definition. Currently the >>>>>> progression >>>>>> terms are only used in conjunction with regulation. >>>>>> >>>>>> The way we represent these in the graph is also inconsistent. An >>>>>> example >>>>>> follows: >>>>>> >>>>>> Case 1: No direct link between the 'regulation of progression >>>>>> through >>>>>> cell cycle' term and 'cell cycle' term exists. >>>>>> >>>>>> regulation of cell cycle >>>>>> --[i]regulation of progression through cell cycle >>>>>> >>>>>> >>>>>> Case 2: Direct link between 'regulation of progression through >>>>>> meiotic >>>>>> cell cycle' and 'meiotic cell cycle' exists. >>>>>> >>>>>> regulation of meiotic cell cycle >>>>>> --[i]regulation of progression through meiotic cell cycle >>>>>> >>>>>> meiotic cell cycle >>>>>> --[p]regulation of progression through meiotic cell cycle >>>>>> >>>>>> >>>>>> We propose: >>>>>> >>>>>> 1) Merging the 'regulation of progression through' terms >>>>>> with their simpler parents when they exist. >>>>>> >>>>>> 2) Renaming the 'regulation of progression through' terms to their >>>>>> simpler forms when the simpler parents do not exist since the parent >>>>>> non-regulates terms are already defined as the progression of... >>>>>> >>>>>> 3) Moving 'cell cycle switching, meiotic to mitotic cell cycle' to >>>>>> become an is_a 'negative regulation of meiotic cell cycle' and an >>>>>> is_a >>>>>> 'positive regulation of mitotic cell cycle'. >>>>>> >>>>>> 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle' >>>>>> to be an is_a 'positive regulation of meiotic cell cycle' and an >>>>>> is_a >>>>>> 'negative regulation of mitotic cell cycle'. We think that the >>>>>> last two >>>>>> terms were why 'regulation of cell cycle' and 'regulation of >>>>>> progression through cell cycle' were originally created as >>>>>> distinct terms. However, the movement of these as in 3 and 4 >>>>>> makes more logical sense since the process they describe stops >>>>>> (negatively regulates) one type of cell cycle and initiates >>>>>> (positively regulates) >>>>>> another. >>>>>> >>> >> >> >> >> > > > From pgaudet at northwestern.edu Mon Dec 10 07:15:58 2007 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Mon, 10 Dec 2007 10:15:58 -0500 Subject: [go] Introducing Siddhartha Basu, dictyBase programer Message-ID: <475D582E.8020701@northwestern.edu> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20071210/fbf10579/attachment.html From jblake at informatics.jax.org Mon Dec 10 07:42:17 2007 From: jblake at informatics.jax.org (Judith Blake) Date: Mon, 10 Dec 2007 10:42:17 -0500 Subject: [go] Introducing Siddhartha Basu, dictyBase programer In-Reply-To: <475D582E.8020701@northwestern.edu> References: <475D582E.8020701@northwestern.edu> Message-ID: <475D5E59.3050602@informatics.jax.org> Welcome Siddhartha, I hope we can meet you at some upcoming GO meeting. Best, Judy Pascale Gaudet wrote: > Dear Colleagues, > > Please join dictyBase in welcoming Dr. Siddhartha Basu as the newest > member of our team. Siddhartha will be involved in many of the > dictyBase ontology-related projects, including the reference genome > software development, our GO curation tool and extending our > implementation of Phenote. > > Siddhartha hails from Kolkata city in India where he received his > Bachelors degree in Chemistry, Master's degeree in Biochemistry, and > Ph.D. in Molecular Microbiology. Siddhartha researched Vibrio cholerae > and its bacteriophages for his Ph.D. work. His post-doctoral work at > SUNY Stony Brook introduced him to computer programming where he > established a biological database called MiGenes, a curated > mitochondrial protein database. We are thrilled to have Siddhartha on > our team and look forward to his contributions to dictyBase. > > The dictyBase Team > http://dictybase.org > ~~~~~~~~~~~~~~~~~~~ > Pascale Gaudet, PhD > Scientific Curator, dictyBase > Northwestern University, Chicago, IL > pgaudet at northwestern.edu > www.dictybase.org > ~~~~~~~~~~~~~~~~~~ From vanauken at caltech.edu Wed Dec 12 14:07:27 2007 From: vanauken at caltech.edu (Kimberly Van Auken) Date: Wed, 12 Dec 2007 14:07:27 -0800 Subject: [go] Re: Fwd: GO and Reverse Engineering of Gene Regulatory Networks In-Reply-To: References: <200712121535.lBCFZpdA009142@fafner.Stanford.EDU> Message-ID: <47605B9F.2090307@caltech.edu> Hi-- This query came to the go-help mailing list this morning. Is there anyone with expertise in reverse engineering of gene regulatory networks who would be willing to comment? Thanks, Kimberly > Date: Wed, 12 Dec 2007 07:35:50 -0800 (PST) > Message-Id: <200712121535.HAA29053 at bread.Stanford.EDU > > > To: f.b.yavari at gmail.com > Subject: GO Help query (from website) > From: noreply at genome.stanford.edu > > contactName: Fatemeh > contactEmail: f.b.yavari at gmail.com > contactText: I wonder if GO annotations are extracted from known > information about genes, I mean if we have GO information for a gene > doesn't it mean that we know its relationships with other gens, its > function, the pathways that it is included in and...? and so when we > have all these information about a gene, we can't use these > information in reverse engineering of gene regulatory networks,right? > I mean we shouldn't use GO information in modeling gene regultory > networks, because they are extracted from exactly what are searching > for, right? > If GOs are used as input information and known biological knowledge > for reverse engineering of GRN, it is lik that we use a special input > to get it in output! Isn't it? > > From rhee at acoma.Stanford.EDU Thu Dec 13 12:30:19 2007 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Thu, 13 Dec 2007 12:30:19 -0800 Subject: [go] a perspective on use and misuse of GO annotations Message-ID: <4761965B.8000309@acoma.stanford.edu> Hi GO consortium, I have been commissioned to write a perspective on the use and misuse of GO annotations by Nature Review Genetics and have collaborated intensively with Sorin Draghichi, Val Wood, and Kara Dolinski on the writing of this manuscript in the past year. We have a close to a final version that we would love to get some feedback from you. It's about 6500 words and needs to be shortened to about 3500-4500 words. In addition to acknowledging the whole GO consortium, we'll acknowledge anyone who provide feedback on the ms. Chris Mungall has already provided some good feedback and it would be great to get more views from others in the group. Please send me your edits/comments by next Thurs, December 20th. I will try to submit it right before X-mas. Thanks and happy holidays, 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Figures-and-Tables-v3.doc Type: application/doc Size: 140800 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20071213/b1371a38/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: NRG-review8.doc Type: application/doc Size: 164352 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/go/attachments/20071213/b1371a38/attachment-0001.bin From suzi at berkeleybop.org Thu Dec 13 15:46:41 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Thu, 13 Dec 2007 15:46:41 -0800 Subject: [go] a perspective on use and misuse of GO annotations In-Reply-To: <4761965B.8000309@acoma.stanford.edu> References: <4761965B.8000309@acoma.stanford.edu> Message-ID: Is this the much anticipated response to the GO-error-rate paper that we were discussing last summer? I hope so. In either case I'll provide some comments. -S On Dec 13, 2007, at 12:30 PM, Sue Rhee wrote: > Hi