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From: SourceForge.net <no...@so...> - 2012-11-28 20:18:58
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Curation tasks item #3588698, was opened at 2012-11-20 01:24 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3588698&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: Valerie Wood (val_wood) Summary: migrate spindle pole to mitotic/meiotic spindle pole Initial Comment: most, but not all of the 214 genes annotated to GO:0005816 - spindle pole body should be moved down to +id: GO:0097431 +name: mitotic spindle pole (some are meiosis specific, should be easy to work out) step 1, fix those from the HTP screen by search and replace of the tem ID in the static file step 2 identifyl meiosis specific step3 search and replace term ID in artemis step4 fix any meiosis specifc manually (add to remapping file for chado loading) step 4 wait for one update cycle stp2 query for remainder and fix manually (should all be in curation tool) (actually may be a little tricker as direct annotations are not to spindle pole, but to children, will work out later....) ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-28 12:18 Message: have done step 1 by remapping GO:0005816 in /pombe-embl/external-go-data/GO_ORFeome_localizations2.txt to GO:0044732 will proceed after the next update ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3588698&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 20:00:32
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Curation tasks item #3588698, was opened at 2012-11-20 01:24 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3588698&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: Valerie Wood (val_wood) >Summary: migrate spindle pole to mitotic/meiotic spindle pole Initial Comment: most, but not all of the 214 genes annotated to GO:0005816 - spindle pole body should be moved down to +id: GO:0097431 +name: mitotic spindle pole (some are meiosis specific, should be easy to work out) step 1, fix those from the HTP screen by search and replace of the tem ID in the static file step 2 identifyl meiosis specific step3 search and replace term ID in artemis step4 fix any meiosis specifc manually (add to remapping file for chado loading) step 4 wait for one update cycle stp2 query for remainder and fix manually (should all be in curation tool) (actually may be a little tricker as direct annotations are not to spindle pole, but to children, will work out later....) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3588698&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 20:00:07
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Curation tasks item #3588698, was opened at 2012-11-20 01:24 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3588698&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: Valerie Wood (val_wood) Summary: migrate spindle pole to meiotic spindle pole Initial Comment: most, but not all of the 214 genes annotated to GO:0005816 - spindle pole body should be moved down to +id: GO:0097431 +name: mitotic spindle pole (some are meiosis specific, should be easy to work out) step 1, fix those from the HTP screen by search and replace of the tem ID in the static file step 2 identifyl meiosis specific step3 search and replace term ID in artemis step4 fix any meiosis specifc manually (add to remapping file for chado loading) step 4 wait for one update cycle stp2 query for remainder and fix manually (should all be in curation tool) (actually may be a little tricker as direct annotations are not to spindle pole, but to children, will work out later....) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3588698&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 19:56:47
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Curation tasks item #3301006, was opened at 2011-05-12 05:57 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3301006&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: Valerie Wood (val_wood) Summary: ftp site Initial Comment: needs a big tidy and archive sorting after we go live ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-28 11:56 Message: done my bit, rest on jira ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3301006&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 19:55:49
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Curation tasks item #3589464, was opened at 2012-11-23 11:36 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3589464&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: GO annotations to "homodimerization activity" etc Initial Comment: historically (and still be lots of databases) these are used for "anything which dimerizes.I have been removing them slowly and making "subunit composition" annotation instead. Most of them will pop out of the matrix intersects..... Should ask for a comment about this to be added to the GO term (I would even propose obsoletion, as it is used incorrectly the majority of the time) ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-28 11:55 Message: https://sourceforge.net/tracker/?func=detail&aid=3385788&group_id=65526&atid=2096421 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3589464&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-28 19:52:56
