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From: SourceForge.net <no...@so...> - 2011-04-19 12:19:18
|
Curation tasks item #3263423, was opened at 2011-03-31 10:31 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263423&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: modification ontology related Initial Comment: Need to 1. Decide which evidence codes are required IDA + 2. Write some text for the curation tool 3. Work out which terms the existing modifications map to (maybe the common ones could be mentioned in the help text) 4. ? ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2011-04-19 12:19 Message: updates: modification, proteolytic cleavage: This is the only one that still looks problematic. Because I don't see anything about cleavage in MOD, it might be best to use either GO or SO for the genes annotated with 'modification, proteolytic cleavage'. We could say that a gene product contains a SO:0100011 'cleaved_peptide_region' (or one of its descendants), or somehow capture that it's a target of GO:0006508 'proteolysis' (most likely GO:0051605 'protein maturation by peptide bond cleavage'). Or even both, if we feel ambitious. I have also put in a query on the MOD tracker (https://sourceforge.net/tracker/?func=detail&aid=3289479&group_id=65472&atid=776607) but of course I have no idea what they'll say. modification, biotinylated: requested MOD term https://sourceforge.net/tracker/?func=detail&aid=3289473&group_id=65472&atid=776607 modification, S-thiolated: requested MOD term modification, carboxymethylated - there's only one gene annotated, so I feel pretty confident it's MOD:01061 S-carboxymethyl-L-cysteine modification, lipoylated - I think it's MOD:00127 N6-lipoyl-L-lysine (see http://www.enzyme-database.org/glossary/lipoyl.html) modification, phosphatidylethanolominated - there's only one gene annotated, so I feel pretty confident it's MOD:00351 N-glycyl-1-(phosphatidyl)ethanolamine modification, phosphopantetheine attachment site - again, only one gene; I think it's MOD:00159 O-phosphopantetheine-L-serine modification, prenylated - I've convinced myself that MOD:00703 isoprenylated residue is fine (also note that rho5 doesn't need this annotation, as it's also annotated to 'modification, farnesylated', which corresponds to a child in MOD) modification, sulfinic acid formation - convinced that this is MOD:00267 L-cysteine sulfinic acid I have emailed the resulting cv-MOD mapping to Kim. m ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2011-03-31 11:20 Message: for #3, I did a quick 'n' dirty search of PSI-MOD: modification, acetylated (11) MOD:00394 acetylated residue modification, biotinylated (2) MOD needs grouping term modification, carboxymethylated (1) MOD needs grouping term modification, disulphide bond (2) MOD:00689 disulfide crosslinked residues modification, farnesylated (10) MOD:00437 farnesylated residue modification, gerenylgerenylated (3) MOD:00441 geranylgeranylated residue (note spelling) modification, glycosylated (84) MOD:00693 glycosylated residue modification, GPI attachment site (42) probably MOD:00818 glycosylphosphatidylinositolated residue modification, hypusination (1) MOD:00125 hypusine modification, lipidated (1) probably MOD:01155 lipoconjugated residue modification, lipoylated (4) maybe same as lipidated? i.e. probably MOD:01155 lipoconjugated residue modification, mannosylated (1) probably MOD:00595 mannosylated residue, tho there's also parent MOD:00727 mannosylated (attached to an amino acid directly OR to another modification) modification, methylated (10) MOD:00427 methylated residue modification, N-myristoylated (2) MOD:00438 myristoylated residue modification, neddylated (3) MOD:01150 neddylated lysine modification, palmitoylated (3) MOD:00440 palmitoylated residue modification, phosphatidylethanolominated (1) looks like MOD probably needs a grouping term (also note spelling should be phosphatidylethanolaminated) modification, phosphopantetheine attachment site (1) is this MOD:00159 O-phosphopantetheine-L-serine? modification, phosphorylated (1254) MOD:00696 phosphorylated residue modification, prenylated (4) would MOD:00703 isoprenylated residue work? If not, they'll need another grouping term modification, proteolytic cleavage (11) don't see anything obvious in MOD modification, RNA trimethylguanosine capped (1) not in MOD cos it's only protein modifications modification, S-thiolated (1) might want something under MOD:00860 sulfur containing residue, but not sure what modification, sulfinic acid formation (1) is this MOD:00267 L-cysteine sulfinic acid? modification, sumoylated (8) MOD:01149 sumoylated lysine modification, ubiquitinated (18) MOD:01148 ubiquitinylated lysine ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-03-31 10:40 Message: 4. When done bounce over to curation tool tracker! ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263423&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-19 10:11:18
|
Curation tasks item #3263423, was opened at 2011-03-31 10:31 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263423&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None >Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: modification ontology related Initial Comment: Need to 1. Decide which evidence codes are required IDA + 2. Write some text for the curation tool 3. Work out which terms the existing modifications map to (maybe the common ones could be mentioned in the help text) 4. ? ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2011-03-31 11:20 Message: for #3, I did a quick 'n' dirty search of PSI-MOD: modification, acetylated (11) MOD:00394 acetylated residue modification, biotinylated (2) MOD needs grouping term modification, carboxymethylated (1) MOD needs grouping term modification, disulphide bond (2) MOD:00689 disulfide crosslinked residues modification, farnesylated (10) MOD:00437 farnesylated residue modification, gerenylgerenylated (3) MOD:00441 geranylgeranylated residue (note spelling) modification, glycosylated (84) MOD:00693 glycosylated residue modification, GPI attachment site (42) probably MOD:00818 glycosylphosphatidylinositolated residue modification, hypusination (1) MOD:00125 hypusine modification, lipidated (1) probably MOD:01155 lipoconjugated residue modification, lipoylated (4) maybe same as lipidated? i.e. probably MOD:01155 lipoconjugated residue modification, mannosylated (1) probably MOD:00595 mannosylated residue, tho there's also parent MOD:00727 mannosylated (attached to an amino acid directly OR to another modification) modification, methylated (10) MOD:00427 methylated residue modification, N-myristoylated (2) MOD:00438 myristoylated residue modification, neddylated (3) MOD:01150 neddylated