GO consortium, > > I have been commissioned to write a perspective on the use and > misuse of > GO annotations by Nature Review Genetics and have collaborated > intensively with Sorin Draghichi, Val Wood, and Kara Dolinski on the > writing of this manuscript in the past year. We have a close to a > final > version that we would love to get some feedback from you. It's about > 6500 words and needs to be shortened to about 3500-4500 words. In > addition to acknowledging the whole GO consortium, we'll acknowledge > anyone who provide feedback on the ms. Chris Mungall has already > provided some good feedback and it would be great to get more views > from > others in the group. > > Please send me your edits/comments by next Thurs, December 20th. I > will > try to submit it right before X-mas. > > Thanks and happy holidays, > 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 rama at genome.Stanford.EDU Fri Dec 14 10:31:42 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Fri, 14 Dec 2007 10:31:42 -0800 Subject: [go] left hand menu on GO website Message-ID: I noticed that the left hand side menu has been changed (has bright blue color as background and items are not grouped). May be there was an email/proposal about this change and I missed it. I could be in the minority, but I find it very hard to navigate with all the items in one long list. If we want the Menu open all the time, can we indent the items that belong to a certain group? Thanks, rama From adiehl at informatics.jax.org Fri Dec 14 10:41:27 2007 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Fri, 14 Dec 2007 18:41:27 +0000 Subject: [go] left hand menu on GO website In-Reply-To: References: Message-ID: <4762CE57.5080803@informatics.jax.org> I like having the menu open all the time, as I always have to open it immediately anyway. But I agree with Rama that indentation of items within groups would be helpful here. Thanks, Alex Rama Balakrishnan wrote: > I noticed that the left hand side menu has been changed (has bright > blue color as background and items are not grouped). > May be there was an email/proposal about this change and I missed it. > I could be in the minority, but I find it very hard to navigate with > all the items in one long list. If we want the Menu open all the time, > can we indent the items that belong to a certain group? > > Thanks, > > rama > -- 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 jdeegan at ebi.ac.uk Fri Dec 14 12:22:11 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Fri, 14 Dec 2007 20:22:11 +0000 Subject: [go] left hand menu on GO website In-Reply-To: <4762CE57.5080803@informatics.jax.org> References: <4762CE57.5080803@informatics.jax.org> Message-ID: <4762E5F3.50401@ebi.ac.uk> Hi, I was assuming that it was an accident and that it would revert when Amelia noticed it. Jen Alexander Diehl wrote: > I like having the menu open all the time, as I always have to open it > immediately anyway. But I agree with Rama that indentation of items > within groups would be helpful here. > > Thanks, > > Alex > > > Rama Balakrishnan wrote: > >> I noticed that the left hand side menu has been changed (has bright >> blue color as background and items are not grouped). >> May be there was an email/proposal about this change and I missed it. >> I could be in the minority, but I find it very hard to navigate with >> all the items in one long list. If we want the Menu open all the time, >> can we indent the items that belong to a certain group? >> >> Thanks, >> >> rama >> > > -- Jennifer Deegan nee Clark EMBL-European Bioinformatics Institute Gene Ontology Consortium From midori at ebi.ac.uk Sat Dec 15 04:25:18 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Sat, 15 Dec 2007 12:25:18 +0000 (GMT) Subject: [go] left hand menu on GO website In-Reply-To: <4762E5F3.50401@ebi.ac.uk> References: <4762CE57.5080803@informatics.jax.org> <4762E5F3.50401@ebi.ac.uk> Message-ID: It seems to be back to normal now, so I suspect Jen's right. m On Fri, 14 Dec 2007, Jennifer Deegan (nee Clark) wrote: > Hi, > > I was assuming that it was an accident and that it would revert when Amelia > noticed it. > > Jen > > Alexander Diehl wrote: >> I like having the menu open all the time, as I always have to open it >> immediately anyway. But I agree with Rama that indentation of items within >> groups would be helpful here. >> >> Thanks, >> >> Alex >> >> >> Rama Balakrishnan wrote: >> >>> I noticed that the left hand side menu has been changed (has bright blue >>> color as background and items are not grouped). >>> May be there was an email/proposal about this change and I missed it. I >>> could be in the minority, but I find it very hard to navigate with all the >>> items in one long list. If we want the Menu open all the time, can we >>> indent the items that belong to a certain group? >>> >>> Thanks, >>> >>> rama >>> >> >> > > > From erika at cribi.unipd.it Sun Dec 16 00:51:04 2007 From: erika at cribi.unipd.it (erika at cribi.unipd.it) Date: Sun, 16 Dec 2007 09:51:04 +0100 (CET) Subject: [go] left hand menu on GO website In-Reply-To: <4762E5F3.50401@ebi.ac.uk> References: <4762CE57.5080803@informatics.jax.org> <4762E5F3.50401@ebi.ac.uk> Message-ID: <1197795064.4764e6f8914ec@webmail.cribi.unipd.it> Hello, I saw this change but I though it was my browser that mixed up everything ;-) Indentation would be helpful. Bye Erika Scrive "Jennifer Deegan (nee Clark)" : > Hi, > > I was assuming that it was an accident and that it would revert when > Amelia noticed it. > > Jen > > Alexander Diehl wrote: > > I like having the menu open all the time, as I always have to open it > > > immediately anyway. But I agree with Rama that indentation of items > > > within groups would be helpful here. > > > > Thanks, > > > > Alex > > > > > > Rama Balakrishnan wrote: > > > >> I noticed that the left hand side menu has been changed (has bright > > >> blue color as background and items are not grouped). > >> May be there was an email/proposal about this change and I missed it. > > >> I could be in the minority, but I find it very hard to navigate with > > >> all the items in one long list. If we want the Menu open all the > time, > >> can we indent the items that belong to a certain group? > >> > >> Thanks, > >> > >> rama > >> > > > > > > > -- > Jennifer Deegan nee Clark > EMBL-European Bioinformatics Institute > Gene Ontology Consortium > Erika Feltrin, PhD Student Bioinformatics Lab c/o CRIBI Padua University via U. Bassi, 58/b 35131 erika at cribi.unipd.it phone + 39.049.827.6165 fax + 39.049.827.6159 Chi sa ridere e\\\' padrone del mondo From jblake at informatics.jax.org Sun Dec 16 17:15:58 2007 From: jblake at informatics.jax.org (Judith Blake) Date: Sun, 16 Dec 2007 20:15:58 -0500 Subject: [go] left hand menu on GO website In-Reply-To: References: <4762CE57.5080803@informatics.jax.org> <4762E5F3.50401@ebi.ac.uk> Message-ID: <4765CDCE.90104@informatics.jax.org> I am glad to see this reset. I think it is cleaner/better this way. judy Midori Harris wrote: > It seems to be back to normal now, so I suspect Jen's right. > m > > On Fri, 14 Dec 2007, Jennifer Deegan (nee Clark) wrote: > >> Hi, >> >> I was assuming that it was an accident and that it would revert when >> Amelia noticed it. >> >> Jen >> >> Alexander Diehl wrote: >>> I like having the menu open all the time, as I always have to open >>> it immediately anyway. But I agree with Rama that indentation of >>> items within groups would be helpful