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Curation tasks item #3523035, was opened at 2012-05-02 07:21 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3523035&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: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: response to toxin Initial Comment: Check annotations to this term (and other terms we don't want to use) ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-28 11:52 Message: Reported to ones which have been made to fix. Reported problem in ontology to GO Blocked SP:KW mapping to "response to toxin" that's it for now so I'll close this, it'll be pretty easy to fix any others which crop up ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3523035&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-27 13:07:04
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Curation tasks item #3590354, was opened at 2012-11-27 05:06 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3590354&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: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: pombe cerevisiae orthologs Initial Comment: based on Sam's feedback, the following duplicates have been removed from V 18 (in drop box) 40 SPBC4.07c YDL007W 3582 SPBC4.07c YDL007W 47 SPCC162.01c NONE 161 SPCC162.01c NONE 1016 SPCC162.01c NONE 48 SPCC162.02c NONE 162 SPCC162.02c NONE 1015 SPCC162.02c NONE 49 SPCC162.03 NONE 163 SPCC162.03 NONE 1014 SPCC162.03 NONE 50 SPCC162.04c NONE 164 SPCC162.04c NONE 236 SPCC162.04c NONE 51 SPCC162.05 YOL096C 4859 SPCC162.05 YOL096C 52 SPCC162.06c YDR486C 1013 SPCC162.06c YDR486C 53 SPCC162.07 YDL161W|YLL038C|YLR206W 4677 SPCC162.07 YDL161W|YLL038C|YLR206W 54 SPCC162.08c YIL149C|YKR095W 4141 SPCC162.08c YKR095W|YIL149C 55 SPCC162.09c YLR450W|YML075C 4493 SPCC162.09c YLR450W|YML075C 56 SPCC162.10 NONE 165 SPCC162.10 NONE 3959 SPCC162.10 NONE 57 SPCC162.11c YNR012W 1012 SPCC162.11c YNR012W 58 SPCC162.12 YPL180W 1011 SPCC162.12 YPL180W ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3590354&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-27 13:06:32
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Curation tasks item #3590354, was opened at 2012-11-27 05:06 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3590354&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: Valerie Wood (val_wood) Summary: pombe cerevisiae orthologs Initial Comment: based on Sam's feedback, the following duplicates have been removed from V 18 (in drop box) 40 SPBC4.07c YDL007W 3582 SPBC4.07c YDL007W 47 SPCC162.01c NONE 161 SPCC162.01c NONE 1016 SPCC162.01c NONE 48 SPCC162.02c NONE 162 SPCC162.02c NONE 1015 SPCC162.02c NONE 49 SPCC162.03 NONE 163 SPCC162.03 NONE 1014 SPCC162.03 NONE 50 SPCC162.04c NONE 164 SPCC162.04c NONE 236 SPCC162.04c NONE 51 SPCC162.05 YOL096C 4859 SPCC162.05 YOL096C 52 SPCC162.06c YDR486C 1013 SPCC162.06c YDR486C 53 SPCC162.07 YDL161W|YLL038C|YLR206W 4677 SPCC162.07 YDL161W|YLL038C|YLR206W 54 SPCC162.08c YIL149C|YKR095W 4141 SPCC162.08c YKR095W|YIL149C 55 SPCC162.09c YLR450W|YML075C 4493 SPCC162.09c YLR450W|YML075C 56 SPCC162.10 NONE 165 SPCC162.10 NONE 3959 SPCC162.10 NONE 57 SPCC162.11c YNR012W 1012 SPCC162.11c YNR012W 58 SPCC162.12 YPL180W 1011 SPCC162.12 YPL180W ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3590354&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-27 12:34:08
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Curation tasks item #3590350, was opened at 2012-11-27 04:33 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3590350&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: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: ortholog updates Initial Comment: The following were annotted as having human orthologs but did not have conserved in vertebrate/metazo...now removed or fixed SPAC1039.11c SPAC23A1.07 SPAC30D11.01c SPAPB24D3.10c SPBC1289.12 removed SPBC1604.01 SPBC1683.02 removed SPBC1861.09 SPBC23E6.02 SPBC776.12c SPBC947.06c SPCC18B5.11c SPCC4B3.15 SPCC645.05c ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3590350&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-27 12:33:48
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Curation tasks item #3590350, was opened at 2012-11-27 04:33 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3590350&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: ortholog updates Initial Comment: The following were annotted as having human orthologs but did not have conserved in vertebrate/metazo...now removed or fixed SPAC1039.11c SPAC23A1.07 SPAC30D11.01c SPAPB24D3.10c SPBC1289.12 removed SPBC1604.01 SPBC1683.02 removed SPBC1861.09 SPBC23E6.02 SPBC776.12c SPBC947.06c SPCC18B5.11c SPCC4B3.15 SPCC645.05c ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3590350&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-23 19:36:48
