From dhowe at cs.uoregon.edu Wed Aug 1 15:59:14 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Wed, 01 Aug 2007 15:59:14 -0700 Subject: [annotation] cilium movement vs.ciliary motility Message-ID: <46B11042.7050802@cs.uoregon.edu> I want to annotate that a gene product is involved in the process of moving cilia. GO has the term 'ciliary or flagellar motility', but this term appears to pertain to organismal locomotion resulting from movement of these structures rather than movement of the structures themselves. Anyone have any thoughts about that? Maybe a new term is needed, though the motion of the cilia and flagella is pretty fundamental. Hard to believe it isn't in the GO somewhere.. -Doug From midori at ebi.ac.uk Wed Aug 1 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 2 Aug 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200708020500.l72506d1432316@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070802/c2b9354b/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070802/c2b9354b/attachment.pl From dph at informatics.jax.org Thu Aug 2 03:48:47 2007 From: dph at informatics.jax.org (David Hill) Date: Thu, 02 Aug 2007 06:48:47 -0400 Subject: [annotation] cilium movement vs.ciliary motility In-Reply-To: <46B11042.7050802@cs.uoregon.edu> References: <46B11042.7050802@cs.uoregon.edu> Message-ID: <46B1B68F.4090500@informatics.jax.org> I think you are correct that these terms describe the cell's motility. I think that this term could have 2 is_a children called ciliary motility and flagellar motility and then in turn these would have parts that describe the movement of an individual cilium or flagellum. These children would also include processes for things like control of coordination and direction. Note also that the current term does not include a stationary cell such as a ciliated epithelial cell since it has a 'localization of cell' parent. So, in this case perhaps we should have a genric term called 'cilium movement' and a specific child for 'cilium movement involved in ciliary motlity'. What do you think Doug? David Doug howe wrote: > I want to annotate that a gene product is involved in the process of > moving cilia. GO has the term 'ciliary or flagellar motility', but > this term appears to pertain to organismal locomotion resulting from > movement of these structures rather than movement of the structures > themselves. Anyone have any thoughts about that? Maybe a new term is > needed, though the motion of the cilia and flagella is pretty > fundamental. Hard to believe it isn't in the GO somewhere.. > > -Doug From dhowe at cs.uoregon.edu Thu Aug 2 08:29:08 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Thu, 02 Aug 2007 08:29:08 -0700 Subject: [annotation] cilium movement vs.ciliary motility In-Reply-To: <46B1B68F.4090500@informatics.jax.org> References: <46B11042.7050802@cs.uoregon.edu> <46B1B68F.4090500@informatics.jax.org> Message-ID: <46B1F844.7010003@cs.uoregon.edu> I think you and Peter hit the nail on the head. I'll start a new SF item to describe cilium and flagellum movement. -Doug David Hill wrote: > I think you are correct that these terms describe the cell's motility. > I think that this term could have 2 is_a children called ciliary > motility and flagellar motility and then in turn these would have > parts that describe the movement of an individual cilium or flagellum. > These children would also include processes for things like control of > coordination and direction. Note also that the current term does not > include a stationary cell such as a ciliated epithelial cell since it > has a 'localization of cell' parent. So, in this case perhaps we > should have a genric term called 'cilium movement' and a specific > child for 'cilium movement involved in ciliary motlity'. What do you > think Doug? > > David > > Doug howe wrote: >> I want to annotate that a gene product is involved in the process of >> moving cilia. GO has the term 'ciliary or flagellar motility', but >> this term appears to pertain to organismal locomotion resulting from >> movement of these structures rather than movement of the structures >> themselves. Anyone have any thoughts about that? Maybe a new term >> is needed, though the motion of the cilia and flagella is pretty >> fundamental. Hard to believe it isn't in the GO somewhere.. >> >> -Doug > From midori at ebi.ac.uk Fri Aug 3 22:00:07 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 4 Aug 2007 05:00:07 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200708040500.l74507K1521521@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070804/bde4ec3f/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070804/bde4ec3f/attachment.pl From midori at ebi.ac.uk Fri Aug 10 22:00:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 11 Aug 2007 05:00:06 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200708110500.l7B506n1343089@mozart.ebi.ac.uk> An HTML attachment was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070823/2fb96f4b/attachment.pl From vanauken at caltech.edu Fri Aug 24 15:07:55 2007 From: vanauken at caltech.edu (Kimberly Van Auken) Date: Fri, 24 Aug 2007 15:07:55 -0700 Subject: [annotation] Question about Isoform Annotation Message-ID: <46CF56BB.9090105@caltech.edu> Hi-- I'm trying to decide the best way to annotate information about the C. elegans GABA receptor. In C. elegans, functional GABA receptors are formed from one or more protein subunits encoded by the same genomic locus, unc-49. To test functionality, the authors of the paper expressed subunits separately and then together and measured the dose-response to, and response to continuous application of, GABA. One subunit has receptor activity on its own, one does not, and expression of both results in a response distinct from that of the first on its own. To summarize: Subunit B: responds Subunit C: doesn't respond Subunits B and C: respond with distinct profile If this was just one isoform, I would annotate the protein to the appropriate receptor activity terms using the IDA evidence code. But is there any way to annotate this complexity using IDA? I can certainly annotate to the B isoform, but I don't want to make the same annotation to the C isoform. One way I can think to capture the complexity would be to annotate to both B and C, but include the other isoform in the WITH column for one B annotation and the only C annotation. Is the WITH column completely off-limits for IDA annotations? Any thoughts on this would be much appreciated! Thanks, Kimberly From dhowe at cs.uoregon.edu Fri Aug 24 15:17:25 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Fri, 24 Aug 2007 15:17:25 -0700 Subject: [annotation] Question about Isoform Annotation In-Reply-To: <46CF56BB.9090105@caltech.edu> References: <46CF56BB.9090105@caltech.edu> Message-ID: <46CF58F5.7000403@cs.uoregon.edu> Sounds like a possible IDA function annotation on Subunit B and a 'contributes_to' function annotation by IGI on subunit C?? -Doug Kimberly Van Auken wrote: > Hi-- > > I'm trying to decide the best way to annotate information about the C. > elegans GABA receptor. > > In C. elegans, functional GABA receptors are formed from one or more > protein subunits encoded > by the same genomic locus, unc-49. > > To test functionality, the authors of the paper expressed subunits > separately and then together > and measured the dose-response to, and response to continuous > application of, GABA. One subunit > has receptor activity on its own, one does not, and expression of both > results in a response distinct > from that of the first on its own. To summarize: > > Subunit B: responds > > Subunit C: doesn't respond > > Subunits B and C: respond with distinct profile > > > If this was just one isoform, I would annotate the protein to the > appropriate receptor activity terms > using the IDA evidence code. But is there any way to annotate this > complexity using IDA? > > I can certainly annotate to the B isoform, but I don't want to make > the same annotation to the C isoform. > > One way I can think to capture the complexity would be to annotate to > both B and C, but include the > other isoform in the WITH column for one B annotation and the only C > annotation. > > Is the WITH column completely off-limits for IDA annotations? > > Any thoughts on this would be much appreciated! > > Thanks, > Kimberly > > > > From vanauken at caltech.edu Fri Aug 24 15:55:39 2007 From: vanauken at caltech.edu (Kimberly Van Auken) Date: Fri, 24 Aug 2007 15:55:39 -0700 Subject: [annotation] Question about Isoform Annotation In-Reply-To: <46CF58F5.7000403@cs.uoregon.edu> References: <46CF56BB.9090105@caltech.edu> <46CF58F5.7000403@cs.uoregon.edu> Message-ID: <46CF61EB.2030000@caltech.edu> Thanks, Doug. I had thought about that, but neither of the gene products is mutant and so I didn't know if IGI was appropriate. Perhaps Subunit C could get a contributes_to qualifier for an IDA annotation and then I could annotate each of the subunits to the CC term receptor complex to fulfill the contributes_to requirement that: All gene products annotated using contributes_to must also be annotated to a cellular component term representing the complex that possesses the activity. --Kimberly Doug howe wrote: > Sounds like a possible IDA function annotation on Subunit B and a > 'contributes_to' function annotation by IGI on subunit C?? > -Doug > > > Kimberly Van Auken wrote: > >> Hi-- >> >> I'm trying to decide the best way to annotate information about the >> C. elegans GABA receptor. >> >> In C. elegans, functional GABA receptors are formed from one or more >> protein subunits encoded >> by the same genomic locus, unc-49. >> >> To test functionality, the authors of the paper expressed subunits >> separately and then together >> and measured the dose-response to, and response to continuous >> application of, GABA. One subunit >> has receptor activity on its own, one does not, and expression of >> both results in a response distinct >> from that of the first on its own. To summarize: >> >> Subunit B: responds >> >> Subunit C: doesn't respond >> >> Subunits B and C: respond with distinct profile >> >> >> If this was just one isoform, I would annotate the protein to the >> appropriate receptor activity terms >> using the IDA evidence code. But is there any way to annotate this >> complexity using IDA? >> >> I can certainly annotate to the B isoform, but I don't want to make >> the same annotation to the C isoform. >> >> One way I can think to capture the complexity would be to annotate to >> both B and C, but include the >> other isoform in the WITH column for one B annotation and the only C >> annotation. >> >> Is the WITH column completely off-limits for IDA annotations? >> >> Any thoughts on this would be much appreciated! >> >> Thanks, >> Kimberly >> >> >> >> > From dhowe at cs.uoregon.edu Fri Aug 24 16:22:55 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Fri, 24 Aug 2007 16:22:55 -0700 Subject: [annotation] Question about Isoform Annotation In-Reply-To: <46CF61EB.2030000@caltech.edu> References: <46CF56BB.9090105@caltech.edu> <46CF58F5.7000403@cs.uoregon.edu> <46CF61EB.2030000@caltech.edu> Message-ID: <46CF684F.8030209@cs.uoregon.edu> Though it is a direct assay, you can only detect it's role in the GABA receptor activity when you introduce both subunit b and subunit c, so it still seems like an IGI to me, though I could see how you might go down either road. Something like this perhaps: Subunit b: 'GABA receptor activity' IDA <--b has activity by itself 'GABA receptor activity' IGI with gene ID for subunit c <--b has altered activity when c is present Subunit c: contributes_to 'GABA receptor activity' IGI with gene ID for subunit b <--c doesn't have activity by itself 'receptor complex' IGI with gene ID for subunit b -Doug Kimberly Van Auken wrote: > Thanks, Doug. > > I had thought about that, but neither of the gene products is mutant > and so I didn't > know if IGI was appropriate. > > Perhaps Subunit C could get a contributes_to qualifier for an IDA > annotation and > then I could annotate each of the subunits to the CC term receptor > complex to fulfill > the contributes_to requirement that: > > All gene products annotated using contributes_to must also be > annotated to a cellular > component term representing the complex that possesses the activity. > > > --Kimberly > > > Doug howe wrote: > >> Sounds like a possible IDA function annotation on Subunit B and a >> 'contributes_to' function annotation by IGI on subunit C?? >> -Doug >> >> >> Kimberly Van Auken wrote: >> >>> Hi-- >>> >>> I'm trying to decide the best way to annotate information about the >>> C. elegans GABA receptor. >>> >>> In C. elegans, functional GABA receptors are formed from one or more >>> protein