here. >>> >>> Thanks, >>> >>> Alex >>> >>> >>> Rama Balakrishnan wrote: >>> >>>> I noticed that the left hand side menu has been changed (has bright >>>> blue color as background and items are not grouped). >>>> May be there was an email/proposal about this change and I missed >>>> it. I could be in the minority, but I find it very hard to >>>> navigate with all the items in one long list. If we want the Menu >>>> open all the time, can we indent the items that belong to a certain >>>> group? >>>> >>>> Thanks, >>>> >>>> rama >>>> >>> >>> >> >> >> From sjcarbon at berkeleybop.org Mon Dec 17 15:34:46 2007 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Mon, 17 Dec 2007 15:34:46 -0800 Subject: [go] AmiGO beta announcement Message-ID: <1197934486.16007.64.camel@accordion> GO Listers, The next version of AmiGO is in the final stages and we felt that now would be a good time to open it up to those outside the working group. For those of you interested in trying and testing out the new version of AmiGO, the main testing server is located at: http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi Questions, comments, and bug reports should be directed to the Web Presence Working Group: web-presence-working-group at genome.stanford.edu In addition, the testing server at Berkeley is refreshed several times a day from CVS and changes made in response to bug reports can be seen as they are patched: http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi Cheers, -Seth From adiehl at informatics.jax.org Mon Dec 17 15:49:15 2007 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Mon, 17 Dec 2007 23:49:15 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: <1197934486.16007.64.camel@accordion> References: <1197934486.16007.64.camel@accordion> Message-ID: <47670AFB.4080408@informatics.jax.org> On this view: http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628&session_id=1458amigo1197932357 the first line of the listed associations reads Qualifier: NOT, Term: GO:0051092 : activation of NF-kappaB transcription factor, link: 63 gene products, which looks like there are 63 NOT annotations to GO:0051092, but in fact clicking on the 63 gene products link shows there are only 2 gene products annotated to this term with a NOT annotation and 61 that are just straight annotations without a qualifier. Thus the original view linked to above misrepresents the situation. I think the NOT annotations should be summarized on a separate line from the non-qualified annotations; ditto for annotations with other qualifiers. By the way I like the beta a lot so far despite this little problem. Thanks, Alex Seth Carbon wrote: > GO Listers, > > The next version of AmiGO is in the final stages and we felt that now > would be a good time to open it up to those outside the working group. > > For those of you interested in trying and testing out the new version of > AmiGO, the main testing server is located at: > > http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi > > Questions, comments, and bug reports should be directed to the Web > Presence Working Group: > > > > web-presence-working-group at genome.stanford.edu > > In addition, the testing server at Berkeley is refreshed several times a > day from CVS and changes made in response to bug reports can be seen as > they are patched: > > http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi > > Cheers, > > -Seth > > > -- 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 sjcarbon at berkeleybop.org Mon Dec 17 15:54:27 2007 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Mon, 17 Dec 2007 15:54:27 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: <1197934486.16007.64.camel@accordion> References: <1197934486.16007.64.camel@accordion> Message-ID: <1197935667.16007.73.camel@accordion> GO Listers, New features that you may want to look for and/or test in the AmiGO beta: *) Term Enrichment tool (accessible from the button/link at the top of every page). *) GO Slimmer tool (also accessible from the button/link at the top of every page). *) New Advanced Search page. *) Searches are now more intelligent (will work harder to get the answers that you probably want). *) Searches are now sorted by relevance. *) The pie charts have been replaced with bar graphs. *) Improved download options (more formats more places). *) Improved user interface (all over the place). Cheers, -Seth On Mon, 2007-12-17 at 15:34 -0800, Seth Carbon wrote: > GO Listers, > > The next version of AmiGO is in the final stages and we felt that now > would be a good time to open it up to those outside the working group. > > For those of you interested in trying and testing out the new version of > AmiGO, the main testing server is located at: > > http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi > > Questions, comments, and bug reports should be directed to the Web > Presence Working Group: > > > > web-presence-working-group at genome.stanford.edu > > In addition, the testing server at Berkeley is refreshed several times a > day from CVS and changes made in response to bug reports can be seen as > they are patched: > > http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi > > Cheers, > > -Seth > > > From rhee at acoma.Stanford.EDU Mon Dec 17 15:57:40 2007 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 17 Dec 2007 15:57:40 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: <1197935667.16007.73.camel@accordion> References: <1197934486.16007.64.camel@accordion> <1197935667.16007.73.camel@accordion> Message-ID: <47670CF4.8070402@acoma.stanford.edu> Fantabulous! I will take it for a spin shortly. So awesome. Sue Seth Carbon wrote: > GO Listers, > > New features that you may want to look for and/or test in the AmiGO > beta: > > *) Term Enrichment tool (accessible from the button/link at the top of > every page). > > *) GO Slimmer tool (also accessible from the button/link at the top of > every page). > > *) New Advanced Search page. > > *) Searches are now more intelligent (will work harder to get the > answers that you probably want). > > *) Searches are now sorted by relevance. > > *) The pie charts have been replaced with bar graphs. > > *) Improved download options (more formats more places). > > *) Improved user interface (all over the place). > > Cheers, > > -Seth > > > On Mon, 2007-12-17 at 15:34 -0800, Seth Carbon wrote: > >> GO Listers, >> >> The next version of AmiGO is in the final stages and we felt that now >> would be a good time to open it up to those outside the working group. >> >> For those of you interested in trying and testing out the new version of >> AmiGO, the main testing server is located at: >> >> http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi >> >> Questions, comments, and bug reports should be directed to the Web >> Presence Working Group: >> >> >> >> web-presence-working-group at genome.stanford.edu >> >> In addition, the testing server at Berkeley is refreshed several times a >> day from CVS and changes made in response to bug reports can be seen as >> they are patched: >> >> http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi >> >> Cheers, >> >> -Seth >> >> >> >> -- 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 jblake at informatics.jax.org Mon Dec 17 17:43:43 2007 From: jblake at informatics.jax.org (Judith Blake) Date: Mon, 17 Dec 2007 20:43:43 -0500 Subject: [go] AmiGO beta announcement In-Reply-To: <1197935667.16007.73.camel@accordion> References: <1197934486.16007.64.camel@accordion> <1197935667.16007.73.camel@accordion> Message-ID: <476725CF.1000802@informatics.jax.org> Seth, all AmiGOers, This is great. Here are some of the many things I like 1. simplicity to start, nice colors 2. ability to select output form 3. ability to customize GOgraphs 4. tips to tell you where you are going 5. ability to download gene details by association files or XML, more download options 6. I like the new header bar and the links to tools 7. I like that the Evidence Codes are spelled out on the Advanced Search page. 8. on the gene product search results page, I like the feature 'perform an action with selected gene products' 9. I like this phrase 'in gene association (tab-delimited) file format' Here are some questions... 