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Curation tasks item #3589464, was opened at 2012-11-23 11:36 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3589464&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: GO annotations to "homodimerization activity" etc Initial Comment: historically (and still be lots of databases) these are used for "anything which dimerizes.I have been removing them slowly and making "subunit composition" annotation instead. Most of them will pop out of the matrix intersects..... Should ask for a comment about this to be added to the GO term (I would even propose obsoletion, as it is used incorrectly the majority of the time) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3589464&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-20 09:24:01
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Curation tasks item #3588698, was opened at 2012-11-20 01:24 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3588698&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: migrate spindle pole to meiotic spindle pole Initial Comment: most, but not all of the 214 genes annotated to GO:0005816 - spindle pole body should be moved down to +id: GO:0097431 +name: mitotic spindle pole (some are meiosis specific, should be easy to work out) step 1, fix those from the HTP screen by search and replace of the tem ID in the static file step 2 identifyl meiosis specific step3 search and replace term ID in artemis step4 fix any meiosis specifc manually (add to remapping file for chado loading) step 4 wait for one update cycle stp2 query for remainder and fix manually (should all be in curation tool) (actually may be a little tricker as direct annotations are not to spindle pole, but to children, will work out later....) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3588698&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-14 17:38:35
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Curation tasks item #3587172, was opened at 2012-11-14 09:38 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3587172&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: sort these before next EMBL submission Initial Comment: Chr 1: ==== WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: pyruvate decarboxylase (predicted) [(emb|CU329670.1|:c103544- 101872, c101869-101836)] -> [emb|CAB03601.3|] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: conserved fungal protein [(emb|CU329670.1|:2499035-2499159, 2499161- 2499353, 2499443-2499824, 2499875-2500236)] - > [emb|CAB16233.3|] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: rRNA processing protein Rrp36, DUF947 family (predicted) [(emb|CU329670.1|:2587729-2587897, 2587952- 2588028, 2588031-2588143, 2588182-2588620)] - > [emb|CAB90149.3|] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: kinetochore protein Nnf1 [(emb|CU329670.1|:4409773-4410192, 4410194- 4410391)] -> [emb|CAB66467.2|] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: mitochondrial ribosomal protein subunit Mrps9 (predicted) [(emb|CU329670.1|:5142407-5142628, 5142631- 5143224)] -> [emb|CAB10130.2|] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329670.1|:c1485023- 1485015] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329670.1|:1704621- 1704628] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329670.1|:c2214776- 2214769] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329670.1|:c2684726- 2684719] [gi|159883886|emb|CU329670.1|: delta, dna len= 5579133] Chr 2: ==== WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: ornithine decarboxylase antizyme with +1 programmed ribosomal frameshift Spa1 [(emb|CU329671.1|:c779869- 779669, c779667-779188)] -> [emb|CAB54822.2|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: translation initiation factor eIF3 alpha subunit (p135) (predicted) [(emb|CU329671.1|:c802851-802839, c802651- 800840, c800838-799142)] -> [emb|CAA19172.3|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: cell surface glycoprotein (predicted), DUF1773 family protein 6 [(emb|CU329671.1|:c1033776-1033610, c1033607- 1032857)] -> [emb|CAO77661.2|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: Lsd90 protein [(emb|CU329671.1|:c1950255-1950053, c1950050- 1948955, c1948953-1947985)] -> [emb|CAB16908.4|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: mitochondrial matrix protein import protein Tam41 (predicted) [(emb|CU329671.1|:c1988353-1988081, c1988015- 1987737, c1987675-1987102, c1987099- 1987044)] -> [emb|CAA20110.3|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: CGI-48 family (predicted) [(emb|CU329671.1|:2048336-2049892, 2049894- 2049896)] -> [emb|CAA18383.2|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: elongin-A, F-box protein Pof4 (predicted) [(emb|CU329671.1|:2053033- 2053517, 2053519-2053600)] -> [emb|CAA18385.2|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: conserved eukaryotic protein [(emb|CU329671.1|:c2108786-2108181, c2108178- 2106448)] -> [emb|CAA22622.3|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: IMPACT domain protein, involved in translation (predicted) [(emb|CU329671.1|:c2220322-2219937, c2219934- 2219430)] -> [emb|CAA18427.3|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: guanyl-nucleotide exchange factor Vps901 (predicted) [(emb|CU329671.1|:2708076-2709415, 2709418- 2709793)] -> [emb|CAA20730.2|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: splicing factor Cwf22 [(emb|CU329671.1|:3037988-3040331, 3040334- 3040650)] -> [emb|CAA20491.4|] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:c1598117- 1598111] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:1598549- 1598558] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:1599745- 1599752] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:c1601011- 1601003] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:1629197- 1629205] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:1643887- 1643896] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:1645083- 1645090] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:c1646349- 1646341] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:3814173- 3814180] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329671.1|:3814596- 3814605] [gi|157310380|emb|CU329671.1|: delta, dna len= 4539804] Chr 3: ==== WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: wtf element Wtf12 [(emb|CU329672.1|:1401530-1401668, 1401900- 1402172, 1402490-1402551, 1402553-1402672)] - > [emb|CAB63875.2|] [gi|157310483|emb|CU329672.1|: delta, dna len= 2452883] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: CDS: meiotic recombination protein (predicted) [(emb|CU329672.1|:c1775429- 1774236, c1774233-1773925)] -> [emb|CAA21438.3|] [gi|157310483|emb|CU329672.1|: delta, dna len= 2452883] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329672.1|:1092972- 1092980] [gi|157310483|emb|CU329672.1|: delta, dna len= 2452883] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329672.1|:c1106022- 1106014] [gi|157310483|emb|CU329672.1|: delta, dna len= 2452883] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329672.1|:c1139579- 1139572] [gi|157310483|emb|CU329672.1|: delta, dna len= 2452883] WARN SEQ_FEAT ShortIntron Introns should be at least 10 nt long FEATURE: intron: [emb|CU329672.1|:1475073- 1475080] [gi|157310483|emb|CU329672.1|: delta, dna len= 2452883] ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3587172&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-12 18:34:51
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Curation tasks item #3586405, was opened at 2012-11-12 10:34 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3586405&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: spbc32H8.15 appears to have a gene next to it Initial Comment: visible when EST track switched on, could be a non coding RNA or a protein coding gene. Dig out coordinates of the feature (I can't figure out how to get these from the browser) and flag the feature ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3586405&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-04 09:06:19
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Curation tasks item #3582683, was opened at 2012-11-02 07:48 Message generated for change (Comment added) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&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: Antonia Lock (antonialock) Assigned to: Valerie Wood (val_wood) Summary: paralogs Initial Comment: Nazia said that on GeneDB paralogs of a gene used to be listed. She said this was true for SPBCPT2R1.01c but this info has disappeared from both pombase and genedb (I can't see it in Artemis either but she said it was CV 'similar to' possibly). Sounds quite useful, where did it go? ---------------------------------------------------------------------- >Comment By: Antonia Lock (antonialock) Date: 2012-11-04 01:06 Message: ah ok. I'll close thix then as it is duplicate ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-03 07:35 Message: Yep the info is stored, will need to chat to Kim as we need to extract some info from the ortholog data for example SPBC12D12.04c YBL105C SPAC17G8.14c YBL105C is not explictly annotated as paralog, which is why I haven't hurried to display (basically it is incomplete), but easy to do. I'll raise the priority after I have fixed the N-C/term issues with the pombe cerevisiae ortholog table. The SF item is this one on the chado tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3399011&group_id=65526&atid=2096276 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-02 08:14 Message: hmmm, yes, there are a bunch of "similar to" cv terms in chado, but with nothing annotated to them: http://curation.pombase.org/pombe/search/type/cvterm?numrows=100&page=1&search-term=similar*&model=chado&submit=search I can't remember what we said we were doing with these ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-03 14:35:14