subunits encoded >>> by the same genomic locus, unc-49. >>> >>> To test functionality, the authors of the paper expressed subunits >>> separately and then together >>> and measured the dose-response to, and response to continuous >>> application of, GABA. One subunit >>> has receptor activity on its own, one does not, and expression of >>> both results in a response distinct >>> from that of the first on its own. To summarize: >>> >>> Subunit B: responds >>> >>> Subunit C: doesn't respond >>> >>> Subunits B and C: respond with distinct profile >>> >>> >>> If this was just one isoform, I would annotate the protein to the >>> appropriate receptor activity terms >>> using the IDA evidence code. But is there any way to annotate this >>> complexity using IDA? >>> >>> I can certainly annotate to the B isoform, but I don't want to make >>> the same annotation to the C isoform. >>> >>> One way I can think to capture the complexity would be to annotate >>> to both B and C, but include the >>> other isoform in the WITH column for one B annotation and the only C >>> annotation. >>> >>> Is the WITH column completely off-limits for IDA annotations? >>> >>> Any thoughts on this would be much appreciated! >>> >>> Thanks, >>> Kimberly >>> >>> >>> >>> >> > From kchris at genome.Stanford.EDU Fri Aug 24 16:35:24 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Fri, 24 Aug 2007 16:35:24 -0700 (PDT) Subject: [annotation] Question about Isoform Annotation In-Reply-To: <46CF684F.8030209@cs.uoregon.edu> References: <46CF56BB.9090105@caltech.edu> <46CF58F5.7000403@cs.uoregon.edu> <46CF61EB.2030000@caltech.edu> <46CF684F.8030209@cs.uoregon.edu> Message-ID: HI Kimberly, Hmmm, I really don't think this is a case for IGI, it's really not a genetic interaction. I think this is the same class of assay that we discussed for the distinction between IMP and IDA. For the IMP vs IDA discussion we agreed that assays where the researcher is using the cell system as an assay for function and not comparing wt vs mutant versions should be IDA. I think the same logic applies here. And to go back to a question from your original post, the with column is not allowed for IDA and will be filtered out by the checking script. Especially if you're already going to annotate both genes to the CC term for 'receptor complex', then I think making the MF 'contributes to: GABA receptor activity' sounds fine. -Karen On Fri, 24 Aug 2007, Doug howe wrote: > Though it is a direct assay, you can only detect it's role in the GABA > receptor activity when you introduce both subunit b and subunit c, so it > still seems like an IGI to me, though I could see how you might go down > either road. Something like this perhaps: > > Subunit b: > 'GABA receptor activity' IDA <--b has activity by itself > 'GABA receptor activity' IGI with gene ID for subunit c <--b has > altered activity when c is present > > Subunit c: > contributes_to 'GABA receptor activity' IGI with gene ID for subunit b > <--c doesn't have activity by itself > 'receptor complex' IGI with gene ID for subunit b > > -Doug > > > Kimberly Van Auken wrote: >> Thanks, Doug. >> >> I had thought about that, but neither of the gene products is mutant and so >> I didn't >> know if IGI was appropriate. >> >> Perhaps Subunit C could get a contributes_to qualifier for an IDA >> annotation and >> then I could annotate each of the subunits to the CC term receptor complex >> to fulfill >> the contributes_to requirement that: >> >> All gene products annotated using contributes_to must also be annotated >> to a cellular >> component term representing the complex that possesses the activity. >> >> >> --Kimberly >> >> >> Doug howe wrote: >> >>> Sounds like a possible IDA function annotation on Subunit B and a >>> 'contributes_to' function annotation by IGI on subunit C?? >>> -Doug >>> >>> >>> Kimberly Van Auken wrote: >>> >>>> Hi-- >>>> >>>> I'm trying to decide the best way to annotate information about the C. >>>> elegans GABA receptor. >>>> >>>> In C. elegans, functional GABA receptors are formed from one or more >>>> protein subunits encoded >>>> by the same genomic locus, unc-49. >>>> >>>> To test functionality, the authors of the paper expressed subunits >>>> separately and then together >>>> and measured