1. when getting gene product results from search on home page, how are these ordered? I don't know how the relevance is determined. For example, if I search on Bmp4, I get 5 gene products in the results. In the fourth one, the match is within a synonym term. Also, the 5th row (human) includes both name and synonyms. I happen to know this, but the results are confusing. I think this is something GOAis working on. 2. The term enrichment is presented well, but I find the 'slimmer' too confusing. I actually wonder if we should think of another name. 'slimmer' is maybe too much GOgroup lingo. I wonder if others think so too. I followed through on the 'more info' and found that the docs aren't quite done here. Maybe this is a place where a 4 click demo might work (very short). 3. When I clicked on 'search' in the dark blue bar, I really expected to go to the Home page. but it went to 'advanced search' instead. I then recognized that the simple search was under the dark blue bar. As a creature of habit, though, I started looking around for a link to the Home page...didn't find it. Hummmmm, disconcerting, but probably ok. 4. When I mouse over the 'help' page, it says it 'help guide for this page', but when I click, that is not what I get. I get a general help page for AmiGO, with nothing about the Advanced Search page. AND FASTA files....what are all those identifiers doing in the DE line? a prosite ID is not equivalent to the protein. ditto ditto on the InterPro domains. Anyway. Looks great. Lots of improvements. Great advance. thanks for all the work on this everyone Judy Seth Carbon wrote: > GO Listers, > > New features that you may want to look for and/or test in the AmiGO > beta: > > *) Term Enrichment tool (accessible from the button/link at the top of > every page). > > *) GO Slimmer tool (also accessible from the button/link at the top of > every page). > > *) New Advanced Search page. > > *) Searches are now more intelligent (will work harder to get the > answers that you probably want). > > *) Searches are now sorted by relevance. > > *) The pie charts have been replaced with bar graphs. > > *) Improved download options (more formats more places). > > *) Improved user interface (all over the place). > > Cheers, > > -Seth > > > On Mon, 2007-12-17 at 15:34 -0800, Seth Carbon wrote: > >> GO Listers, >> >> The next version of AmiGO is in the final stages and we felt that now >> would be a good time to open it up to those outside the working group. >> >> For those of you interested in trying and testing out the new version of >> AmiGO, the main testing server is located at: >> >> http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi >> >> Questions, comments, and bug reports should be directed to the Web >> Presence Working Group: >> >> >> >> web-presence-working-group at genome.stanford.edu >> >> In addition, the testing server at Berkeley is refreshed several times a >> day from CVS and changes made in response to bug reports can be seen as >> they are patched: >> >> http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi >> >> Cheers, >> >> -Seth >> >> >> >> > > From val at sanger.ac.uk Tue Dec 18 01:37:21 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Tue, 18 Dec 2007 09:37:21 UT Subject: [go] AmiGO beta announcement Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20071218/980e3370/attachment.pl From ma11 at gen.cam.ac.uk Tue Dec 18 02:06:41 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Tue, 18 Dec 2007 10:06:41 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: References: Message-ID: <632B84D4-4B7E-4793-862C-09B293EE13DD@gen.cam.ac.uk> Seth and the Amigo working group This looks great, and so fast ! I agree with Val that we should really encourage people to use full id's, ie. GO:0000123, and not 0000123 or 123. I guess the Help page has not yet been redone, as this directs to the old Help. I have not tested the GO Slimmer (I don't mind the name as much as some !) but does it allow the user to keep his slimmed ontology (ie without any instance data) ? When you look at a graphical view why is "all" repeated in the root box ? Does this come from: [Term] id: all name: all namespace: universal def: "This term is the most general term possible" [] Why are some, but not all, GO slims hyperlinked ? eg from the page for "metallochaperone activity" there are two subsets (slims?, why use two words?), and only the pir one is linked: * goslim_pir * gosubset_prok (ah, is it just gosubset_prok that is never linked ?) I see treeview is limited to 500 lines. Is this for the server's benefit or the user's ? If the latter could there be a "view all" option ? Looking at the PIR slim in Treeview I got this when invited to try "compact view of the graph": * fatal message AmiGO could not find any terms to perform your query upon. Please go back and select one or more terms. and this when invited to see the old GO format: $all ; all %biological_process ; GO:0008150 %reproduction ; GO:0000003 Indeed the same terms in OBO or RDF format. Something wrong here. Thanks all for the magnificant work. Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20071218/5c1ac33b/attachment.html From Mary_Dolan at umit.maine.edu Tue Dec 18 07:28:43 2007 From: Mary_Dolan at umit.maine.edu (Mary Dolan) Date: Tue, 18 Dec 2007 10:28:43 -0500 Subject: [go] AmiGO beta announcement In-Reply-To: <1197934486.16007.64.camel@accordion> References: <1197934486.16007.64.camel@accordion> Message-ID: Seth Carbon on Monday, December 17, 2007 at 6:34 PM -0500 wrote: >http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi Hi, Seth. I think it all looks terrific! The pages are clear and inviting. I like the way AmiGO seems more a part of GO then before but still a self-contained tool. Great work! A few things... 1. GO Term Enrichment a. Does not say which evidence codes will be used in the analysis. b. Will users know what is meant by: "The default settings are sane." 2. Blurbs are reversed for: http://wiki.geneontology.org/index.php/AmiGO_Manual:_Slimmer http://wiki.geneontology.org/index.php/AmiGO_Manual:_Term_Enrichment 3. Using "Browse" I got a software error filtering for source "MGI" and species "Mus musculus" and view "compact": "cannot filter by both speciesdb and taxid at /share/goweb/www-data/html/dev/go-perl/GO/Model/Root.pm line 65" Maybe that restriction should be made more explicit --or forbidden. 