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pombase-go-annotation — PomBase GO annotations
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From: SourceForge.net <no...@so...> - 2012-10-08 23:59:43
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GO annotation item #3396780, was opened at 2011-08-23 02:02 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3396780&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: potassium ion transport Initial Comment: probably most of these experimental annotations can be moved down to "potassium ion transmembrane transport" SPAC15A10.06 SPCC965.06 tpr1 trk1 trk1 trk2 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 16:59 Message: have annotations from mapping so closing for now ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3396780&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 23:52:27
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GO annotation item #2971333, was opened at 2010-03-16 08:30 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=2971333&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: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: N-glycosylation annotation specificity Initial Comment: dolichol linked oligosaccharide biosynthetic process (sub type of N-glycosylation) ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 16:52 Message: all genes annoted to dolichol linked oligosaccharide biosynthetic process in SGD are already annotated to this in Pombase s o closing ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=2971333&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 23:37:44
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GO annotation item #2727014, was opened at 2009-04-02 08:57 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=2727014&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: 3 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: GO: column 12 Initial Comment: should be SO ID or term (checking) ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 16:37 Message: ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2009-09-19 10:55 Message: > I thought a while ago that the scope of column12 was extended so > that we can > distinguish protein coding genes/rRNAs/tRNAs and use different types > of > identifers in addition to "gene". > > I was checking the documentation to verify this and find out how to > use > the field. > > the current documentation still states: > one of gene (SO:0000704), transcript (SO:0000673), protein (SO: > 0000358), > protein_structure, complex > > Does this need to be updated? can I use tRNA/rRNA in this field, or > should > it be the SO ID? IDs are in general preferable, but SO didn't exist when the GAF format came into existence, so we are stuck with using the names, otherwise we break backwards compatibility. Also the SO ID for protein above is problematic as it denotes a SO attribute. It seems the docs still state gene, transcript, protein, protein_structure, and complex. I'm not aware of any uses of complex, and I suspect the protein / protein_structure distinction reflects a confusion between biological entities vs database records (I confess I don't really understand the GOA pdb files, the IDs in there do not appear to be genuine PDB IDs). I think you should be able to use other SO types (denoted by label not ID ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=2727014&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 23:30:29
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GO annotation item #3309888, was opened at 2011-05-31 13:08 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3309888&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: GO annotations with no PMID /TRAINING? Initial Comment: The following genes have annotations which dhould have PMIDs attached as they have exp evidence codes. They are currently GOC:unpublished. Tracking down these should be annotation priorities when we get going (training exercise?) 1 acp2 1 alg11 1 apc10 1 ask1 1 atf1 1 atf31 1 bgs1 1 bir1 1 bqt2 1 ccr1 1 cdc2 1 cdt2 1 cpc2 1 crn1 1 cut8 1 dad1 1 dhp1 1 dis1 1 dpb3 1 duo1 1 fap2 1 fas1 1 for3 1 fub2 1 gas4 1 git11 1 gle1 1 gwt1 1 his5 1 mak2 1 mak3 1 mbx1 1 mcp6 1 mcp7 1 met9 1 meu13 1 mfr1 1 mus81 1 myo1 1 nrf1 1 nup40 1 orc4 1 pct1 1 pef1 1 pmc4 1 mfr1 1 mus81 1 myo1 1 nrf1 1 nup40 1 orc4 1 pct1 1 pef1 1 pmc4 1 png1 1 prp45 1 psf2 1 psm1 1 rad31 1 rem1 1 rho1 1 rpa43 1 rpt2 1 sam1 1 sbp1 1 shk1 1 sif3 1 slx1 1 smn1 1 spc34 1 spt16 1 stt3 1 sxa1 1 tpi1 1 ucp3 1 ura1 1 wis4 1 yip12 1 ynd1 2 ebp2 2 fap1 2 fin1 2 mag1 2 pmk1 2 ppk18 2 qcr8 2 swi6 3 gpi8 4 dpm3 4 sod22 5 rpc40 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 16:30 Message: closing as I cant see the annotations referred to, and i checked the first 7 if any do exist they will get fixed eventually ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-06-22 11:33 Message: not SPBC30B4.06c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-06-22 11:32 Message: new list: IMP alg11 apc10 bqt2 can1 dis1 fin1 mbx1 mcl1 rho1 IGI acp1 acp2 ask1 bir1 cdt2 dad1 dhp1 dpb3 dpm3 duo1 ecm33 fub2 gar1 gpi8 gwt1 his5 mag1 mak2 mak3 mfr1 nrf1 pef1 pmk1 png1 psf2 qcr8 rad31 rpc40 rpt2 sam1 sbp1 sod22 spc34 stt3 tpi1 ucp3 ura1 wis4 ynd1 IDA atf31 bgs1 fap1 fap2 gas4 gle1 met9 myo1 orc4 pmc4 ppk18 SPBC30B4.06c swi6 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2011-06-10 10:09 Message: a quick Friday-afternoon spot check reveals that the list is now out of sync with the GAF file ... e.g. 1 acp2 everything on web page has a PMID now 1 apc10 GO:0008054 IMP has PMID:17072883 in current file 1 ask1 GO:0034613 IGI has PMID:17072883 in current file 1 atf1 GO:0005515 not in current file 1 atf31 GO:0005634 has PMID:17072883 in current file (in addition to PMID:16823372) .. so I think it would make sense to regenerate the list before we do much more to hunt publications. m ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-05-31 13:11 Message: 1 alg11 done ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3309888&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 20:47:56
