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From: SourceForge.net <no...@so...> - 2012-12-03 11:16:52
|
Chado item #3590723, was opened at 2012-11-28 08:01 Message generated for change (Settings changed) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590723&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: Closed >Resolution: Fixed Priority: 7 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: 'from=' data missing from GAF for IC Initial Comment: Problem! The GAFs being written out from Chado don't have anything in column 8 (with/from) where the evidence (col 7) is IC. I used pombase-build-2012-11-25-v2-l1.gaf to the GAF in the GO repository. I looked a couple other GAFs from the dumps as well, and none had the data (tried pombase-build-2012-10-19-v1-l1.gaf, pombase-build-2012-11-05-v1-l1.gaf, pombase-build-2012-11-18-v2-l1.gaf). I didn't try to chase up every annotation, but the handful I spot-checked all had the requisite data in the embl files. Just one example: FT /GO="aspect=P; term=histone acetylation; GOid=GO:0016573; FT evidence=IC; db_xref=GO_REF:0000001; from=GO:0035267; FT date=20090301" becomes PomBase SPAC1F5.11c tra2 GO:0016573 GO_REF:0000001 IC P NuA4 complex phosphatidylinositol pseudokinase complex subunit Tra2 protein taxon:4896 20090301 PomBase The GO filter-gene-association.pl script is totally supposed to catch these, but equally totally failed -- it told me "Congratulations, there are no errors." and I didn't realize until today that it was lying. I'm reporting that to GO. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-12-02 07:36 Message: That looks MUCH better - thanks! I'll fix the problem lines, and sooner or later GO SVN will be back among the living and I'll commit the new GAF ... ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-12-02 00:21 Message: This is fixed in the latest load: http://curation.pombase.org/kmr44/dumps/pombase-build-2012-11-28-v3-l1/ Sorry, the GAF writer was ignoring the froms. The fix added the from to most of the IC annotations. I've made a file with the ones that look like problems: Dropbox/pombase/Chado/GAF_IC_annotation_problems.txt There's only a handful. Some have no from, some have a from that isn't a GO term (maybe that's OK?) and there is one IMP annotation that has a from in Chado, but perhaps shouldn't. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590723&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-12-03 11:16:41
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Chado item #3586386, was opened at 2012-11-12 08:57 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586386&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: Closed >Resolution: Fixed Priority: 3 Private: No Submitted By: Valerie Wood (val_wood) >Assigned to: Kim Rutherford (kim_rutherford) Summary: filtering IEA odd behaviuor Initial Comment: GO:0004674 protein serine/threonine kinase activity IEA KW-0723 GO_REF:0000004 has_substrate mei2 IDA Watanabe Y et al. (1997) has_substrate ste11 IDA Li P et al. (1996) has_substrate cpc2 IDA McLeod M et al. (2000) in current data, so even though there are IDA's the IEA is kept This is in NG28 so we should check what 29 looks like. This could be something to do with extnsions not being included in filtering, but I though thsi was fixed. Anyway, not urgent, we'll see what 29 looks like, just wanted to flag it ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-12-03 03:16 Message: as in SF 3590727, happy with IEA numbers now ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-11-30 03:12 Message: What gene was your example from? In this case the IDAs are all for annotation extensions. It wouldn't surprise me too much if there was a bug in how that was handled. I'll investigate. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-28 08:02 Message: Also see SF 3590727 on what reaches the GAF. https://sourceforge.net/tracker/?func=detail&aid=3590727&group_id=65526&atid=2096276 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586386&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-12-03 11:16:08
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Chado item #3590727, was opened at 2012-11-28 08:02 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&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: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: IC (and IEA?) filtering Initial Comment: In my investigations for the missing 'from' .problem (SF 3590723), I also noticed that the number of IC annotations that reach the GAF has varied over time by far more than can be explained by actual annotation changes. Examples: pombase-build-2012-10-19-v1-l1.gaf - 215 pombase-build-2012-11-05-v1-l1.gaf - 214 pombase-build-2012-11-18-v2-l1.gaf - 1126 pombase-build-2012-11-25-v2-l1.gaf - 1122 % grep -c 'evidence=IC' *contig finds about 1500 matches Val has also commented on the number of IEA annotations (6559 in the file committed to GOC). Is something up with filtering? Also see SF 3586386, which was about v28 and what shows up on pombase gene pages. https://sourceforge.net/tracker/?func=detail&aid=3586386&group_id=65526&atid=2096276 ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-12-03 03:16 Message: The 11-28-v2 GAF has just over 4700 IEAs, which Val says is about right. I don't know what to make of the IC count changes, but the current 1100-odd makes sense, so I'll call this fixed. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-12-02 10:38 Message: The current IC count is 1127. I can't explain the change in count over time. As far as I can see there haven't been any code changes that code have made a difference. Is 6559 IEAs too high? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-28 09:04 Message: It could be because the filtering filters IC/TAS/NAS/IEA redundently with no precedence for any particular evidence code? I think there is an item about this on the chado tracker with low priority... (so we are seeing ICs replaced by IEAs?... but this wouldn't explain the increase in both, or the non-filtering reported in the other ticket ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-12-02 18:38:14