4. So I removed the species restriction, it worked fine. But then gave an error clicking on the bar graph icon for the Bar Chart Viewer: "Unfortunately AmiGO cannot create a bar chart with the current filter settings." Again, maybe that restriction should be made more explicit --or forbidden (i.e. no bar chart icon if the user has set filters). Mary Mary E. Dolan, Ph.D. ************************************ Mouse Genome Informatics Consortium, The Jackson Laboratory mdolan at informatics.jax.org (207)288-6439 Research Faculty, NCGIA Department of Spatial Information Science and Engineering, University of Maine Boardman Hall 329 University of Maine Orono, Maine 04469 fax: 207.581.2206 mary_dolan at umit.maine.edu ************************************ From sjcarbon at berkeleybop.org Tue Dec 18 10:34:17 2007 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Tue, 18 Dec 2007 10:34:17 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: References: Message-ID: <1198002857.25203.8.camel@accordion> On Tue, 2007-12-18 at 09:37 +0000, Valerie Wood wrote: > Hi Seth, > > Just a small thing: > > For the 'slimmer' we have: > Input your GO slim terms > Enter GO ids (such as GO:0005764, 0005764, and 5764), term names, or synonyms. > > Didn't we decide to only allow complete GO IDs, and to remove synonyms? The GO IDs is not such a problem, but synonymns could be synonyms of more than one term. This has been fixed on the toy server. Cheers, -Seth > Val > > Seth Carbon wrote: > > GO Listers, > > > > The next version of AmiGO is in the final stages and we felt that now > > would be a good time to open it up to those outside the working group. > > > > For those of you interested in trying and testing out the new version of > > AmiGO, the main testing server is located at: > > > > http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi > > > > Questions, comments, and bug reports should be directed to the Web > > Presence Working Group: > > > > > > > > web-presence-working-group at genome.stanford.edu > > > > In addition, the testing server at Berkeley is refreshed several times a > > day from CVS and changes made in response to bug reports can be seen as > > they are patched: > > > > http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi > > > > Cheers, > > > > -Seth > > > > > > > > > From sjcarbon at berkeleybop.org Tue Dec 18 11:46:59 2007 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Tue, 18 Dec 2007 11:46:59 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: <632B84D4-4B7E-4793-862C-09B293EE13DD@gen.cam.ac.uk> References: <632B84D4-4B7E-4793-862C-09B293EE13DD@gen.cam.ac.uk> Message-ID: <1198007219.25203.19.camel@accordion> On Tue, 2007-12-18 at 10:06 +0000, Michael Ashburner wrote: > I guess the Help page has not yet been redone, as this directs to the > old Help. We're currently working to get the old help into the new AmiGO manual on the public wiki. > I have not tested the GO Slimmer (I don't mind the name as much as > some !) but does it allow > the user to keep his slimmed ontology (ie without any instance data) ? Not at this time, but features like this are slated for future releases. > When you look at a graphical view why is "all" repeated in the root > box ? Does this come from: > [Term] > id: all > name: all > namespace: universal > def: "This term is the most general term possible" [] Yes it is; this will be removed from the ontology. > I see treeview is limited to 500 lines. Is this for the server's > benefit or the user's ? If the latter could there be a "view all" > option ? This is a limitation of the current software being used to render the treeview. Again, this will be slated for future versions. Amelia and I will look into the issues with the slims. Cheers, -Seth From sjcarbon at berkeleybop.org Tue Dec 18 12:16:41 2007 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Tue, 18 Dec 2007 12:16:41 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: <632B84D4-4B7E-4793-862C-09B293EE13DD@gen.cam.ac.uk> References: <632B84D4-4B7E-4793-862C-09B293EE13DD@gen.cam.ac.uk> Message-ID: <1198009001.25203.26.camel@accordion> On Tue, 2007-12-18 at 10:06 +0000, Michael Ashburner wrote: > Why are some, but not all, GO slims hyperlinked ? The short answer is that there is a limit on the size of subsets that can be reasonably manipulated in AmiGO at this point. In the case of the what is in the database so far, gosubset_prok falls outside this limit and is not linkable (so gosubset_prok is the odd one out). > Looking at the PIR slim in Treeview I got this when invited to try > "compact view of the graph": > * fatal message AmiGO could not find any terms to perform your > query upon. Please go back and select one or more terms. We have fixed this bug. Thanks for the feedback! Cheers, -Seth From aji at ebi.ac.uk Tue Dec 18 12:33:57 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Tue, 18 Dec 2007 20:33:57 +0000 (GMT) Subject: [go] AmiGO beta announcement In-Reply-To: <47670AFB.4080408@informatics.jax.org> Message-ID: Hi Alex, >http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628&session_id=1458amigo1197932357 > >the first line of the listed associations reads Qualifier: NOT, Term: >GO:0051092 : activation of NF-kappaB transcription factor, link: 63 gene >products, [snip] I guess this has the potential to be confusing. Currently the gene product counts displayed by AmiGO do not include the 'not' annotations, but presumably users may still want to know the number of gene products associated with a certain term even if for a given gene product, the term association has the operator 'not'. One possibility might be to swap the order of the columns so that the qualifier / operator column appears next to the evidence code column instead. Do other people find this confusing, and if so, would swapping the columns help? Thanks, Amelia. -- Amelia Ireland GO Editorial Office, European Bioinformatics Institute, UK. Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From mgiglio at som.umaryland.edu Tue Dec 18 12:45:51 2007 From: mgiglio at som.umaryland.edu (Gwinn Giglio, Michelle) Date: Tue, 18 Dec 2007 15:45:51 -0500 Subject: [go] AmiGO beta announcement In-Reply-To: <1198009001.25203.26.camel@accordion> Message-ID: Hi, I'm not sure the gosubset_prok should be listed as a slim - its not really a slim - its just the whole GO with euk specific terms subtracted out. It's really nothing like a slim. I have a prok GO slim that I built recently. At some point I wasn't sure how/where to submit it and I asked about it and then discussion ensued and then I got distracted with other things. Now I can't remember if I brought it with me from TIGR but I should be able to get it. Michelle On 12/18/07 3:16 PM, "Seth Carbon" wrote: > > On Tue, 2007-12-18 at 10:06 +0000, Michael Ashburner wrote: >> Why are some, but not all, GO slims hyperlinked ? > > The short answer is that there is a limit on the size of subsets that > can be reasonably manipulated in AmiGO at this point. In the case of the > what is in the database so far, gosubset_prok falls outside this limit > and is not linkable (so gosubset_prok is the odd one out). > >> Looking at the PIR slim in Treeview I got this when invited to try >> "compact view of the graph": >> * fatal message AmiGO could not find any terms to perform your >> query upon. Please go back and select one or more terms. > > We have fixed this bug. > > Thanks for the feedback! > > Cheers, > > -Seth > > From adiehl at informatics.jax.org Tue Dec 18 13:25:42 2007 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Tue, 18 Dec 2007 21:25:42 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: References: Message-ID: <47683AD6.80705@informatics.jax.org> Amelia, When I had more time today, I compared the display to the current version of Amigo and figured out my confusion. The "63 gene products" link is of