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pombase-phenotype — PomBase phenotype ontology and annotation
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From: SourceForge.net <no...@so...> - 2012-12-03 15:13:20
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Fission yeast phenotype item #3592113, was opened at 2012-12-03 07:13 Message generated for change (Tracker Item Submitted) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3592113&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: minichromosome loss Initial Comment: increased/normal minichromosome loss ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3592113&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-12-01 11:27:44
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Fission yeast phenotype item #3591626, was opened at 2012-12-01 03:27 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3591626&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: FYPO:0001779 Initial Comment: has a comment which appears to belong to another term... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3591626&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-30 15:32:48
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Fission yeast phenotype item #3591382, was opened at 2012-11-30 07:32 Message generated for change (Tracker Item Submitted) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3591382&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: normal cellular response to acidity Initial Comment: normal cellular response to acidity ps. I saw that the other terms for sensitive to acidity/alkalinity set the benchmark at pH 7, wouldn't it make more sense to set it to standard medium i.e. just under 6? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3591382&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-30 15:01:59
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Fission yeast phenotype item #3590714, was opened at 2012-11-28 07:00 Message generated for change (Comment added) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590714&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: annotation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: diploids Initial Comment: Hi Midori, 1. I'm trying to figure out if the term below is what I am after. The diploid mutant described become haploid at a higher rate than wt through 'premature mitosis'. I suppose premature mitosis fits chromosome loss in a way - it doesn't have time to replicate its chromosomes so they are 'lost'. Is this how the term was intended to be used? ID FYPO:0001386 Term name increased haploidization Definition A cell phenotype in which non-sporulating diploid cells become haploid by chromosome loss at a higher frequency than normal. If that is the case, then I'm thinking that chromosome loss must occur in one of two ways, either premature mitosis, as described above, or via segregation defects (which is what the 'unstable diploid' term refers to: ID FYPO:0001781 Term name unstable diploid Definition A cell phenotype in which cells are unable to maintain a diploid state. Cells may die or become aneuplaid or haploid.) For instance, if a cell has 4 chromosomes to divvy into 2 new cells, and progeny A gets 1 chromosome and progeny B gets 3, then progeny A dies and B becomes aneuploid (this state is unstable, so it will eventually become haploid). Perhaps there are more ways that I didn't think of in how diploids are unable to maintain their chromosomes - if not, then these two terms should perhaps become sibling terms? ---------------------------------------------------------------------- >Comment By: Antonia Lock (antonialock) Date: 2012-11-30 07:01 Message: ok cool, sounds good ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-30 06:50 Message: Now that I've looked at both papers, I suggest: Merge FYPO:0001386 and FYPO:0001781, and define the resulting term as "A cell phenotype in which non-sporulating diploid cells become haploid, without undergoing meiosis, at a higher frequency than normal". I'll move the bit about chromosome loss to a comment. For stm1 overexpression, I think I'd annotate to premature mitosis separately, since they also see it in haploids in Fig. 2. ---------------------------------------------------------------------- Comment By: Antonia Lock (antonialock) Date: 2012-11-29 09:15 Message: yeah I think I'd be in favor of merging too. They used an array of evidence. I thought it was a reasonable conclusion. pmid:17346842 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:25 Message: I'll have to think about this a bit more. From the paper I was annotating when I added FYPO:0001386, it's clear that there's no evidence specifically for premature mitosis. I'm now wondering if FYPO:0001386 and FYPO:0001781 should be merged, because the difference may not mean much. I think chromosome loss usually means lost during segregation, either because the chromosome structure is wonky (which in turn could be due to incomplete replication) or because the segregation machinery itself doesn't work properly. What's the paper you're reading? How did they detect premature mitosis? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590714&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-30 14:50:14