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Chado item #3590727, was opened at 2012-11-28 08:02 Message generated for change (Comment added) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&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: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: IC (and IEA?) filtering Initial Comment: In my investigations for the missing 'from' .problem (SF 3590723), I also noticed that the number of IC annotations that reach the GAF has varied over time by far more than can be explained by actual annotation changes. Examples: pombase-build-2012-10-19-v1-l1.gaf - 215 pombase-build-2012-11-05-v1-l1.gaf - 214 pombase-build-2012-11-18-v2-l1.gaf - 1126 pombase-build-2012-11-25-v2-l1.gaf - 1122 % grep -c 'evidence=IC' *contig finds about 1500 matches Val has also commented on the number of IEA annotations (6559 in the file committed to GOC). Is something up with filtering? Also see SF 3586386, which was about v28 and what shows up on pombase gene pages. https://sourceforge.net/tracker/?func=detail&aid=3586386&group_id=65526&atid=2096276 ---------------------------------------------------------------------- >Comment By: Kim Rutherford (kim_rutherford) Date: 2012-12-02 10:38 Message: The current IC count is 1127. I can't explain the change in count over time. As far as I can see there haven't been any code changes that code have made a difference. Is 6559 IEAs too high? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-28 09:04 Message: It could be because the filtering filters IC/TAS/NAS/IEA redundently with no precedence for any particular evidence code? I think there is an item about this on the chado tracker with low priority... (so we are seeing ICs replaced by IEAs?... but this wouldn't explain the increase in both, or the non-filtering reported in the other ticket ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-12-02 15:37:01
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Chado item #3590723, was opened at 2012-11-28 08:01 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590723&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: 7 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: 'from=' data missing from GAF for IC Initial Comment: Problem! The GAFs being written out from Chado don't have anything in column 8 (with/from) where the evidence (col 7) is IC. I used pombase-build-2012-11-25-v2-l1.gaf to the GAF in the GO repository. I looked a couple other GAFs from the dumps as well, and none had the data (tried pombase-build-2012-10-19-v1-l1.gaf, pombase-build-2012-11-05-v1-l1.gaf, pombase-build-2012-11-18-v2-l1.gaf). I didn't try to chase up every annotation, but the handful I spot-checked all had the requisite data in the embl files. Just one example: FT /GO="aspect=P; term=histone acetylation; GOid=GO:0016573; FT evidence=IC; db_xref=GO_REF:0000001; from=GO:0035267; FT date=20090301" becomes PomBase SPAC1F5.11c tra2 GO:0016573 GO_REF:0000001 IC P NuA4 complex phosphatidylinositol pseudokinase complex subunit Tra2 protein taxon:4896 20090301 PomBase The GO filter-gene-association.pl script is totally supposed to catch these, but equally totally failed -- it told me "Congratulations, there are no errors." and I didn't realize until today that it was lying. I'm reporting that to GO. ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-12-02 07:36 Message: That looks MUCH better - thanks! I'll fix the problem lines, and sooner or later GO SVN will be back among the living and I'll commit the new GAF ... ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-12-02 00:21 Message: This is fixed in the latest load: http://curation.pombase.org/kmr44/dumps/pombase-build-2012-11-28-v3-l1/ Sorry, the GAF writer was ignoring the froms. The fix added the from to most of the IC annotations. I've made a file with the ones that look like problems: Dropbox/pombase/Chado/GAF_IC_annotation_problems.txt There's only a handful. Some have no from, some have a from that isn't a GO term (maybe that's OK?) and there is one IMP annotation that has a from in Chado, but perhaps shouldn't. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590723&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-12-02 08:21:35