course tied only to the term, not to the combination of qualifier and term. In the old version, a similar system was used, but the link was called "view associations" which seems more directly tied to the term itself and not the combination of the qualifier and the term. On the other hand I like seeing immediately the number of gene products associated with the term, and as you point out switching the order of the columns might make this more clear. The number too, is a bit confusing, as it does not seem to correspond to the number of genes listed when you click the link, but perhaps I am missing another subtle feature here as well. It is also true that in a logical sense NOT annotations are really different from regular annotations and when we make a NOT annotation, we are specifically saying that a given gene product is not associated with a given function, process, or component. Thus NOT annotations should ideally be excluded from the count of gene products associated with a term, just as when people do term enrichment analysis or GO slim analysis, we recommend they exclude the NOT annotations. But it comes down to trying to display the greatest amount of information in the least amount of GUI space, and in most cases the new version of Amigo succeeds admirably at this task. I'll stop fussing now and see if anyone else cares to comment here, Thanks, Alex Amelia Ireland wrote: > Hi Alex, > > >> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >> >> the first line of the listed associations reads Qualifier: NOT, Term: >> GO:0051092 : activation of NF-kappaB transcription factor, link: 63 gene >> products, >> > [snip] > > I guess this has the potential to be confusing. Currently the gene product > counts displayed by AmiGO do not include the 'not' annotations, but > presumably users may still want to know the number of gene products > associated with a certain term even if for a given gene product, the > term association has the operator 'not'. > > One possibility might be to swap the order of the columns so that the > qualifier / operator column appears next to the evidence code column > instead. > > Do other people find this confusing, and if so, would swapping the columns > help? > > Thanks, > Amelia. > > -- 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 ma11 at gen.cam.ac.uk Tue Dec 18 14:08:54 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Tue, 18 Dec 2007 22:08:54 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: References: Message-ID: Yes I agree Michelle, it is a subset, NOT a slim. Michael On 18 Dec 2007, at 20:45, Gwinn Giglio, Michelle wrote: > > > Hi, > > I'm not sure the gosubset_prok should be listed as a slim - its not > really a > slim - its just the whole GO with euk specific terms subtracted > out. It's > really nothing like a slim. > > I have a prok GO slim that I built recently. At some point I > wasn't sure > how/where to submit it and I asked about it and then discussion > ensued and > then I got distracted with other things. Now I can't remember if I > brought > it with me from TIGR but I should be able to get it. > > Michelle > > > > On 12/18/07 3:16 PM, "Seth Carbon" wrote: > >> >> On Tue, 2007-12-18 at 10:06 +0000, Michael Ashburner wrote: >>> Why are some, but not all, GO slims hyperlinked ? >> >> The short answer is that there is a limit on the size of subsets that >> can be reasonably manipulated in AmiGO at this point. In the case >> of the >> what is in the database so far, gosubset_prok falls outside this >> limit >> and is not linkable (so gosubset_prok is the odd one out). >> >>> Looking at the PIR slim in Treeview I got this when invited to try >>> "compact view of the graph": >>> * fatal message AmiGO could not find any terms to perform >>> your >>> query upon. Please go back and select one or more terms. >> >> We have fixed this bug. >> >> Thanks for the feedback! >> >> Cheers, >> >> -Seth >> >> > From sjcarbon at berkeleybop.org Tue Dec 18 14:18:27 2007 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Tue, 18 Dec 2007 14:18:27 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: References: Message-ID: <1198016307.25203.30.camel@accordion> On Tue, 2007-12-18 at 22:08 +0000, Michael Ashburner wrote: > Yes I agree Michelle, it is a subset, NOT a slim. These have been removed in CVS. Cheers, -Seth > Michael > On 18 Dec 2007, at 20:45, Gwinn Giglio, Michelle wrote: > > > > > > > Hi, > > > > I'm not sure the gosubset_prok should be listed as a slim - its not > > really a > > slim - its just the whole GO with euk specific terms subtracted > > out. It's > > really nothing like a slim. > > > > I have a prok GO slim that I built recently. At some point I > > wasn't sure > > how/where to submit it and I asked about it and then discussion > > ensued and > > then I got distracted with other things. Now I can't remember if I > > brought > > it with me from TIGR but I should be able to get it. > > > > Michelle > > > > > > > > On 12/18/07 3:16 PM, "Seth Carbon" wrote: > > > >> > >> On Tue, 2007-12-18 at 10:06 +0000, Michael Ashburner wrote: > >>> Why are some, but not all, GO slims hyperlinked ? > >> > >> The short answer is that there is a limit on the size of subsets that > >> can be reasonably manipulated in AmiGO at this point. In the case > >> of the > >> what is in the database so far, gosubset_prok falls outside this > >> limit > >> and is not linkable (so gosubset_prok is the odd one out). > >> > >>> Looking at the PIR slim in Treeview I got this when invited to try > >>> "compact view of the graph": > >>> * fatal message AmiGO could not find any terms to perform > >>> your > >>> query upon. Please go back and select one or more terms. > >> > >> We have fixed this bug. > >> > >> Thanks for the feedback! > >> > >> Cheers, > >> > >> -Seth > >> > >> > > > > From aji at ebi.ac.uk Tue Dec 18 14:57:40 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Tue, 18 Dec 2007 22:57:40 +0000 (GMT) Subject: [go] AmiGO beta announcement In-Reply-To: Message-ID: Hi Mary, >3. Using "Browse" I got a software error filtering for source "MGI" and species "Mus musculus" and view "compact": >"cannot filter by both speciesdb and taxid at /share/goweb/www-data/html/dev/go-perl/GO/Model/Root.pm line 65" >Maybe that restriction should be made more explicit --or forbidden. OK, I'll see if I can find a way around this problem - or at least make the error page look a bit prettier. >4. So I removed the species restriction, it worked fine. But then gave an error clicking on the bar graph icon for the Bar Chart Viewer: >"Unfortunately AmiGO cannot create a bar chart with the current filter settings." >Again, maybe that restriction should be made more explicit --or forbidden (i.e. no bar chart icon if the user has set filters). I've changed that to allow bar charts to be constructed with those filter settings. Thanks for the feedback! Amelia. -- Amelia Ireland GO Editorial Office, European Bioinformatics Institute, UK. Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From sjcarbon at berkeleybop.org Tue Dec 18 14:58:06 2007 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Tue, 18 Dec 2007 14:58:06 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: References: <1197934486.16007.64.camel@accordion> Message-ID: <1198018686.25203.47.camel@accordion> On Tue, 2007-12-18 at 10:28 -0500, Mary Dolan wrote: > 1. GO Term Enrichment > a. Does not say which evidence codes will be used in the analysis. > b. Will users know what is meant by: "The default settings are sane." I have changed the wording and added a bit of text to the manual. We are still working on NDs and the roots. > 2. Blurbs are reversed for: > http://wiki.geneontology.org/index.php/AmiGO_Manual:_Slimmer > http://wiki.geneontology.org/index.php/AmiGO_Manual:_Term_Enrichment Thanks! Fixed! Hopefully, we can start fleshing out the manual soon. Cheers, -Seth From jdeegan at ebi.ac.uk Wed Dec 19 02:30:46 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Wed, 19 Dec 2007 10:30:46 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: <1198018686.25203.47.camel@accordion> References: <1197934486.16007.64.camel@accordion> <1198018686.25203.47.camel@accordion> Message-ID: <4768F2D6.5080903@ebi.ac.uk> Hi, The new setup looks great. :-) What is the largest number of annotations that can be handled by the GO Slimmer? We had a question about this on gohelp today. If you could put a little note about this on the GO slimmer page then that might help future users. Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From dph at informatics.jax.org Wed Dec 19 05:10:07 2007 From: dph at informatics.jax.org (David Hill) Date: Wed, 19 Dec 2007 08:10:07 -0500 Subject: [go] AmiGO beta announcement In-Reply-To: <1197935667.16007.73.camel@accordion> References: <1197934486.16007.64.camel@accordion> <1197935667.16007.73.camel@accordion> Message-ID: <4769182F.6030808@informatics.jax.org> Seth (and others who contributed), This is really great! It's clean and straightforward. I am still playing around with it but like what I'm seeing. I tried the term enrichment tool. It should provide which set of annotations it is using and which version of the GO it is using, maybe right at the top of the results. At some point we may want an option to incorporate the ortholog annotations into this, but I think that's down the road. Did we ever decide to incorporate your term suggestion tool into AMIGO? I can't remember where that was supposed to go. I'll let you know if I have more comments as I do more. David Seth Carbon wrote: > GO Listers, > > New features that you may want to look for and/or test in the AmiGO > beta: > > *) Term Enrichment tool (accessible from the button/link at the top of > every page). > > *) GO Slimmer tool (also accessible from the button/link at the top of > every page). > > *) New Advanced Search page. > > *) Searches are now more intelligent (will work harder to get the > answers that you probably want). > > *) Searches are now sorted by relevance. > > *) The pie charts have been replaced with bar graphs. > > *) Improved download options (more formats more places). > > *) Improved user interface (all over the place). > > Cheers, > > -Seth > > > On Mon, 2007-12-17 at 15:34 -0800, Seth Carbon wrote: > >> GO Listers, >> >> The next version of AmiGO is in the final stages and we felt that now >> would be a good time to open it up to those outside the working group. >> >> For those of you interested in trying and testing out the new version of >> AmiGO, the main testing server is located at: >> >> http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi >> >> Questions, comments, and bug reports should be directed to the Web >> Presence Working Group: >> >> >> >> web-presence-working-group at genome.stanford.edu >> >> In addition, the testing server at Berkeley is refreshed several times a >> day from CVS and changes made in response to bug reports can be seen as >> they are patched: >> >> http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi >> >> Cheers, >> >> -Seth >> >> >> >> > > From jdeegan at ebi.ac.uk Wed Dec 19 07:31:31 2007 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Wed, 19 Dec 2007 15:31:31 +0000 Subject: [go] Alert: Proposal to obsolete GO:0000504: proteasome regulatory particle (sensu Bacteria) term that does not impact existing annotation Message-ID: <47693953.8020201@ebi.ac.uk> The proposal has been made to obsolete GO:0000504: proteasome regulatory particle (sensu Bacteria). There exist today no annotations to this term. The term is used in no mappings. The reasons for this proposal are that there is no ubiquitin in bacteria and they don?t have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase (PAN). The discussion is to be found at http://gocwiki.geneontology.org/index.php/Meeting_Notes_3#proteasome The full set of edits to remove sensu from the proteasome terms have been made already and are being held in a branch file at http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/proteasome.obo If you have any comments on the changes we would be very pleased to hear them. UNLESS OBJECTIONS ARE RECEIVED BY 7th January WE WILL ASSUME THAT YOU AGREE TO THIS CHANGE. -- Jennifer Deegan nee Clark EMBL-European Bioinformatics Institute Gene Ontology Consortium From eurie at genome.Stanford.EDU Wed Dec 19 09:19:24 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Wed, 19 Dec 2007 09:19:24 -0800 Subject: [go] Alert: Proposal to obsolete GO:0050517: inositol hexakisphosphate kinase activity that impacts existing annotations Message-ID: <25CA40BC-A339-4424-B13F-3A53AD01D16F@genome.stanford.edu> The proposal has been made to obsolete GO:0050517: inositol hexakisphosphate kinase activity. There exists annotations to this term as follows (data from AmiGO): * S. pombe GeneDB: 2 objects * Flybase: 1 object * RGD: 1 object * UniProt: 2 objects * SGD: 1 object The term is used in the following mappings: ec2go:EC:2.7.4.21 > GO:inositol hexakisphosphate kinase activity ; GO: 0050517 metacyc2go:MetaCyc:2.7.1.152-RXN > GO:inositol hexakisphosphate kinase activity ; GO:0050517 The reason for this proposal is that this activity is currently defined as catalyzing two reactions based on a gene product. The reactions listed in the definition can be catalyzed independently by other gene products. The SourceForge discussion is to be found on https://sourceforge.net/tracker/? func=detail&atid=440764&aid=1849773&group_id=36855 UNLESS OBJECTIONS ARE RECEIVED BY 7th January WE WILL ASSUME THAT YOU AGREE TO THIS CHANGE. From eurie at genome.Stanford.EDU Wed Dec 19 09:19:59 2007 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Wed, 19 Dec 2007 09:19:59 -0800 Subject: [go] Alert: Proposal to obsolete GO:0050516: inositol polyphosphate multikinase activity that impacts existing annotations Message-ID: The proposal has been made to obsolete GO:0050516: inositol polyphosphate multikinase activity. There exists annotations to this term as follows (data from AmiGO): * SGD: 1 object * TAIR: 2 objects * Flybase: 1 object * MGI: 1 object * RGD: 1 object The term is used in the following mappings: ec2go:EC:2.7.1.151 > GO:inositol polyphosphate multikinase activity ; GO:0050516 metacyc2go:MetaCyc:2.7.1.151-RXN > GO:inositol polyphosphate multikinase activity ; GO:0050516 The reason for this proposal is that this activity is currently defined as catalyzing two sequential reactions based on a gene product. However, "inositol polyphosphate multikinase activity" in some organisms can catalyze additional reactions. In addition, the reactions listed in the definition can be catalyzed independently by other gene products. The SourceForge discussion is to be found on https://sourceforge.net/tracker/? func=detail&atid=440764&aid=1849773&group_id=36855 UNLESS OBJECTIONS ARE RECEIVED BY 7th January WE WILL ASSUME THAT YOU AGREE TO THIS CHANGE. From hitz at genome.Stanford.EDU Wed Dec 19 08:45:57 2007 From: hitz at genome.Stanford.EDU (Ben Hitz) Date: Wed, 19 