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Fission yeast phenotype item #3590714, was opened at 2012-11-28 07:00 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590714&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: annotation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: diploids Initial Comment: Hi Midori, 1. I'm trying to figure out if the term below is what I am after. The diploid mutant described become haploid at a higher rate than wt through 'premature mitosis'. I suppose premature mitosis fits chromosome loss in a way - it doesn't have time to replicate its chromosomes so they are 'lost'. Is this how the term was intended to be used? ID FYPO:0001386 Term name increased haploidization Definition A cell phenotype in which non-sporulating diploid cells become haploid by chromosome loss at a higher frequency than normal. If that is the case, then I'm thinking that chromosome loss must occur in one of two ways, either premature mitosis, as described above, or via segregation defects (which is what the 'unstable diploid' term refers to: ID FYPO:0001781 Term name unstable diploid Definition A cell phenotype in which cells are unable to maintain a diploid state. Cells may die or become aneuplaid or haploid.) For instance, if a cell has 4 chromosomes to divvy into 2 new cells, and progeny A gets 1 chromosome and progeny B gets 3, then progeny A dies and B becomes aneuploid (this state is unstable, so it will eventually become haploid). Perhaps there are more ways that I didn't think of in how diploids are unable to maintain their chromosomes - if not, then these two terms should perhaps become sibling terms? ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-30 06:50 Message: Now that I've looked at both papers, I suggest: Merge FYPO:0001386 and FYPO:0001781, and define the resulting term as "A cell phenotype in which non-sporulating diploid cells become haploid, without undergoing meiosis, at a higher frequency than normal". I'll move the bit about chromosome loss to a comment. For stm1 overexpression, I think I'd annotate to premature mitosis separately, since they also see it in haploids in Fig. 2. ---------------------------------------------------------------------- Comment By: Antonia Lock (antonialock) Date: 2012-11-29 09:15 Message: yeah I think I'd be in favor of merging too. They used an array of evidence. I thought it was a reasonable conclusion. pmid:17346842 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:25 Message: I'll have to think about this a bit more. From the paper I was annotating when I added FYPO:0001386, it's clear that there's no evidence specifically for premature mitosis. I'm now wondering if FYPO:0001386 and FYPO:0001781 should be merged, because the difference may not mean much. I think chromosome loss usually means lost during segregation, either because the chromosome structure is wonky (which in turn could be due to incomplete replication) or because the segregation machinery itself doesn't work properly. What's the paper you're reading? How did they detect premature mitosis? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590714&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 17:34:03
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Fission yeast phenotype item #3590649, was opened at 2012-11-28 02:05 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: abnormal protein structure / misfolded protein Initial Comment: abnormal protein structure / misfolded protein (experiments were done with CD/NMR, so I mean the global protein fold if that makes a difference) ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-29 09:34 Message: cant a misfolded protein be ab observable characteristic? is it a problem with the resolution (you can't actually see it?) ---------------------------------------------------------------------- Comment By: Antonia Lock (antonialock) Date: 2012-11-29 09:30 Message: but surely it's an observable characteristic? - It's completely your call Midori. I suppose most point mutations that result in differences between mutant and wild-type cells will either alter the protein fold or bugger up any protein-other molecule interactions, so it's not exactly a ground breaking piece of information. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:39 Message: In that example the disease is the phenotype. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-29 08:37 Message: "protein misfolding" sounds phenotypey to me? i.e as in disease phenotype in a protein misfolding disorder ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:26 Message: I think I see what you want to capture with this -- that a mutation causes a protein to fold incorrectly. But I'm inclined not to add the term, because I'm having trouble convincing myself that protein structure is really a phenotype. It's not something that happens to the organism (the cell, for yeasties) as a result of the mutation. I'll keep thinking ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 17:30:39
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Fission yeast phenotype item #3590649, was opened at 2012-11-28 02:05 Message generated for change (Comment added) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: abnormal protein structure / misfolded protein Initial Comment: abnormal protein structure / misfolded protein (experiments were done with CD/NMR, so I mean the global protein fold if that makes a difference) ---------------------------------------------------------------------- >Comment By: Antonia Lock (antonialock) Date: 2012-11-29 09:30 Message: but surely it's an observable characteristic? - It's completely your call Midori. I suppose most point mutations that result in differences between mutant and wild-type cells will either alter the protein fold or bugger up any protein-other molecule interactions, so it's not exactly a ground breaking piece of information. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:39 Message: In that example the disease is the phenotype. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-29 08:37 Message: "protein misfolding" sounds phenotypey to me? i.e as in disease phenotype in a protein misfolding disorder ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:26 Message: I think I see what you want to capture with this -- that a mutation causes a protein to fold incorrectly. But I'm inclined not to add the term, because I'm having trouble convincing myself that protein structure is really a phenotype. It's not something that happens to the organism (the cell, for yeasties) as a result of the mutation. I'll keep thinking ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 17:15:48