the dose-response to, and response to continuous application >>>> of, GABA. One subunit >>>> has receptor activity on its own, one does not, and expression of both >>>> results in a response distinct >>>> from that of the first on its own. To summarize: >>>> >>>> Subunit B: responds >>>> >>>> Subunit C: doesn't respond >>>> >>>> Subunits B and C: respond with distinct profile >>>> >>>> >>>> If this was just one isoform, I would annotate the protein to the >>>> appropriate receptor activity terms >>>> using the IDA evidence code. But is there any way to annotate this >>>> complexity using IDA? >>>> >>>> I can certainly annotate to the B isoform, but I don't want to make the >>>> same annotation to the C isoform. >>>> >>>> One way I can think to capture the complexity would be to annotate to >>>> both B and C, but include the >>>> other isoform in the WITH column for one B annotation and the only C >>>> annotation. >>>> >>>> Is the WITH column completely off-limits for IDA annotations? >>>> >>>> Any thoughts on this would be much appreciated! >>>> >>>> Thanks, >>>> Kimberly >>>> >>>> >>>> >>>> >>> >> > From midori at ebi.ac.uk Sat Aug 25 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sun, 26 Aug 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200708260500.l7Q506C1210312@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070826/97407391/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070826/97407391/attachment.pl From vpetri at mcw.edu Mon Aug 27 06:52:18 2007 From: vpetri at mcw.edu (Petri, Victoria) Date: Mon, 27 Aug 2007 08:52:18 -0500 Subject: [annotation] Question about Isoform Annotation In-Reply-To: <46CF61EB.2030000@caltech.edu> References: <46CF56BB.9090105@caltech.edu> <46CF58F5.7000403@cs.uoregon.edu> <46CF61EB.2030000@caltech.edu> Message-ID: <1448A38A42714048B9C53E473E13CCF0010A5FED@davis.hmgc.mcw.edu> Hi Kimberly, I see it as a call for contributes_to for subunit C. I think that the complex - subunit b and subunit c - represents the physiologically significant unit and therefore the physiologically significant activity is the response profile exhibited by c when b is present. The function of c is then to modulate the activity b would otherwise have on its own and probably not the optimal response. In this respect, b contributes to the 'proper' activity of the receptor complex. Yes, the two subunits get the CC complex term which clarifies the picture to the users that most likely encountered similar situations. Best, Victoria Victoria Petri, Ph.D. Research Scientist Rat Genome Database (http://rgd.mcw.edu) Bioinformatics Program Human and Molecular Genetics Center Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI 53226 (414) 456-7507 Fax (414) 456-6595 vpetri at mcw.edu vpetri at mail.brc.mcw.edu -----Original Message----- From: owner-annotation at genome.stanford.edu [mailto:owner-annotation at genome.stanford.edu] On Behalf Of Kimberly Van Auken Sent: Friday, August 24, 2007 5:56 PM To: dhowe at cs.uoregon.edu Cc: annotation at genome.stanford.edu Subject: Re: [annotation] Question about Isoform Annotation Thanks, Doug. I had thought about that, but neither of the gene products is mutant and so I didn't know if IGI was appropriate. Perhaps Subunit C could get a contributes_to qualifier for an IDA annotation and then I could annotate each of the subunits to the CC term receptor complex to fulfill the contributes_to requirement that: All gene products annotated using contributes_to must also be annotated to a cellular component term representing the complex that possesses the activity. --Kimberly Doug howe wrote: > Sounds like a possible IDA function annotation on Subunit B and a > 'contributes_to' function annotation by IGI on subunit C?? > -Doug > > > Kimberly Van Auken wrote: > >> Hi-- >> >> I'm trying to decide the best way to annotate information about the >> C. elegans GABA receptor. >> >> In C. elegans, functional GABA receptors are formed from one or more >> protein subunits encoded >> by the same genomic locus, unc-49. >> >> To test functionality, the authors of the paper expressed subunits >> separately and then together >> and measured the dose-response to, and response to continuous >> application of, GABA. One subunit >> has receptor activity