Dec 2007 08:45:57 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: <4768F2D6.5080903@ebi.ac.uk> References: <1197934486.16007.64.camel@accordion> <1198018686.25203.47.camel@accordion> <4768F2D6.5080903@ebi.ac.uk> Message-ID: Probably, we don't know yet. It would be great if someone can test this (at what number does it go "unresponsive" ) on the goweb-dev server, so we can cap it before we go to production. Ben On Dec 19, 2007, at 2:30 AM, Jennifer Deegan (nee Clark) wrote: > Hi, > > The new setup looks great. :-) > > What is the largest number of annotations that can be handled by > the GO Slimmer? We had a question about this on gohelp today. If > you could put a little note about this on the GO slimmer page then > that might help future users. > > > Thanks, > > Jen > > -- > Jennifer Deegan (nee Clark) > EMBL-European Bioinformatics Institute > Gene Ontology Consortium -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu From hitz at genome.Stanford.EDU Wed Dec 19 09:59:40 2007 From: hitz at genome.Stanford.EDU (Benjamin Hitz) Date: Wed, 19 Dec 2007 09:59:40 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: <4769182F.6030808@informatics.jax.org> References: <1197934486.16007.64.camel@accordion> <1197935667.16007.73.camel@accordion> <4769182F.6030808@informatics.jax.org> Message-ID: The Last updated date at the footer of every page shows when the database (terms, associations, and sequences) was loaded. I agree it could be more obvious. Ben > Seth (and others who contributed), > > This is really great! It's clean and straightforward. I am still > playing around with it but like what I'm seeing. I tried the term > enrichment tool. It should provide which set of annotations it is > using and which version of the GO it is using, maybe right at the > top of the results. At some point we may want an option to > incorporate the ortholog annotations into this, but I think that's > down the road. > > Did we ever decide to incorporate your term suggestion tool into > AMIGO? I can't remember where that was supposed to go. > > I'll let you know if I have more comments as I do more. > > David > > Seth Carbon wrote: >> GO Listers, >> >> New features that you may want to look for and/or test in the AmiGO >> beta: >> >> *) Term Enrichment tool (accessible from the button/link at the >> top of >> every page). >> >> *) GO Slimmer tool (also accessible from the button/link at the >> top of >> every page). >> >> *) New Advanced Search page. >> >> *) Searches are now more intelligent (will work harder to get the >> answers that you probably want). >> >> *) Searches are now sorted by relevance. >> >> *) The pie charts have been replaced with bar graphs. >> >> *) Improved download options (more formats more places). >> >> *) Improved user interface (all over the place). >> >> Cheers, >> >> -Seth >> >> >> On Mon, 2007-12-17 at 15:34 -0800, Seth Carbon wrote: >> >>> GO Listers, >>> >>> The next version of AmiGO is in the final stages and we felt that >>> now >>> would be a good time to open it up to those outside the working >>> group. >>> >>> For those of you interested in trying and testing out the new >>> version of >>> AmiGO, the main testing server is located at: >>> >>> http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi >>> >>> Questions, comments, and bug reports should be directed to the Web >>> Presence Working Group: >>> >>> >>> >>> web-presence-working-group at genome.stanford.edu >>> >>> In addition, the testing server at Berkeley is refreshed several >>> times a >>> day from CVS and changes made in response to bug reports can be >>> seen as >>> they are patched: >>> >>> http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi >>> >>> Cheers, >>> >>> -Seth >>> >>> >>> >>> >> >> -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu From val at sanger.ac.uk Wed Dec 19 11:29:06 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 19 Dec 2007 19:29:06 UT Subject: [go] AmiGO beta announcement Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/go/attachments/20071219/0ba9a51a/attachment.pl From rhee at acoma.Stanford.EDU Wed Dec 19 23:35:44 2007 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Wed, 19 Dec 2007 23:35:44 -0800 Subject: [go] total genes/gene products annotated versus genome size Message-ID: <476A1B50.3040802@acoma.stanford.edu> Dear GO consortium, It looks like different GOC members are submitting annotations to different objects (genes, proteins, transcripts) and the total number of the same objects in the genome is not included in the association files. Also, some databases are submitting 'genes' but it looks like they are more like transcripts (e.g. TAIR). Therefore, it is difficult for me (or anyone else) to generate a simple table as follows. Michael suggested that I use genes rather than gene products for this table, but I am having trouble doing this by querying the GO database. If the organism(s) that you are submitting annotation files are included in the following table, would you kindly send me tthe following three numbers? 1. total number of genes (including protein-coding, RNA and pseudogenes) in the genome as of October 2007 2. total number of genes annotated with GO as of October 2007 3. total number of genes annotated with evidence codes IDA, IMP, IGI, IPI, IEP as of October 2007 Thanks much, Sue species (NCBI taxon ID) experi-mental anno-tations total anno-tations % expt anno-tations annotated gene products total gene products^a % annotated^b % known in genome^c baker?s yeast (4932) 23993 36746 65.3% 6476 7137 90.7% 59.2% fission yeast (4896) 12343 33385 37.0% 5243 5463 96.0% 35.5% fruit fly (7227) 14148 20303 69.7% 10581 30971 34.2% 23.8% worm (6239) 27472 68594 40.1% 12534 28866 43.4% 17.4% Candida albicans (5476) 3413 5326 64.1% 1262 6344 19.9% 12.7% arabidopsis (3702) 14060 103850 13.5% 34683 42929 80.8% 10.9% mouse (10090) 28540 133743 21.3% 18052 35466 50.9% 10.9% human^d (9606) 12437 166419 7.5% 33760 37,106 91.0% 6.8% slime mold (44689) 2691 30299 8.9% 4328 6729 64.3% 5.7% Pseudomonas aeruginosa PAO1 (208964) 1123 7377 15.2% 1519 5670 26.8% 4.1% rat^d (10116) 12986 135246 9.6% 11606 37,106 31.3% 3.0% zebrafish (7955) 4204 70340 6.0% 13194 27532 47.9% 2.9% Plasmodium falciparum (5833) 196 12026 1.6% 3165 5595 56.6% 0.9% Trypanosoma brucei (5691) 438 19006 2.3% 3921 10966 35.8% 0.8% rice (39947) 265 49582 0.5% 37548 58587 64.1% 0.3% cow^d (9913) 278 85951 0.3% 22727 42836 53.1% 0.2% chicken^d (9031) 179 55498 0.3% 16067 33566 47.9% 0.2% -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/go/attachments/20071219/69f64524/attachment.html From aji at ebi.ac.uk Thu Dec 20 04:56:04 2007 From: aji at ebi.ac.uk (Amelia Ireland) Date: Thu, 20 Dec 2007 12:56:04 +0000 (GMT) Subject: [go] AmiGO beta announcement In-Reply-To: <4769182F.6030808@informatics.jax.org> Message-ID: Back in Gotham City, David Hill wrote: >Seth (and others who contributed), Seth did the term enrichment and mapper, I worked on improving the search and the core AmiGO functionality, and the Web Presence Working Group provided key feedback to help guide things in the right direction! Ben and Chris were also instrumental in getting things working behind the scenes at Stanford and in the database respectively. >It should provide which set of annotations it is using and which >version of the GO it is using, maybe right at the top of the results. For general AmiGO stuff, the DB version is at the bottom of the page, as Ben noted. I don't know whether includ