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Chado item #3590723, was opened at 2012-11-28 08:01 Message generated for change (Comment added) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590723&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: 7 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: 'from=' data missing from GAF for IC Initial Comment: Problem! The GAFs being written out from Chado don't have anything in column 8 (with/from) where the evidence (col 7) is IC. I used pombase-build-2012-11-25-v2-l1.gaf to the GAF in the GO repository. I looked a couple other GAFs from the dumps as well, and none had the data (tried pombase-build-2012-10-19-v1-l1.gaf, pombase-build-2012-11-05-v1-l1.gaf, pombase-build-2012-11-18-v2-l1.gaf). I didn't try to chase up every annotation, but the handful I spot-checked all had the requisite data in the embl files. Just one example: FT /GO="aspect=P; term=histone acetylation; GOid=GO:0016573; FT evidence=IC; db_xref=GO_REF:0000001; from=GO:0035267; FT date=20090301" becomes PomBase SPAC1F5.11c tra2 GO:0016573 GO_REF:0000001 IC P NuA4 complex phosphatidylinositol pseudokinase complex subunit Tra2 protein taxon:4896 20090301 PomBase The GO filter-gene-association.pl script is totally supposed to catch these, but equally totally failed -- it told me "Congratulations, there are no errors." and I didn't realize until today that it was lying. I'm reporting that to GO. ---------------------------------------------------------------------- >Comment By: Kim Rutherford (kim_rutherford) Date: 2012-12-02 00:21 Message: This is fixed in the latest load: http://curation.pombase.org/kmr44/dumps/pombase-build-2012-11-28-v3-l1/ Sorry, the GAF writer was ignoring the froms. The fix added the from to most of the IC annotations. I've made a file with the ones that look like problems: Dropbox/pombase/Chado/GAF_IC_annotation_problems.txt There's only a handful. Some have no from, some have a from that isn't a GO term (maybe that's OK?) and there is one IMP annotation that has a from in Chado, but perhaps shouldn't. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590723&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-30 11:12:35
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Chado item #3586386, was opened at 2012-11-12 08:57 Message generated for change (Comment added) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586386&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: 3 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: filtering IEA odd behaviuor Initial Comment: GO:0004674 protein serine/threonine kinase activity IEA KW-0723 GO_REF:0000004 has_substrate mei2 IDA Watanabe Y et al. (1997) has_substrate ste11 IDA Li P et al. (1996) has_substrate cpc2 IDA McLeod M et al. (2000) in current data, so even though there are IDA's the IEA is kept This is in NG28 so we should check what 29 looks like. This could be something to do with extnsions not being included in filtering, but I though thsi was fixed. Anyway, not urgent, we'll see what 29 looks like, just wanted to flag it ---------------------------------------------------------------------- >Comment By: Kim Rutherford (kim_rutherford) Date: 2012-11-30 03:12 Message: What gene was your example from? In this case the IDAs are all for annotation extensions. It wouldn't surprise me too much if there was a bug in how that was handled. I'll investigate. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-28 08:02 Message: Also see SF 3590727 on what reaches the GAF. https://sourceforge.net/tracker/?func=detail&aid=3590727&group_id=65526&atid=2096276 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586386&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-29 10:41:16
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Chado item #3590980, was opened at 2012-11-29 02:41 Message generated for change (Tracker Item Submitted) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590980&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: 8 Private: No Submitted By: Kim Rutherford (kim_rutherford) Assigned to: Kim Rutherford (kim_rutherford) Summary: Update gene_association.goa_uniprot.pombe every load Initial Comment: The pombe GOA file needs to be recreated every load. The full file is here: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz We need to extract just rows wth the various pombe taxon IDs. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590980&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 19:57:38
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Chado item #3553913, was opened at 2012-08-02 22:09 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3553913&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: 7 Private: No Submitted By: Kim Rutherford (kim_rutherford) Assigned to: Kim Rutherford (kim_rutherford) Summary: Phenotypes not attached to alleles from EMBL files Initial Comment: The phenotype annotations from the EMBL files are attached to genes in Chado but should be attached to alleles. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-10-21 15:02 Message: The problem with the code is fixed so when there is an allele= in the controlled_curation the phenotype is correctly attached to the allele feature in Chado. There are still some phenotypes that don't have an allele=. The next log files will warn about that. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-10-20 15:55 Message: Is this done? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3553913&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 17:04:24
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Chado item #3590727, was opened at 2012-11-28 08:02 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&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: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: IC (and IEA?) filtering Initial Comment: In my investigations for the missing 'from' .problem (SF 3590723), I also noticed that the number of IC annotations that reach the GAF has varied over time by far more than can be explained by actual annotation changes. Examples: pombase-build-2012-10-19-v1-l1.gaf - 215 pombase-build-2012-11-05-v1-l1.gaf - 214 pombase-build-2012-11-18-v2-l1.gaf - 1126 pombase-build-2012-11-25-v2-l1.gaf - 1122 % grep -c 'evidence=IC' *contig finds about 1500 matches Val has also commented on the number of IEA annotations (6559 in the file committed to GOC). Is something up with filtering? Also see SF 3586386, which was about v28 and what shows up on pombase gene pages. https://sourceforge.net/tracker/?func=detail&aid=3586386&group_id=65526&atid=2096276 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-28 09:04 Message: It could be because the filtering filters IC/TAS/NAS/IEA redundently with no precedence for any particular evidence code? I think there is an item about this on the chado tracker with low priority... (so we are seeing ICs replaced by IEAs?... but this wouldn't explain the increase in both, or the non-filtering reported in the other ticket ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 16:02:43
