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pombase-curation-tool — Canto curation tool issues
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From: SourceForge.net <no...@so...> - 2012-05-18 10:56:56
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Curation tool item #3527835, was opened at 2012-05-18 03:50 Message generated for change (Comment added) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3527835&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: Antonia Lock (antonialock) Assigned to: Kim Rutherford (kim_rutherford) Summary: bugs following recent update (20120518) Initial Comment: First one spotted: when on a gene page, the link to go back to the summary page is not working see for instance http://oliver0.sysbiol.cam.ac.uk/pombe/curs/47419e0c2f2a5f42/gene/1 ---------------------------------------------------------------------- >Comment By: Kim Rutherford (kim_rutherford) Date: 2012-05-18 03:56 Message: Now fixed. Sorry about that. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3527835&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-05-18 10:50:33
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Curation tool item #3527835, was opened at 2012-05-18 03:50 Message generated for change (Tracker Item Submitted) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3527835&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: Antonia Lock (antonialock) Assigned to: Kim Rutherford (kim_rutherford) Summary: bugs following recent update (20120518) Initial Comment: First one spotted: when on a gene page, the link to go back to the summary page is not working see for instance http://oliver0.sysbiol.cam.ac.uk/pombe/curs/47419e0c2f2a5f42/gene/1 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3527835&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-05-18 06:38:10
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Curation tool item #3527392, was opened at 2012-05-16 13:24 Message generated for change (Comment added) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3527392&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: Antonia Lock (antonialock) Assigned to: Kim Rutherford (kim_rutherford) Summary: New phenotype evidence code: chromatography evidence Initial Comment: Hi Kim, Could you please add a new phenotype evidence code? The one I want is ECO:0000325 [Term] id: ECO:0000325 name: chromatography evidence def: "A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase." [ECO:MCC] synonym: "chromatographic evidence" EXACT [] is_a: ECO:0000006 ! experimental evidence created_by: mchibucos creation_date: 2012-05-16T11:46:27Z ---------------------------------------------------------------------- >Comment By: Kim Rutherford (kim_rutherford) Date: 2012-05-17 23:38 Message: Done. I haven't updated the main tool recently and there are quite a few fixes and changes that have come in now I've updated. Please look out for any weirdness, especially with gene names and products. I'll fix things as soon as you let me know. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3527392&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-05-16 20:24:43
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Curation tool item #3527392, was opened at 2012-05-16 13:24 Message generated for change (Tracker Item Submitted) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3527392&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: Antonia Lock (antonialock) Assigned to: Kim Rutherford (kim_rutherford) Summary: New phenotype evidence code: chromatography evidence Initial Comment: Hi Kim, Could you please add a new phenotype evidence code? The one I want is ECO:0000325 [Term] id: ECO:0000325 name: chromatography evidence def: "A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase." [ECO:MCC] synonym: "chromatographic evidence" EXACT [] is_a: ECO:0000006 ! experimental evidence created_by: mchibucos creation_date: 2012-05-16T11:46:27Z ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3527392&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-05-16 11:04:37
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Curation tool item #3523268, was opened at 2012-05-03 08:35 Message generated for change (Settings changed) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3523268&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: Kim Rutherford (kim_rutherford) >Summary: We need to store and index the alt_id fields from OBO files Initial Comment: curs/82154f75e067e7cd review session, gives: (en) Please come back later ---------------------------------------------------------------------- >Comment By: Kim Rutherford (kim_rutherford) Date: 2012-05-16 04:04 Message: I don't know why I closed this as it's still a major problem. It needs to be fixed before the tool goes public. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-07 23:52 Message: Should we keep this item open for the bigger fix of handling merged IDs, or do you do this (it sounds like you just manually fixed?) Val ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-05-07 23:42 Message: The 141ca8ee8d8465c0 session worked as well now. It was the same problem. I checked all the sessions for that FYPO ID and fixed 3763e4e9332ec42e too. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-05-07 23:18 Message: The 82154f75e067e7cd session is now fixed. It failed because of FYPO:0000018. It looks like that term was used in the annotation then the term was deleted. The ID is now an alt_id: [Term] id: FYPO:0000779 name: dumbbell-shaped cells alt_id: FYPO:0000018 The curation tool doesn't index or store the alt_ids so when it tried to display that annotation, it fails to find it and dies. I've fixed the ID by hand in the database so you can get to the session now. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-05 08:02 Message: this session has disappeared too.... http://oliver0.sysbiol.cam.ac.uk/pombe/curs/141ca8ee8d8465c0 Could you take a look? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3523268&group_id=65526 |
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