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Curation tasks item #3582683, was opened at 2012-11-02 07:48 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&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: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Valerie Wood (val_wood) Summary: paralogs Initial Comment: Nazia said that on GeneDB paralogs of a gene used to be listed. She said this was true for SPBCPT2R1.01c but this info has disappeared from both pombase and genedb (I can't see it in Artemis either but she said it was CV 'similar to' possibly). Sounds quite useful, where did it go? ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-03 07:35 Message: Yep the info is stored, will need to chat to Kim as we need to extract some info from the ortholog data for example SPBC12D12.04c YBL105C SPAC17G8.14c YBL105C is not explictly annotated as paralog, which is why I haven't hurried to display (basically it is incomplete), but easy to do. I'll raise the priority after I have fixed the N-C/term issues with the pombe cerevisiae ortholog table. The SF item is this one on the chado tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3399011&group_id=65526&atid=2096276 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-02 08:14 Message: hmmm, yes, there are a bunch of "similar to" cv terms in chado, but with nothing annotated to them: http://curation.pombase.org/pombe/search/type/cvterm?numrows=100&page=1&search-term=similar*&model=chado&submit=search I can't remember what we said we were doing with these ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-02 15:14:38
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Curation tasks item #3582683, was opened at 2012-11-02 07:48 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&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: Valerie Wood (val_wood) Summary: paralogs Initial Comment: Nazia said that on GeneDB paralogs of a gene used to be listed. She said this was true for SPBCPT2R1.01c but this info has disappeared from both pombase and genedb (I can't see it in Artemis either but she said it was CV 'similar to' possibly). Sounds quite useful, where did it go? ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-02 08:14 Message: hmmm, yes, there are a bunch of "similar to" cv terms in chado, but with nothing annotated to them: http://curation.pombase.org/pombe/search/type/cvterm?numrows=100&page=1&search-term=similar*&model=chado&submit=search I can't remember what we said we were doing with these ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-02 14:48:18
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Curation tasks item #3582683, was opened at 2012-11-02 07:48 Message generated for change (Tracker Item Submitted) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&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: Valerie Wood (val_wood) Summary: paralogs Initial Comment: Nazia said that on GeneDB paralogs of a gene used to be listed. She said this was true for SPBCPT2R1.01c but this info has disappeared from both pombase and genedb (I can't see it in Artemis either but she said it was CV 'similar to' possibly). Sounds quite useful, where did it go? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-27 08:24:38
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Curation tasks item #3580846, was opened at 2012-10-27 01:24 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3580846&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: Valerie Wood (val_wood) Summary: supporting refs for divergent orthologs Initial Comment: Go through my old cerevisiae ortholog table release notes and add evidences for some of the distant ortholog predictions. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3580846&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-24 21:26:28
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Curation tasks item #3579866, was opened at 2012-10-24 14:26 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3579866&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: work out waht to do with legacy gene expression Initial Comment: From Antonia: Just realized that there are quite a few controlled curations with gene expressions not in the format of a curated northern blot or whatever (see http://old.genedb.org/genedb/Curation?startLetter=g&size=100&organism=pombe ) these show up in the gene expression box (for an example see isa1) Some make sense for our current format (eg. expressed during S phase) some don't (eg. promoter contains DRE element) the ones that don't make sense look weird on the gene pages. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3579866&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-21 22:02:24