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Chado item #3586386, was opened at 2012-11-12 08:57 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586386&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: 3 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: filtering IEA odd behaviuor Initial Comment: GO:0004674 protein serine/threonine kinase activity IEA KW-0723 GO_REF:0000004 has_substrate mei2 IDA Watanabe Y et al. (1997) has_substrate ste11 IDA Li P et al. (1996) has_substrate cpc2 IDA McLeod M et al. (2000) in current data, so even though there are IDA's the IEA is kept This is in NG28 so we should check what 29 looks like. This could be something to do with extnsions not being included in filtering, but I though thsi was fixed. Anyway, not urgent, we'll see what 29 looks like, just wanted to flag it ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-28 08:02 Message: Also see SF 3590727 on what reaches the GAF. https://sourceforge.net/tracker/?func=detail&aid=3590727&group_id=65526&atid=2096276 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586386&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 16:02:03
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Chado item #3590727, was opened at 2012-11-28 08:02 Message generated for change (Tracker Item Submitted) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&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: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: IC (and IEA?) filtering Initial Comment: In my investigations for the missing 'from' .problem (SF 3590723), I also noticed that the number of IC annotations that reach the GAF has varied over time by far more than can be explained by actual annotation changes. Examples: pombase-build-2012-10-19-v1-l1.gaf - 215 pombase-build-2012-11-05-v1-l1.gaf - 214 pombase-build-2012-11-18-v2-l1.gaf - 1126 pombase-build-2012-11-25-v2-l1.gaf - 1122 % grep -c 'evidence=IC' *contig finds about 1500 matches Val has also commented on the number of IEA annotations (6559 in the file committed to GOC). Is something up with filtering? Also see SF 3586386, which was about v28 and what shows up on pombase gene pages. https://sourceforge.net/tracker/?func=detail&aid=3586386&group_id=65526&atid=2096276 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 16:01:06
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Chado item #3590723, was opened at 2012-11-28 08:01 Message generated for change (Tracker Item Submitted) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590723&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: 7 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: 'from=' data missing from GAF for IC Initial Comment: Problem! The GAFs being written out from Chado don't have anything in column 8 (with/from) where the evidence (col 7) is IC. I used pombase-build-2012-11-25-v2-l1.gaf to the GAF in the GO repository. I looked a couple other GAFs from the dumps as well, and none had the data (tried pombase-build-2012-10-19-v1-l1.gaf, pombase-build-2012-11-05-v1-l1.gaf, pombase-build-2012-11-18-v2-l1.gaf). I didn't try to chase up every annotation, but the handful I spot-checked all had the requisite data in the embl files. Just one example: FT /GO="aspect=P; term=histone acetylation; GOid=GO:0016573; FT evidence=IC; db_xref=GO_REF:0000001; from=GO:0035267; FT date=20090301" becomes PomBase SPAC1F5.11c tra2 GO:0016573 GO_REF:0000001 IC P NuA4 complex phosphatidylinositol pseudokinase complex subunit Tra2 protein taxon:4896 20090301 PomBase The GO filter-gene-association.pl script is totally supposed to catch these, but equally totally failed -- it told me "Congratulations, there are no errors." and I didn't realize until today that it was lying. I'm reporting that to GO. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590723&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-26 16:36:41
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Chado item #3586373, was opened at 2012-11-12 07:57 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586373&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: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: global updates for a couple of publications Initial Comment: PMID:20519959 FYPO:0000124 FYPO:0000049 annotations can be globally updated to have the following conditions added: PCO:0000012 (YE3S) PCO:0000005 (25-32 degrees) evidence "cell growth assay" also same conditions and evidence for these terms for PMID:20473289 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-26 08:36 Message: Ignore comment about PMID:20404563 (18) PMID:18622392 (19) PMID:18310029 (21) PMID:15116432 (24) PMID:15821139 (18) I've done it with some perl val ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-26 08:08 Message: If its easy, these pubications all have "no allele qualifier" for phenotypes http://curation.pombase.org/kmr44/dumps/pombase-build-2012-11-18-v2-l1/warnings/qualifier_problems.tx For all of these allele=deletion PMID:20404563 (18) PMID:18622392 (19) PMID:18310029 (21) PMID:15116432 (24) PMID:15821139 (18) If we can do this during loading, we can prioritise the remaining papers through the curation system (preferably via community curation) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-12 08:18 Message: they also need PCO:0000090 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-12 07:59 Message: note these are all annotations in artemis so could this be done during loading (its a few 1000 annotations in total) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586373&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-26 16:08:07