on its own, one does not, and expression of >> both results in a response distinct >> from that of the first on its own. To summarize: >> >> Subunit B: responds >> >> Subunit C: doesn't respond >> >> Subunits B and C: respond with distinct profile >> >> >> If this was just one isoform, I would annotate the protein to the >> appropriate receptor activity terms >> using the IDA evidence code. But is there any way to annotate this >> complexity using IDA? >> >> I can certainly annotate to the B isoform, but I don't want to make >> the same annotation to the C isoform. >> >> One way I can think to capture the complexity would be to annotate to >> both B and C, but include the >> other isoform in the WITH column for one B annotation and the only C >> annotation. >> >> Is the WITH column completely off-limits for IDA annotations? >> >> Any thoughts on this would be much appreciated! >> >> Thanks, >> Kimberly >> >> >> >> > From dhowe at cs.uoregon.edu Tue Aug 28 11:21:27 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Tue, 28 Aug 2007 11:21:27 -0700 Subject: [annotation] ISS for hydrophobicity Message-ID: <46D467A7.7080600@cs.uoregon.edu> I want to annotate to 'integral to membrane' based on the authors citing hydrophobicity analysis and concluding that it is a transmembrane protein. I know we have discussed this before... What is the current policy on this annotation? ISS using nothing in the 'with' field (this appears to be disallowed at the moment)? -Doug From kchris at genome.Stanford.EDU Tue Aug 28 11:34:50 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Tue, 28 Aug 2007 11:34:50 -0700 (PDT) Subject: [annotation] ISS for hydrophobicity In-Reply-To: <46D467A7.7080600@cs.uoregon.edu> References: <46D467A7.7080600@cs.uoregon.edu> Message-ID: Hi Doug, At the Jan 07 GO meeting we did agree to require that the with column be filled for ISS. We also agreed that it would be allowed to put the name of a method in the with field. My example at the time was various snoRNA predictions based on sequence. However, we have not yet worked out the specifics of how to be able to include names of methods in the with column. I am writing up a summary of the issue to send to the GO list to start the discussion before I go on maternity leave (last day working till next year will be Sept 14), so if you send me the paper and the specifics of what you would like to be able to annotate from the paper, I'll include it in my item. thanks, -Karen On Tue, 28 Aug 2007, Doug howe wrote: > I want to annotate to 'integral to membrane' based on the authors citing > hydrophobicity analysis and concluding that it is a transmembrane protein. I > know we have discussed this before... > What is the current policy on this annotation? ISS using nothing in the > 'with' field (this appears to be disallowed at the moment)? > -Doug > From dhowe at cs.uoregon.edu Thu Aug 30 10:34:05 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Thu, 30 Aug 2007 10:34:05 -0700 Subject: [annotation] IDA or IGI Message-ID: <46D6FF8D.9060300@cs.uoregon.edu> A paper reports that mafb is involved in 'anterior posterior pattern formation'. This is demonstrated by injecting mafb mRNA into vhnf1 mutants embryos, which have AP patterning defects. Would this be annotated as: mafb 'anterior posterior pattern formation' IDA? mafb 'anterior posterior pattern formation' IGI w/ the vhnf1 mutant? -Doug From nash at genome.Stanford.EDU Thu Aug 30 10:54:07 2007 From: nash at genome.Stanford.EDU (Rob Nash) Date: Thu, 30 Aug 2007 10:54:07 -0700 Subject: [annotation] IDA or IGI In-Reply-To: <46D6FF8D.9060300@cs.uoregon.edu> References: <46D6FF8D.9060300@cs.uoregon.edu> Message-ID: <9EE33935-7AC1-4F78-913C-FE70D3EB62D9@genome.stanford.edu> Hi, I would say this is a clear case for the later. Since this is a mutant phenotype suppressed by introduction of mafb, this would be an IGI using the with you have suggested. Cheers, Rob On Aug 30, 2007, at 10:34 AM, Doug howe wrote: > A paper reports that mafb is involved in 'anterior posterior > pattern formation'. This is demonstrated by injecting mafb mRNA > into vhnf1 mutants embryos, which have AP patterning defects. > Would this be annotated as: > > mafb 'anterior posterior pattern formation' IDA? > mafb 'anterior