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GO annotation item #3422852, was opened at 2011-10-13 00:25 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3422852&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: new mitochondrial complex Initial Comment: MitOS http://www.ncbi.nlm.nih.gov/pubmed/21987634?dopt=Abstract annotate when SGD have curated this ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3422852&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 20:42:13
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GO annotation item #3475589, was opened at 2012-01-18 10:26 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3475589&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: Elongator complex-> tRNA wobble uridine modification Initial Comment: annotate all elongator complex http://old.genedb.org/genedb/GOcomponent?action=search&organism=pombe&search=Elongator+holoenzyme+complex%7C_%7C+%28GO%3A0033588%29 to tRNA wobble uridine modification GO:0002098 by ISS to SGD ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 13:42 Message: done ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3475589&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 20:29:06
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GO annotation item #2859847, was opened at 2009-09-16 02:13 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=2859847&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: Out of Date Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: document issues with RCA Initial Comment: for slimming and enrichment - critera for review - use in analysis (use translation as an example) compare numbers -are reported erros fed back to data producecers? if not how will they be corrected announce GO slim ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 13:29 Message: This is about issues with RCA generally if they come from function predictions. it doesn't really affect us as our RCA's are not of this type ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=2859847&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 20:26:27
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GO annotation item #3232310, was opened at 2011-03-21 08:30 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3232310&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: 1 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Nobody/Anonymous (nobody) Summary: GO: replace TAS annotations Initial Comment: March 2011 1460 Should be able to replace all with experimental or ISS from trac ticket: https://sourceforge.net/apps/trac/pombase/ticket/11 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 13:26 Message: reducing automatically..... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3232310&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 20:25:33
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GO annotation item #3232317, was opened at 2011-03-21 08:36 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3232317&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: 1 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Nobody/Anonymous (nobody) Summary: replace IEA mappings with manual (or remove) Initial Comment: The IEA data is filtered against the manual annotation to remove redundancy so the number of IEAs is moving towards zero (the total would now be ~50000) There's a spreadsheet/graph previously used in publications and reports in the dropbox FILES TO RELOCATE/GO_totals_graph.xls IEA totals Mar 11 3308 Feb 10 4743 Aug 09 4907 May 09 4613 We could just get this snapshot from the old annotation files... from trac ticket: https://sourceforge.net/apps/trac/pombase/ticket/19 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 13:25 Message: These are reducing automatically by redundency filtering against experimental data and conversion to manual ISO's ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 02:21 Message: Jul11 3523 (should come done again when F_P Link annotations are back (better evidence codes) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-10 12:40 Message: 03/02/2011 43551 prefiltering 18605 post filtering ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3232317&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 20:20:51
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GO annotation item #3354224, was opened at 2011-07-05 04:25 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3354224&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: Out of Date Priority: 2 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: getting fission yeast annotation into GOA Initial Comment: Need to figure out how to get the remaining 3068 into GOA..... SUMMARY ======= Number of lines processed: 36568 Total number of annotations: 36543 Number of annotations assigned by GeneDB_Spombe: 32543 Number of annotations assigned by RefGenome: 232 Number of annotation assigned by other sources: 3768 Total number of annotations excluded: 3068 Number of annotations excluded with reason "With_string should not be supplied for evidence code": 2 Number of annotations excluded with reason "No mapping to UniProt": 1257 Number of annotations excluded with reason "With_string not recognised or not valid for evidence code": 1809 Total number of warnings: 272 Number of annotations with warning "Unrecognised or unsupported relation(s) in annotation_extension": 272 Number of annotations output: 29827 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 00:04 Message: wrong item, moving back ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 00:03 Message: moving to Chado tracker ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-05 05:05 Message: uploaded exclusions .log. Tony can regenerate this as required Fixing these 2 which were IEP with a "with" field Number of annotations excluded with reason "With_string should not be supplied for evidence code": 2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3354224&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 20:16:47