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Chado item #3586373, was opened at 2012-11-12 07:57 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586373&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: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: global updates for a couple of publications Initial Comment: PMID:20519959 FYPO:0000124 FYPO:0000049 annotations can be globally updated to have the following conditions added: PCO:0000012 (YE3S) PCO:0000005 (25-32 degrees) evidence "cell growth assay" also same conditions and evidence for these terms for PMID:20473289 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-26 08:08 Message: If its easy, these pubications all have "no allele qualifier" for phenotypes http://curation.pombase.org/kmr44/dumps/pombase-build-2012-11-18-v2-l1/warnings/qualifier_problems.tx For all of these allele=deletion PMID:20404563 (18) PMID:18622392 (19) PMID:18310029 (21) PMID:15116432 (24) PMID:15821139 (18) If we can do this during loading, we can prioritise the remaining papers through the curation system (preferably via community curation) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-12 08:18 Message: they also need PCO:0000090 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-12 07:59 Message: note these are all annotations in artemis so could this be done during loading (its a few 1000 annotations in total) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586373&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-26 14:46:38
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Chado item #3537225, was opened at 2012-06-22 10:07 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3537225&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: 7 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: phenotype relations query Initial Comment: once the annotations are loaded, could you let us know how many phenotype annotation (and the PMIDs) use has_target has_regulation_target localizes it is likely we will need to substitute most of these for assayed_during (If there is any way to let us know this via the curation tool before the final load, even better, we can fix them) Thanks Val ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-26 06:46 Message: There are lots on the annotation extension page: http://curation.pombase.org/pombe/tools/ann_ex_locations Randomly selected one: allele=hrk1-V19E(V19E), annotation_extension=localizes(GeneDB_Spombe:SPCC962.02c) from d4e73d1a93ec5860 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-26 06:35 Message: At some point can we get a list of relations used for phenotype extensions? We thought that we had remapped all localizes etc to assayed_using These relations are not in the relevant extensions obo file (see details below), but they do not give any warnings (and we have examples of these relations in use for phenotypes) I should have recorded and example, but I didn't can anybody add one? val ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-12 03:51 Message: closing this as the relations has_target has_regulation_target localizes are not in the allowed relations for phenotypes, so assuming they would spawn warnings..... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3537225&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-26 14:35:44
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Chado item #3537225, was opened at 2012-06-22 10:07 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3537225&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: 7 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: phenotype relations query Initial Comment: once the annotations are loaded, could you let us know how many phenotype annotation (and the PMIDs) use has_target has_regulation_target localizes it is likely we will need to substitute most of these for assayed_during (If there is any way to let us know this via the curation tool before the final load, even better, we can fix them) Thanks Val ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-26 06:35 Message: At some point can we get a list of relations used for phenotype extensions? We thought that we had remapped all localizes etc to assayed_using These relations are not in the relevant extensions obo file (see details below), but they do not give any warnings (and we have examples of these relations in use for phenotypes) I should have recorded and example, but I didn't can anybody add one? val ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-12 03:51 Message: closing this as the relations has_target has_regulation_target localizes are not in the allowed relations for phenotypes, so assuming they would spawn warnings..... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3537225&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-26 14:30:51