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Curation tasks item #3553913, was opened at 2012-08-02 22:09 Message generated for change (Comment added) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&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=2096421&aid=3553913&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-20 20:27:44
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Curation tasks item #3470272, was opened at 2012-01-06 05:56 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3470272&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: 2 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Nobody/Anonymous (nobody) >Summary: ncRNA annotation Initial Comment: In GeneDB only protein-coding genes had "characterisation status" annotated. In PomBase we should be able to assign status to a lot of the ncRNA genes as well. Note that not all of the status designations would be applicable to ncRNAs, but we can use "published" and "role inferred from homology". Any others? Also update http://www.pombase.org/status/gene-characterisation table and descriptions when RNAs have status. Also see items on ncRNA GO annotation https://sourceforge.net/tracker/?func=detail&aid=3232326&group_id=65526&atid=2096329 https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3316936&group_id=65526 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-20 13:27 Message: intergenic ncRNA which are not rNA, tRNA, SN/SNoRNA are generally refered to as "linc, or lncRNA (SO needs this synonym) http://www.sequenceontology.org/browser/current_cvs/term/SO:0001641 ..probably also need a SO term for "antisense RNA" ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3470272&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-17 16:31:22
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Curation tasks item #3577859, was opened at 2012-10-17 09:30 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3577859&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: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: unknowns Initial Comment: reference only I went through the "unknowns" list at the weekend and was able to update the following to inferred biological role: some they all changed from status 10 to 7 SPBC1703.03c /GO="aspect=P; term=ribosomal large subunit biogenesis; GOid=GO:0042273; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000002221; date=20121013" /primary_name=lin1 /synonym=snu40 /product="U5 snRNP subunit Snu40" /GO="aspect=C; term=snRNP U5; GOid=GO:0005682; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000001199; date=20060802" /GO="aspect=P; term=assembly of spliceosomal tri-snRNP; GOid=GO:0000244; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:O95400; date=20121013" /GO="aspect=C; term=U5 snRNP; GOid=GO:0005682; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:O95400; date=20121013" /primary_name=lin1 /synonym=snu40 /product="U5 snRNP subunit Snu40" /product="cactin, spliceosome complex subunit (predicted)" /systematic_id="SPBC2F12.12c" /GO="aspect=C; term=catalytic step 2 spliceosome; GOid=GO:0071013; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:Q8WUQ7; date=20121013" /GO="aspect=P; term=nuclear mRNA splicing, via spliceosome; GOid=GO:0000398; evidence=ISS; db_xref=GO_REF:0000001; from=GO:0071013; date=20121013" /systematic_id="SPCC18.15" /product="WD repeat protein, involved in diphthamide biosynthesis" /GO="aspect=P; term=endocytic recycling; GOid=GO:0032456; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000000450; date=20120703" /GO="aspect=P; term=peptidyl-diphthamide biosynthetic process from peptidyl-histidine; GOid=GO:0017183; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000000450; date=20120703" /primary_name="rtt10" /systematic_id="SPBC1306.02" /product="WD repeat protein, human WDR6 family, involved in endocytic recycling" /synonym="SPBC4.08" /controlled_curation="term=phenotype, viable; allele=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /GO="aspect=C; term=endosome; GOid=GO:0005768; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:; date=20120604" /GO="aspect=P; term=endocytic recycling; GOid=GO:0032456; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000006104; date=20120604" /systematic_id="SPAC1952.06c" /product="spliceosomal complex subunit (predicted)" /GO="aspect=C; term=spliceosomal complex; GOid=GO:0005681; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:Q8WYA6; date=20121013" /GO="aspect=P; term=mRNA splicing, via spliceosome; GOid=GO:0000398; evidence=IC; db_xref=GO_REF:0000001; from=GO:0005681; date=20121013" /systematic_id="SPBC2G5.01" /GO="aspect=C; term=endoplasmic reticulum; GOid=GO:0005783; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000005304; date=20051107" /GO="aspect=P; term=ER-nucleus signaling pathway; GOid=GO:0006984; evidence=ISS; db_xref=GO_REF:0000001; with=MGI:1914413; date=20121013" /colour=7 /product="ER