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GO annotation item #2612089, was opened at 2009-02-18 02:04 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=2612089&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: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: GO: replace NAS annotations Initial Comment: 629 to replace or remove 17th Feb ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 13:16 Message: don't need SF item for this, they will gradually disappear as they are now filtered if redundent ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2009-08-21 08:30 Message: care- except "hardiwred terms for slimming etc" ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=2612089&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-09-13 16:12:22
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GO annotation item #3558385, was opened at 2012-08-16 03:23 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3558385&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: Midori Harris (gomidori) Summary: rti1 GO:0000739 Initial Comment: term will go obsolete update when SGD RAD52 (S000004494) is updated ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-09-13 09:12 Message: SGD just deleted theirs, so have done the same ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3558385&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-17 09:08:55
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GO annotation item #3554304, was opened at 2012-08-04 09:25 Message generated for change (Settings changed) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3554304&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: Valerie Wood (val_wood) Assigned to: Midori Harris (gomidori) Summary: response to pheomone -> cellular response to pheromone Initial Comment: All these annotations need to move down to http://old.genedb.org/amigo-cgi/term-details.cgi?term=GO:0019236&session_id=2760amigo1344097385 cellular response to pheromone ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-08-15 09:39 Message: I have changed all the direct annotations in Artemis. The rest either already have paths to cellular response to pheromone or will get them when I move GO:0000749 (https://sourceforge.net/tracker/?func=detail&aid=3557957&group_id=36855&atid=440764). My guess is that Antonia has used the cellular terms all along, since that' how you trained her ;) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3554304&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-16 10:23:43
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GO annotation item #3558385, was opened at 2012-08-16 03:23 Message generated for change (Tracker Item Submitted) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3558385&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: Midori Harris (gomidori) Summary: rti1 GO:0000739 Initial Comment: term will go obsolete update when SGD RAD52 (S000004494) is updated ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3558385&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-15 16:39:03
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GO annotation item #3554304, was opened at 2012-08-04 09:25 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3554304&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: 5 Private: No Submitted By: Valerie Wood (val_wood) >Assigned to: Midori Harris (gomidori) Summary: response to pheomone -> cellular response to pheromone Initial Comment: All these annotations need to move down to http://old.genedb.org/amigo-cgi/term-details.cgi?term=GO:0019236&session_id=2760amigo1344097385 cellular response to pheromone ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-08-15 09:39 Message: I have changed all the direct annotations in Artemis. The rest either already have paths to cellular response to pheromone or will get them when I move GO:0000749 (https://sourceforge.net/tracker/?func=detail&aid=3557957&group_id=36855&atid=440764). My guess is that Antonia has used the cellular terms all along, since that' how you trained her ;) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3554304&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-07-12 13:22:56
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GO annotation item #3541611, was opened at 2012-07-09 07:42 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3541611&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: Midori Harris (gomidori) Summary: NTR sensitive to potassium chloride Initial Comment: note to self Doms spt7 ada1 sgf11 sus1 spt3 gcn5 ada2 ada3 sgf29 ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-07-12 06:22 Message: sensitive to potassium chloride FYPO:0001214 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3541611&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-07-10 16:42:31
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GO annotation item #3542073, was opened at 2012-07-10 09:35 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3542073&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: NTR: eiosome filament Initial Comment: A filamentous cortical structure formed by the eiosome component Pil1. parent eisosome and cytoskeleton PMID:21900489 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-07-10 09:42 Message: ....wrong tracker ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3542073&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-07-10 16:35:07
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GO annotation item #3542073, was opened at 2012-07-10 09:35 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3542073&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: NTR: eiosome filament Initial Comment: A filamentous cortical structure formed by the eiosome component Pil1. parent eisosome and cytoskeleton PMID:21900489 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3542073&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-07-04 10:45:24