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Chado item #3588341, was opened at 2012-11-18 09:04 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3588341&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: Closed Resolution: Duplicate Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: phenotype extensions relations Initial Comment: At some point can we get a list of relations used for phenotype extensions? We thought that we had remapped all localizes etc to assayed_using ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-26 06:30 Message: Yep but the other item is closed. I'll reopen and add a comment val ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-19 02:52 Message: isn't this the same question as in https://sourceforge.net/tracker/?func=detail&aid=3537225&group_id=65526&atid=2096276 ? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3588341&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-26 14:28:53
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Chado item #3367967, was opened at 2011-07-15 06:41 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3367967&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: Accepted >Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Kim Rutherford (kim_rutherford) Summary: GO/ FYPO export from Chado Initial Comment: when we export the GO data we need to make sure that only synonyms are in the synonym column, not like current GAF ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-26 06:28 Message: Lowering priority, we can raise when the FYPO export is more urgent val ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-11-06 02:25 Message: I think the GAF part is done, but I haven't started on the FYPO export yet. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-10-09 00:46 Message: I think so, it is the newer way, and I'm not sure but I think GPAD expects it, so it would make both the same ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-10-08 17:04 Message: Do you think a SO ID would be better? It's easy enough to change. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-10-08 16:37 Message: You probably know this but column 12 (the feature type) can contain the SO feature ID. val ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-10-07 21:40 Message: The ND rows are now in, with no complaints from filter-gene-association.pl ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-10-07 16:42 Message: This is mostly done. The GO filter-gene-association.pl script now reports only 20-ish errors, which we are looking at. I haven't added the ND annotations. I'll do that next. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-30 21:35 Message: There's another problem with dates. Some are stored in the GO way "20121022" (from GAF files) and some are stored in the ISO standard way "2012-10-22" (from the curation tool). The GAF files I'm writing have both formats, which the GAF file checker disapproves of. I'll rationalise things. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-29 02:28 Message: It turns out that I had implement the column 17 stuff months ago and then forgot. So it's already done. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-09-27 04:09 Message: might as well do it then (and see if it freaks 'em out as much as it did when we put stuff in column 16 ;) ) ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-27 03:57 Message: Thanks. It should be easy to add it where there is a "column_17" property in Chado. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-09-27 03:55 Message: > do we need to put anything in column 17? It's only desirable for the tiny number of annotations where there's a tag like "column_17=PR:000027503;". Even for them, it's optional on GO's end, and the reason to include it is to provide a bit more specificity about what form of a gene product is doing the business. If you do include it, just write out the "PR:000027503" part. There will probably be more column 17 entries in future, but they'll accumulate slowly. m ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-27 03:51 Message: The GAF writing is coming along, there are still some problems to fix but it now puts things like "happens_during(GO:0071276),has_regulation_target(SPBC660.07)" in column 16. You've probably told me before, but do we need to put anything in column 17? This page implies that it's optional: http://www.geneontology.org/GO.format.gaf-2_0.shtml ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-25 02:37 Message: The Chado database was missing some dates too - all dates from the input GAF files weren't being stored. That's fixed too and I'm now re-loading. I don't think that's a problem for Ensembl as the dates aren't soon on pombase.org. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-09-05 06:46 Message: This fits with what I would say. At present i delete psudos before submission. if a psudo warrnts any kind of annotation we would probably remove the pseudo tag and make another feature like a non coding RNA with a regultory role ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-05 03:14 Message: Right so. Thanks for that. I won't include the pseudogenes in the GAF output. Unfortunately I've meanwhile found a worse anomaly in Chado - there are lots of annotations without evidence code. I'm trying to track down how that happened. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-09-05 03:09 Message: Your question has prompted me to trawl through a fairly old (March 2006) exchange on GO & SO mailing lists, which can be scary. It starts here: https://mailman.stanford.edu/pipermail/go-discuss/2006-March/001782.html ... goes on and on, and some of it comes out in separate threads in the archive: https://mailman.stanford.edu/pipermail/go-discuss/2006-March/thread.html ... and it boils down to "it's complicated". But I think some usable simple answers would be ... > Does it make sense for pseudogenes to have GO annotation? Probably not; maybe with some rare exceptions, but if we did just say "never" we probably wouldn't lose much. The exceptions would come up if someone finds that a "pseudogene" is transcribed, and the transcript does something, usually regulatory, e.g. acts as antisense RNA for a "live" copy of the gene. But the email exchange included arguments that if that happens the feature shouldn't be called a pseudogene anyway ... but what if the community expect to see it called a pseudogene ... argh argh aaargh. That leads me to the second simple answer: > If so, should the annotation be exported to the GAF file? No. As long as we call something a pseudogene, we should not export any GO annotations for it to the GAF, even if we want to have the annotations for one of the exceptional circumstances. We don't want to piss them off, and we *really* don't want to reopen the can of pseudo-worms! m ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-04 21:06 Message: Does it make sense for pseudogenes to have GO annotation? If so, should the annotation be exported to the GAF file?: http://www.pombase.org/spombe/result/SPAC23D3.05c ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-08-02 04:24 Message: Only add NDs for protein coding genes. Add an ND annotation for each aspect that has no other annotation. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-07-09 03:46 Message: What's the format of the "ND mapping" file? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-09 03:16 Message: When we do the export we need to also create a ND mapping for when a gene product is missing a particular aspect. I checked the weekend before I went away that these were all valid (most are for conserved unknowns and sequence orphans, and as far as I am aware there are no outstanding appers for any of these. The numbers will be quite low (see Venn attached) (in fact the numbers will be slightly less than this because I managed to squeeze a few more ISS annotations in) ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-07-08 02:32 Message: I've added a separate tracker item for the GeneDB style mapping files: https://sourceforge.net/tracker/?func=detail&aid=3541336&group_id=65526&atid=2096276 ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-07-06 03:23 Message: Apparently I implemented some of this back in January. I don't remember doing it, but it probably wasn't someone else. The code as is doesn't write out the annotation extensions, so that still needs doing. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-07 08:41 Message: Also we need to replace some "Mappign files" generated from GeneDB They are all simple tab delimited format Mapping files described here: http://www.pombase.org/downloads/data-mapping ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-23 14:31 Message: GPAD/GPI documentation http://www.geneontology.org/GO.format.gpi.shtml http://www.geneontology.org/GO.format.gpad.shtml Not sure this documentation is up to date, check before use ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-06 14:05 Message: extending this item to cover phenotype annotations Sent this to Chris M when done ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2011-12-30 02:32 Message: I'll do the GAF export first as it's easier and probably more immediately useful. It's also easy to test because we can compare the output to the current GeneDB GAF files. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3367967&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-26 14:27:59
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Chado item #3586319, was opened at 2012-11-12 00:30 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586319&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: Closed Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Kim Rutherford (kim_rutherford) Summary: contigs used in Chado load Initial Comment: could you put a copy of the contigs which are used for a specific chado load here? http://curation.pombase.org/kmr44/dumps/ I will tell Mark to get the contigs for the ftp directory currently ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Cosmid_assembly_data/ (but will move to EBI soon) from here ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-26 06:27 Message: appears to be done. I have added an note to the jira ticket about ftp site to get the files from here when pombase is updated val ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-11-12 00:45 Message: That's make's sense. I'll alter the load script. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586319&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-26 14:25:49
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Chado item #3586319, was opened at 2012-11-12 00:30 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586319&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: Closed Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Kim Rutherford (kim_rutherford) Summary: contigs used in Chado load Initial Comment: could you put a copy of the contigs which are used for a specific chado load here? http://curation.pombase.org/kmr44/dumps/ I will tell Mark to get the contigs for the ftp directory currently ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Cosmid_assembly_data/ (but will move to EBI soon) from here ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-11-12 00:45 Message: That's make's sense. I'll alter the load script. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3586319&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-20 10:24:19