posterior pattern formation' IGI w/ the vhnf1 mutant? > > -Doug Rob Nash, Ph.D. Senior Scientific Curator Saccharomyces Genome Database Department of Genetics Stanford University Medical Center Stanford, CA 94305-5120 USA phone: (650) 725-8956 fax: (650) 725-1534 email: nash at genome.stanford.edu http://www.yeastgenome.org/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070830/2fb1fd98/attachment.html From rama at genome.Stanford.EDU Thu Aug 30 11:11:39 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Thu, 30 Aug 2007 11:11:39 -0700 Subject: [annotation] IDA or IGI In-Reply-To: <9EE33935-7AC1-4F78-913C-FE70D3EB62D9@genome.stanford.edu> References: <46D6FF8D.9060300@cs.uoregon.edu> <9EE33935-7AC1-4F78-913C-FE70D3EB62D9@genome.stanford.edu> Message-ID: <3204C1C8-4D03-4FE0-A651-94B6AE8D0ED4@genome.stanford.edu> I agree. Rama On Aug 30, 2007, at 10:54 AM, Rob Nash wrote: > Hi, > > I would say this is a clear case for the later. Since this is a > mutant phenotype suppressed by introduction of mafb, this would be > an IGI using the with you have suggested. > > Cheers, > Rob > > > On Aug 30, 2007, at 10:34 AM, Doug howe wrote: > >> A paper reports that mafb is involved in 'anterior posterior >> pattern formation'. This is demonstrated by injecting mafb mRNA >> into vhnf1 mutants embryos, which have AP patterning defects. >> Would this be annotated as: >> >> mafb 'anterior posterior pattern formation' IDA? >> mafb 'anterior posterior pattern formation' IGI w/ the vhnf1 >> mutant? >> >> -Doug > > Rob Nash, Ph.D. > Senior Scientific Curator > Saccharomyces Genome Database > Department of Genetics > Stanford University Medical Center > Stanford, CA 94305-5120 USA > phone: (650) 725-8956 fax: (650) 725-1534 > email: nash at genome.stanford.edu > http://www.yeastgenome.org/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070830/148950d0/attachment.html From tberardi at acoma.Stanford.EDU Thu Aug 30 11:20:00 2007 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Thu, 30 Aug 2007 11:20:00 -0700 Subject: [annotation] IDA or IGI In-Reply-To: <3204C1C8-4D03-4FE0-A651-94B6AE8D0ED4@genome.stanford.edu> References: <46D6FF8D.9060300@cs.uoregon.edu> <9EE33935-7AC1-4F78-913C-FE70D3EB62D9@genome.stanford.edu> <3204C1C8-4D03-4FE0-A651-94B6AE8D0ED4@genome.stanford.edu> Message-ID: <46D70A50.1020906@acoma.stanford.edu> Me three. Tanya Rama Balakrishnan wrote: > I agree. > > Rama > > On Aug 30, 2007, at 10:54 AM, Rob Nash wrote: > >> Hi, >> >> I would say this is a clear case for the later. Since this is a mutant >> phenotype suppressed by introduction of mafb, this would be an IGI >> using the with you have suggested. >> >> Cheers, >> Rob >> >> >> On Aug 30, 2007, at 10:34 AM, Doug howe wrote: >> >>> A paper reports that mafb is involved in 'anterior posterior pattern >>> formation'. This is demonstrated by injecting mafb mRNA into vhnf1 >>> mutants embryos, which have AP patterning defects. Would this be >>> annotated as: >>> >>> mafb 'anterior posterior pattern formation' IDA? >>> mafb 'anterior posterior pattern formation' IGI w/ the vhnf1 mutant? >>> >>> -Doug >> >> Rob Nash, Ph.D. >> Senior Scientific Curator >> Saccharomyces Genome Database >> Department of Genetics >> Stanford University Medical Center >> Stanford, CA 94305-5120 USA >> phone: (650) 725-8956 fax: (650) 725-1534 >> email: nash at genome.stanford.edu >> http://www.yeastgenome.org/ >> >> > -- ------------------------------------------------------------------------------------------ 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 dph at informatics.jax.org Thu Aug 30 11:42:50 2007 From: dph at informatics.jax.org (David Hill) Date: Thu, 30 Aug 2007 14:42:50 -0400 Subject: [annotation] IDA or IGI In-Reply-To: <46D6FF8D.9060300@cs.uoregon.edu> References: <46D6FF8D.9060300@cs.uoregon.edu> Message-ID: <46D70FAA.2010900@informatics.jax.org> I vote for IGI. Doug howe wrote: > A paper reports that mafb is involved in 'anterior posterior pattern > formation'. This is demonstrated by injecting mafb mRNA into vhnf1 > mutants embryos, which have AP patterning defects. Would this be > annotated as: > > mafb 'anterior posterior pattern formation' IDA? > mafb 'anterior posterior pattern formation' IGI w/ the vhnf1 mutant? > > -Doug