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Fission yeast phenotype item #3590714, was opened at 2012-11-28 07:00 Message generated for change (Comment added) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590714&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: annotation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: diploids Initial Comment: Hi Midori, 1. I'm trying to figure out if the term below is what I am after. The diploid mutant described become haploid at a higher rate than wt through 'premature mitosis'. I suppose premature mitosis fits chromosome loss in a way - it doesn't have time to replicate its chromosomes so they are 'lost'. Is this how the term was intended to be used? ID FYPO:0001386 Term name increased haploidization Definition A cell phenotype in which non-sporulating diploid cells become haploid by chromosome loss at a higher frequency than normal. If that is the case, then I'm thinking that chromosome loss must occur in one of two ways, either premature mitosis, as described above, or via segregation defects (which is what the 'unstable diploid' term refers to: ID FYPO:0001781 Term name unstable diploid Definition A cell phenotype in which cells are unable to maintain a diploid state. Cells may die or become aneuplaid or haploid.) For instance, if a cell has 4 chromosomes to divvy into 2 new cells, and progeny A gets 1 chromosome and progeny B gets 3, then progeny A dies and B becomes aneuploid (this state is unstable, so it will eventually become haploid). Perhaps there are more ways that I didn't think of in how diploids are unable to maintain their chromosomes - if not, then these two terms should perhaps become sibling terms? ---------------------------------------------------------------------- >Comment By: Antonia Lock (antonialock) Date: 2012-11-29 09:15 Message: yeah I think I'd be in favor of merging too. They used an array of evidence. I thought it was a reasonable conclusion. pmid:17346842 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:25 Message: I'll have to think about this a bit more. From the paper I was annotating when I added FYPO:0001386, it's clear that there's no evidence specifically for premature mitosis. I'm now wondering if FYPO:0001386 and FYPO:0001781 should be merged, because the difference may not mean much. I think chromosome loss usually means lost during segregation, either because the chromosome structure is wonky (which in turn could be due to incomplete replication) or because the segregation machinery itself doesn't work properly. What's the paper you're reading? How did they detect premature mitosis? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590714&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 16:39:30
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Fission yeast phenotype item #3590649, was opened at 2012-11-28 02:05 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: abnormal protein structure / misfolded protein Initial Comment: abnormal protein structure / misfolded protein (experiments were done with CD/NMR, so I mean the global protein fold if that makes a difference) ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:39 Message: In that example the disease is the phenotype. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-29 08:37 Message: "protein misfolding" sounds phenotypey to me? i.e as in disease phenotype in a protein misfolding disorder ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:26 Message: I think I see what you want to capture with this -- that a mutation causes a protein to fold incorrectly. But I'm inclined not to add the term, because I'm having trouble convincing myself that protein structure is really a phenotype. It's not something that happens to the organism (the cell, for yeasties) as a result of the mutation. I'll keep thinking ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 16:37:06
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Fission yeast phenotype item #3590649, was opened at 2012-11-28 02:05 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: abnormal protein structure / misfolded protein Initial Comment: abnormal protein structure / misfolded protein (experiments were done with CD/NMR, so I mean the global protein fold if that makes a difference) ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-29 08:37 Message: "protein misfolding" sounds phenotypey to me? i.e as in disease phenotype in a protein misfolding disorder ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:26 Message: I think I see what you want to capture with this -- that a mutation causes a protein to fold incorrectly. But I'm inclined not to add the term, because I'm having trouble convincing myself that protein structure is really a phenotype. It's not something that happens to the organism (the cell, for yeasties) as a result of the mutation. I'll keep thinking ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 16:26:03
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Fission yeast phenotype item #3590649, was opened at 2012-11-28 02:05 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: abnormal protein structure / misfolded protein Initial Comment: abnormal protein structure / misfolded protein (experiments were done with CD/NMR, so I mean the global protein fold if that makes a difference) ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:26 Message: I think I see what you want to capture with this -- that a mutation causes a protein to fold incorrectly. But I'm inclined not to add the term, because I'm having trouble convincing myself that protein structure is really a phenotype. It's not something that happens to the organism (the cell, for yeasties) as a result of the mutation. I'll keep thinking ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590649&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 16:25:30