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Chado item #3515094, was opened at 2012-04-05 01:56 Message generated for change (Comment added) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3515094&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: Fixed Priority: 4 Private: No Submitted By: Kim Rutherford (kim_rutherford) Assigned to: Kim Rutherford (kim_rutherford) Summary: Fix incorrect curation tool load warning Initial Comment: This warning should be fixed - there isn't actually a problem: error in 011e491e: in SPAC22E12.07.1, duplicated annotation extension for exists_during (GO:0007127) ---------------------------------------------------------------------- >Comment By: Kim Rutherford (kim_rutherford) Date: 2012-11-20 02:24 Message: This warning seems to be gone now. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3515094&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-19 10:57:43
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Chado item #3564992, was opened at 2012-09-05 05:18 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3564992&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: 7 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: existing interaction weirdness Initial Comment: This is just a little odd, no worse: on the page for gene A, I'm seeing two existing interaction annotations involving only gene B and gene C. http://curation.pombase.org/pombe/curs/982304b134332abd/gene/3 screenshot on the way ... ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-19 02:57 Message: another example, transferred from other item: ------ when i am on this page ~curs/ff6fc192a2bc990a/gene/5 I see lots of interactors for sre2, but all of the interactions from the paper are showing, not just the ones for sre2 v ----- ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-19 02:56 Message: I think so. I'll keep this one open, because it's got a bit more commentary, and it was Kim who put it in this tracker. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-18 10:55 Message: Hi Midori, is this the same problem reported here on the curation tool tracker? val https://sourceforge.net/tracker/?func=detail&aid=3558452&group_id=65526&atid=2525791 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-09-07 04:24 Message: Uh-oh. I hope it turns out not to be horrible. I have seen it again, in a session I approved for Val (08dc04f357b0310b) -- I added a gene, then added an interaction involving that gene, and saw the existing interactions for something else. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-07 04:20 Message: Er, yeh, that's a bit odd. I hope it's not a deep Chado problem. I'll investigate. I've put priority up because there might be a data problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3564992&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-19 10:56:35
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Chado item #3564992, was opened at 2012-09-05 05:18 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3564992&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: 7 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: existing interaction weirdness Initial Comment: This is just a little odd, no worse: on the page for gene A, I'm seeing two existing interaction annotations involving only gene B and gene C. http://curation.pombase.org/pombe/curs/982304b134332abd/gene/3 screenshot on the way ... ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-19 02:56 Message: I think so. I'll keep this one open, because it's got a bit more commentary, and it was Kim who put it in this tracker. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-18 10:55 Message: Hi Midori, is this the same problem reported here on the curation tool tracker? val https://sourceforge.net/tracker/?func=detail&aid=3558452&group_id=65526&atid=2525791 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-09-07 04:24 Message: Uh-oh. I hope it turns out not to be horrible. I have seen it again, in a session I approved for Val (08dc04f357b0310b) -- I added a gene, then added an interaction involving that gene, and saw the existing interactions for something else. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-07 04:20 Message: Er, yeh, that's a bit odd. I hope it's not a deep Chado problem. I'll investigate. I've put priority up because there might be a data problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3564992&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-19 10:52:52
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Chado item #3588341, was opened at 2012-11-18 09:04 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3588341&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: Duplicate Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: phenotype extensions relations Initial Comment: At some point can we get a list of relations used for phenotype extensions? We thought that we had remapped all localizes etc to assayed_using ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-19 02:52 Message: isn't this the same question as in https://sourceforge.net/tracker/?func=detail&aid=3537225&group_id=65526&atid=2096276 ? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3588341&group_id=65526 |