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GO annotation item #3536606, was opened at 2012-06-20 06:59 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3536606&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: Midori Harris (gomidori) Summary: rae1 GO:0055126 Initial Comment: term will go obsolete update when SGD:S000000909 GLE2 is updated (ISS) ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-07-04 03:45 Message: they've just deleted their GO:0055126 annotation, so I've done likewise ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3536606&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-06-26 10:53:50
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GO annotation item #3538071, was opened at 2012-06-26 03:52 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3538071&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: SP_KW:KW-0675 receptor mappings, possibly lots Initial Comment: There are a number of fission yeast gene products mapping to "receptor activity" which are not receptors in the "GO sense" "Combining with an extracellular or intracellular messenger to initiate a change in cell activity" most of these are using receptor quite loosely to indicate protein, or other moiety binding O43032 SPBC3B9.03 could be "GO:0005047 signal recognition particle binding" O13950 SPAC23H4.07c ditto O94270 GO:0045015 SPBP8B7.22 HDEL sequence binding O13813 tom22 not sure what the correct function here should be but it is not the existing GO:0005047signal recognition particle binding which should also be removed (I will report this separately to Ivo at Uniprot, this term is specific for the SRP) I won't pick any problems up for SP_KW:KW-0675 mapping in the future as I am filtering it for PomBase Many thanks Val ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-06-26 03:53 Message: wrong tracker ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3538071&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-06-26 10:52:50
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GO annotation item #3538071, was opened at 2012-06-26 03:52 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3538071&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: SP_KW:KW-0675 receptor mappings, possibly lots Initial Comment: There are a number of fission yeast gene products mapping to "receptor activity" which are not receptors in the "GO sense" "Combining with an extracellular or intracellular messenger to initiate a change in cell activity" most of these are using receptor quite loosely to indicate protein, or other moiety binding O43032 SPBC3B9.03 could be "GO:0005047 signal recognition particle binding" O13950 SPAC23H4.07c ditto O94270 GO:0045015 SPBP8B7.22 HDEL sequence binding O13813 tom22 not sure what the correct function here should be but it is not the existing GO:0005047signal recognition particle binding which should also be removed (I will report this separately to Ivo at Uniprot, this term is specific for the SRP) I won't pick any problems up for SP_KW:KW-0675 mapping in the future as I am filtering it for PomBase Many thanks Val ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3538071&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-06-22 15:38:03
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GO annotation item #3471904, was opened at 2012-01-10 07:50 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3471904&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: Midori Harris (gomidori) Assigned to: Midori Harris (gomidori) Summary: annotate PBF complex Initial Comment: When GO SFs 3471874 & 3471897 and SO SF 3471903 are done, annotate sep1, fkh2, mbx1 to - PBF complex GO:new - trsc reg GO:new (or, if SF 3471897 rejected, GO:0006357 ext happens_during(GO:0000216)); ext has_regulation_target [genes in list for cv term "transcriptionally regulated by PBF transcription complex"] - GO:0000982 ext SO:new note: GO annotation details in temporary file raise priority when necessary terms are in GO & SO ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-06-22 08:38 Message: done at last? ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-01-31 08:15 Message: note to self: PBF CC term and GO:982+SO term done ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3471904&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-06-20 13:59:33
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GO annotation item #3536606, was opened at 2012-06-20 06:59 Message generated for change (Tracker Item Submitted) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3536606&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: Midori Harris (gomidori) Summary: rae1 GO:0055126 Initial Comment: term will go obsolete update when SGD:S000000909 GLE2 is updated (ISS) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3536606&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-06-18 13:26:35
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GO annotation item #3535943, was opened at 2012-06-18 01:57 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3535943&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: Accepted Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Midori Harris (gomidori) Summary: tgs1 GO:0006387 Initial Comment: update because GO:0006387 is going obsolete ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-06-18 06:26 Message: done; also curated rest of paper (not much) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3535943&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-06-18 08:57:55
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GO annotation item #3535943, was opened at 2012-06-18 01:57 Message generated for change (Tracker Item Submitted) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3535943&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: Midori Harris (gomidori) Summary: tgs1 GO:0006387 Initial Comment: update because GO:0006387 is going obsolete ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096329&aid=3535943&group_id=65526 |
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