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Fission yeast phenotype item #3590714, was opened at 2012-11-28 07:00 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590714&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: annotation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: diploids Initial Comment: Hi Midori, 1. I'm trying to figure out if the term below is what I am after. The diploid mutant described become haploid at a higher rate than wt through 'premature mitosis'. I suppose premature mitosis fits chromosome loss in a way - it doesn't have time to replicate its chromosomes so they are 'lost'. Is this how the term was intended to be used? ID FYPO:0001386 Term name increased haploidization Definition A cell phenotype in which non-sporulating diploid cells become haploid by chromosome loss at a higher frequency than normal. If that is the case, then I'm thinking that chromosome loss must occur in one of two ways, either premature mitosis, as described above, or via segregation defects (which is what the 'unstable diploid' term refers to: ID FYPO:0001781 Term name unstable diploid Definition A cell phenotype in which cells are unable to maintain a diploid state. Cells may die or become aneuplaid or haploid.) For instance, if a cell has 4 chromosomes to divvy into 2 new cells, and progeny A gets 1 chromosome and progeny B gets 3, then progeny A dies and B becomes aneuploid (this state is unstable, so it will eventually become haploid). Perhaps there are more ways that I didn't think of in how diploids are unable to maintain their chromosomes - if not, then these two terms should perhaps become sibling terms? ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 08:25 Message: I'll have to think about this a bit more. From the paper I was annotating when I added FYPO:0001386, it's clear that there's no evidence specifically for premature mitosis. I'm now wondering if FYPO:0001386 and FYPO:0001781 should be merged, because the difference may not mean much. I think chromosome loss usually means lost during segregation, either because the chromosome structure is wonky (which in turn could be due to incomplete replication) or because the segregation machinery itself doesn't work properly. What's the paper you're reading? How did they detect premature mitosis? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590714&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:50:55
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Fission yeast phenotype item #3590648, was opened at 2012-11-28 01:54 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590648&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: phosphoglycerate mutase activity Initial Comment: 1. abolished phosphoglycerate mutase activity 2. increased phosphoglycerate mutase activity 3. normal phosphoglycerate mutase activity thanks! ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 07:50 Message: abnormal phosphoglycerate mutase activity FYPO:0001831 abolished phosphoglycerate mutase activity FYPO:0001832 increased phosphoglycerate mutase activity FYPO:0001833 normal phosphoglycerate mutase activity FYPO:0001834 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590648&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:46:01
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Fission yeast phenotype item #3590412, was opened at 2012-11-27 10:02 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590412&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: decreased cell growth on gluconate carbon source Initial Comment: decreased cell growth on gluconate carbon source ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 07:46 Message: decreased cell growth on gluconate carbon source FYPO:0001830 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590412&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:41:58
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Fission yeast phenotype item #3590377, was opened at 2012-11-27 07:13 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590377&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) >Assigned to: Midori Harris (gomidori) Summary: normal cell growth on gluconate carbon source Initial Comment: normal cell growth on gluconate carbon source ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 07:41 Message: normal cell growth on gluconate carbon source FYPO:0001829 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590377&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:37:07
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Fission yeast phenotype item #3590376, was opened at 2012-11-27 07:12 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590376&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: abolished glucose import Initial Comment: abolished glucose import ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 07:37 Message: abnormal glucose import FYPO:0001827 abolished glucose import FYPO:0001828 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590376&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:31:30
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Fission yeast phenotype item #3590115, was opened at 2012-11-26 09:09 Message generated for change (Settings changed) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590115&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: sodium export Initial Comment: increased sodium export abolished sodium export children of FYPO:0001721 ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 07:31 Message: increased sodium export FYPO:0001825 sodium export abolished FYPO:0001826 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590115&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:19:54
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Fission yeast phenotype item #3590113, was opened at 2012-11-26 08:54 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590113&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Midori Harris (gomidori) Summary: sensitive to ... Initial Comment: chlorpromazine CHEBI:3647 trifluoperazine CHEBI:45951 ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 07:19 Message: sensitive to chlorpromazine FYPO:0001823 sensitive to trifluoperazine FYPO:0001824 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3590113&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:12:54