protein involved in unfolded protein response (predicted)" /db_xref="SPD:17/17F11" /systematic_id="SPBC2G5.01" reference only SPBC1703.03c /GO="aspect=P; term=ribosomal large subunit biogenesis; GOid=GO:0042273; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000002221; date=20121013" /primary_name=lin1 /synonym=snu40 /product="U5 snRNP subunit Snu40" /GO="aspect=C; term=snRNP U5; GOid=GO:0005682; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000001199; date=20060802" /GO="aspect=P; term=assembly of spliceosomal tri-snRNP; GOid=GO:0000244; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:O95400; date=20121013" /GO="aspect=C; term=U5 snRNP; GOid=GO:0005682; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:O95400; date=20121013" /primary_name=lin1 /synonym=snu40 /product="U5 snRNP subunit Snu40" /product="cactin, spliceosome complex subunit (predicted)" /systematic_id="SPBC2F12.12c" /GO="aspect=C; term=catalytic step 2 spliceosome; GOid=GO:0071013; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:Q8WUQ7; date=20121013" /GO="aspect=P; term=nuclear mRNA splicing, via spliceosome; GOid=GO:0000398; evidence=ISS; db_xref=GO_REF:0000001; from=GO:0071013; date=20121013" /systematic_id="SPCC18.15" /product="WD repeat protein, involved in diphthamide biosynthesis" /GO="aspect=P; term=endocytic recycling; GOid=GO:0032456; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000000450; date=20120703" /GO="aspect=P; term=peptidyl-diphthamide biosynthetic process from peptidyl-histidine; GOid=GO:0017183; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000000450; date=20120703" /primary_name="rtt10" /systematic_id="SPBC1306.02" /product="WD repeat protein, human WDR6 family, involved in endocytic recycling" /synonym="SPBC4.08" /controlled_curation="term=phenotype, viable; allele=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /GO="aspect=C; term=endosome; GOid=GO:0005768; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:; date=20120604" /GO="aspect=P; term=endocytic recycling; GOid=GO:0032456; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000006104; date=20120604" /systematic_id="SPAC1952.06c" /product="spliceosomal complex subunit (predicted)" /GO="aspect=C; term=spliceosomal complex; GOid=GO:0005681; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:Q8WYA6; date=20121013" /GO="aspect=P; term=mRNA splicing, via spliceosome; GOid=GO:0000398; evidence=IC; db_xref=GO_REF:0000001; from=GO:0005681; date=20121013" /systematic_id="SPBC2G5.01" /GO="aspect=C; term=endoplasmic reticulum; GOid=GO:0005783; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000005304; date=20051107" /GO="aspect=P; term=ER-nucleus signaling pathway; GOid=GO:0006984; evidence=ISS; db_xref=GO_REF:0000001; with=MGI:1914413; date=20121013" /colour=7 /product="ER protein involved in unfolded protein response (predicted)" /db_xref="SPD:17/17F11" /systematic_id="SPBC2G5.01" ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-17 09:31 Message: for reference only ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3577859&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-17 16:30:51
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Curation tasks item #3577859, was opened at 2012-10-17 09:30 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3577859&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: unknowns Initial Comment: reference only I went through the "unknowns" list at the weekend and was able to update the following to inferred biological role: some they all changed from status 10 to 7 SPBC1703.03c /GO="aspect=P; term=ribosomal large subunit biogenesis; GOid=GO:0042273; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000002221; date=20121013" /primary_name=lin1 /synonym=snu40 /product="U5 snRNP subunit Snu40" /GO="aspect=C; term=snRNP U5; GOid=GO:0005682; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000001199; date=20060802" /GO="aspect=P; term=assembly of spliceosomal tri-snRNP; GOid=GO:0000244; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:O95400; date=20121013" /GO="aspect=C; term=U5 snRNP; GOid=GO:0005682; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:O95400; date=20121013" /primary_name=lin1 /synonym=snu40 /product="U5 snRNP subunit Snu40" /product="cactin, spliceosome complex subunit (predicted)" /systematic_id="SPBC2F12.12c" /GO="aspect=C; term=catalytic step 2 spliceosome; GOid=GO:0071013; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:Q8WUQ7; date=20121013" /GO="aspect=P; term=nuclear mRNA splicing, via spliceosome; GOid=GO:0000398; evidence=ISS; db_xref=GO_REF:0000001; from=GO:0071013; date=20121013" /systematic_id="SPCC18.15" /product="WD repeat protein, involved in diphthamide biosynthesis" /GO="aspect=P; term=endocytic recycling; GOid=GO:0032456; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000000450; date=20120703" /GO="aspect=P; term=peptidyl-diphthamide biosynthetic process from