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Fission yeast phenotype item #3589932, was opened at 2012-11-25 10:10 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589932&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Closed Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: increased amount of heterothallic H+ cells Initial Comment: increased amount of heterothallic H+ cells a population phenotype in which an increasing amount of cells in an originally homothallic (h90) population express P-specific information from the mat1 locus. ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 07:12 Message: OK, I'll use h+ in the term name. I asked because I think I've seen lower case pretty much exclusively, but since I worked on That Other Yeast I don't count myself as an expert on pombe nomenclature ;) ---------------------------------------------------------------------- Comment By: Antonia Lock (antonialock) Date: 2012-11-29 07:09 Message: hmm, I often write h90, H+ and H- but thinking about it h+ and h- might be 'correct' spelling ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 06:58 Message: increased number of heterothallic H+ cells FYPO:0001821 does it matter whether the H is upper or lower case? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589932&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:09:54
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Fission yeast phenotype item #3589932, was opened at 2012-11-25 10:10 Message generated for change (Comment added) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589932&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Closed Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: increased amount of heterothallic H+ cells Initial Comment: increased amount of heterothallic H+ cells a population phenotype in which an increasing amount of cells in an originally homothallic (h90) population express P-specific information from the mat1 locus. ---------------------------------------------------------------------- >Comment By: Antonia Lock (antonialock) Date: 2012-11-29 07:09 Message: hmm, I often write h90, H+ and H- but thinking about it h+ and h- might be 'correct' spelling ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 06:58 Message: increased number of heterothallic H+ cells FYPO:0001821 does it matter whether the H is upper or lower case? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589932&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 15:08:49
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Fission yeast phenotype item #3589933, was opened at 2012-11-25 10:11 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589933&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: mating cassette duplications Initial Comment: mating cassette duplications A phenotype where a cell acquire duplications of its mating cassettes I guess this would be an example of gross chromosomal rearrangements (or is duplications not rearrangements)? ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 07:08 Message: mating cassette duplication FYPO:0001822 I made it a sibling of gross chromosomal rearrangement, because "gross" means very large, and the mating cassettes aren't that big. (I'm not sure exactly where the cutoff between gross and not-gross would be, but I'm nevertheless confident that mating cassettes are on the smaller side.) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589933&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 14:58:18
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Fission yeast phenotype item #3589932, was opened at 2012-11-25 10:10 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589932&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: increased amount of heterothallic H+ cells Initial Comment: increased amount of heterothallic H+ cells a population phenotype in which an increasing amount of cells in an originally homothallic (h90) population express P-specific information from the mat1 locus. ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 06:58 Message: increased number of heterothallic H+ cells FYPO:0001821 does it matter whether the H is upper or lower case? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589932&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 14:52:01
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Fission yeast phenotype item #3589419, was opened at 2012-11-23 06:27 Message generated for change (Settings changed) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589419&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None >Status: Closed Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: normal lithium response Initial Comment: normal cellular response (/growth) to lithium ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-29 06:51 Message: normal cellular response to lithium ion FYPO:0001820 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589419&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 14:51:54
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Fission yeast phenotype item #3589419, was opened at 2012-11-23 06:27 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589419&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: new ontology term Group: None Status: Open >Resolution: Accepted Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Midori Harris (gomidori) Summary: normal lithium response Initial Comment: normal cellular response (/growth) to lithium ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 06:51 Message: normal cellular response to lithium ion FYPO:0001820 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589419&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 14:36:12
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Fission yeast phenotype item #3589409, was opened at 2012-11-23 06:05 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589409&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: new ontology term Group: None >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) >Assigned to: Midori Harris (gomidori) Summary: ntr: abolished catalytic activity Initial Comment: abolished phosphoribosylamine-glycine ligase activity abolished phosphoribosylformylglycinamidine cyclo-ligase activity PMID:967158 ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-29 06:36 Message: abnormal phosphoribosylamine-glycine ligase activity FYPO:0001816 abolished phosphoribosylamine-glycine ligase activity FYPO:0001817 abnormal phosphoribosylformylglycinamidine cyclo-ligase activity FYPO:0001818 abolished phosphoribosylformylglycinamidine cyclo-ligase activity FYPO:0001819 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3589409&group_id=65526 |
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