peptidyl-histidine; GOid=GO:0017183; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000000450; date=20120703" /primary_name="rtt10" /systematic_id="SPBC1306.02" /product="WD repeat protein, human WDR6 family, involved in endocytic recycling" /synonym="SPBC4.08" /controlled_curation="term=phenotype, viable; allele=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /GO="aspect=C; term=endosome; GOid=GO:0005768; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:; date=20120604" /GO="aspect=P; term=endocytic recycling; GOid=GO:0032456; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000006104; date=20120604" /systematic_id="SPAC1952.06c" /product="spliceosomal complex subunit (predicted)" /GO="aspect=C; term=spliceosomal complex; GOid=GO:0005681; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:Q8WYA6; date=20121013" /GO="aspect=P; term=mRNA splicing, via spliceosome; GOid=GO:0000398; evidence=IC; db_xref=GO_REF:0000001; from=GO:0005681; date=20121013" /systematic_id="SPBC2G5.01" /GO="aspect=C; term=endoplasmic reticulum; GOid=GO:0005783; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000005304; date=20051107" /GO="aspect=P; term=ER-nucleus signaling pathway; GOid=GO:0006984; evidence=ISS; db_xref=GO_REF:0000001; with=MGI:1914413; date=20121013" /colour=7 /product="ER protein involved in unfolded protein response (predicted)" /db_xref="SPD:17/17F11" /systematic_id="SPBC2G5.01" reference only SPBC1703.03c /GO="aspect=P; term=ribosomal large subunit biogenesis; GOid=GO:0042273; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000002221; date=20121013" /primary_name=lin1 /synonym=snu40 /product="U5 snRNP subunit Snu40" /GO="aspect=C; term=snRNP U5; GOid=GO:0005682; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000001199; date=20060802" /GO="aspect=P; term=assembly of spliceosomal tri-snRNP; GOid=GO:0000244; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:O95400; date=20121013" /GO="aspect=C; term=U5 snRNP; GOid=GO:0005682; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:O95400; date=20121013" /primary_name=lin1 /synonym=snu40 /product="U5 snRNP subunit Snu40" /product="cactin, spliceosome complex subunit (predicted)" /systematic_id="SPBC2F12.12c" /GO="aspect=C; term=catalytic step 2 spliceosome; GOid=GO:0071013; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:Q8WUQ7; date=20121013" /GO="aspect=P; term=nuclear mRNA splicing, via spliceosome; GOid=GO:0000398; evidence=ISS; db_xref=GO_REF:0000001; from=GO:0071013; date=20121013" /systematic_id="SPCC18.15" /product="WD repeat protein, involved in diphthamide biosynthesis" /GO="aspect=P; term=endocytic recycling; GOid=GO:0032456; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000000450; date=20120703" /GO="aspect=P; term=peptidyl-diphthamide biosynthetic process from peptidyl-histidine; GOid=GO:0017183; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000000450; date=20120703" /primary_name="rtt10" /systematic_id="SPBC1306.02" /product="WD repeat protein, human WDR6 family, involved in endocytic recycling" /synonym="SPBC4.08" /controlled_curation="term=phenotype, viable; allele=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /GO="aspect=C; term=endosome; GOid=GO:0005768; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:; date=20120604" /GO="aspect=P; term=endocytic recycling; GOid=GO:0032456; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000006104; date=20120604" /systematic_id="SPAC1952.06c" /product="spliceosomal complex subunit (predicted)" /GO="aspect=C; term=spliceosomal complex; GOid=GO:0005681; evidence=ISS; db_xref=GO_REF:0000001; with=UniProtKB:Q8WYA6; date=20121013" /GO="aspect=P; term=mRNA splicing, via spliceosome; GOid=GO:0000398; evidence=IC; db_xref=GO_REF:0000001; from=GO:0005681; date=20121013" /systematic_id="SPBC2G5.01" /GO="aspect=C; term=endoplasmic reticulum; GOid=GO:0005783; evidence=ISS; db_xref=GO_REF:0000001; with=SGD:S000005304; date=20051107" /GO="aspect=P; term=ER-nucleus signaling pathway; GOid=GO:0006984; evidence=ISS; db_xref=GO_REF:0000001; with=MGI:1914413; date=20121013" /colour=7 /product="ER protein involved in unfolded protein response (predicted)" /db_xref="SPD:17/17F11" /systematic_id="SPBC2G5.01" ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3577859&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-09 17:47:11
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Curation tasks item #3466153, was opened at 2011-12-27 14:31 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3466153&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: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: standardize warnings Initial Comment: some existing warnings can be combined/streamlined ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-09 10:47 Message: I have standardized existing warnings but they will need checking later..... will close this for now ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3466153&group_id=65526 |