lysine modification, palmitoylated (3) MOD:00440 palmitoylated residue modification, phosphatidylethanolominated (1) looks like MOD probably needs a grouping term (also note spelling should be phosphatidylethanolaminated) modification, phosphopantetheine attachment site (1) is this MOD:00159 O-phosphopantetheine-L-serine? modification, phosphorylated (1254) MOD:00696 phosphorylated residue modification, prenylated (4) would MOD:00703 isoprenylated residue work? If not, they'll need another grouping term modification, proteolytic cleavage (11) don't see anything obvious in MOD modification, RNA trimethylguanosine capped (1) not in MOD cos it's only protein modifications modification, S-thiolated (1) might want something under MOD:00860 sulfur containing residue, but not sure what modification, sulfinic acid formation (1) is this MOD:00267 L-cysteine sulfinic acid? modification, sumoylated (8) MOD:01149 sumoylated lysine modification, ubiquitinated (18) MOD:01148 ubiquitinylated lysine ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-03-31 10:40 Message: 4. When done bounce over to curation tool tracker! ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263423&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-19 09:20:49
|
Curation tasks item #3289377, was opened at 2011-04-19 09:20 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=3289377&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: 9 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: GO central GO update Initial Comment: Do update to pick up i) new annotations for deletion project ii) PAINT iii) New GOA iv) Obsoletion fixes etc ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3289377&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-19 07:22:27
|
Curation tasks item #3289291, was opened at 2011-04-19 07:22 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=3289291&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: Versioning Initial Comment: Versioning for Ensembl will start Pombase 1.1 where 1. Is the sequence assembly version and .1 is the annotation version. GeneDB files need backwardly naming: GeneDB 1_date GeneDB 2_date ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3289291&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-19 06:40:40
|
Curation tasks item #3232445, was opened at 2011-03-21 16:10 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3232445&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None >Priority: 8 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Valerie Wood (val_wood) Summary: EMBL resubmission Initial Comment: To pick up new features http://www.genedb.org/genedb/pombe/newgenes.jsp and gene structure changes http://www.genedb.org/genedb/pombe/coordChanges.jsp and recent Broad updates (lots) FIRST check NCBI name problem fixed check dummy PMID fixed also fix strain of mating type contig instructions are in sequence update AFTER report update to Uniprot pomblelist NCBI Raja pir/ ensembl/biogrid Eleanor gp2protein from trac ticket: https://sourceforge.net/apps/trac/pombase/ticket/29 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3232445&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-16 17:49:40
|
Curation tasks item #3232448, was opened at 2011-03-21 16:12 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3232448&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: 6 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Valerie Wood (val_wood) Summary: Sequence update, followed by EMBL update Initial Comment: • Hideki, gap filling ? • Sasaki M, Idiris A, Tada A, Kumagai H, Giga-Hama Y, Tohda H. Yeast. 2008 Sep;25(9):673-9.PMID: 18727152 new telomeric clone pending http://www.sanger.ac.uk/Projects/S_pombe/sequence_updates.shtml http://www.sanger.ac.uk/Projects/S_pombe/sequence_discrepancies.shtml from trac ticket: https://sourceforge.net/apps/trac/pombase/ticket/30 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-04-16 17:49 Message: read in UTR files to ensure sequence updates propagated ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3232448&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-16 17:48:39
|
Curation tasks item #3288250, was opened at 2011-04-16 17:48 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=3288250&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: UTR datasets Initial Comment: Make available ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3288250&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-11 18:01:48
|
Curation tasks item #3284714, was opened at 2011-04-11 18:01 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=3284714&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: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: confirmed introns Initial Comment: Would be nice to add confirmed introns for all Solexa and Broad data ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3284714&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-10 19:38:13
|
Curation tasks item #3283812, was opened at 2011-04-10 19:38 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=3283812&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: annotate alternative transcripts Initial Comment: See GeneDB listed also /ID="SPAC31G5.09c" /note="alternative UTRs for this feature are represented by different polyA sites" ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3283812&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-04 21:45:10
|
Curation tasks item #3274373, was opened at 2011-04-04 16:18 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3274373&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: mating type region update Initial Comment: Need to follow this up at some point. MAy need to check further with Juan... Yes, what Xavi did is perfect. He's put together mat2 and mat3 with adjacent regions (which should be present in all h90 strains). In h90 cells, mat1 would switch between having a p cassette or a m cassette. In 972 h- there is a deletion of mat2-p. However, in some h+ strains there is a deletion of mat3-M, but more frequently there are mutations that prevent the switching from P to M, although mat2-P is still there. Therefore, one would have to assemble a different region for each strain. I think the configuration of the different h+ and h- strains is described in the very old pombe book. Anyway, most of the time people don't even know which h+ or h- allele they have. I think it would help to annotate mat1-m and mat3-m as such in the main contig (rather than calling them matmi_1 and _2 - or at least add a note), so that people know which one they are looking at. Also, it would help to annotate the features of the mating type region that Xavi put in his contig and that are present in 972 (like the IR-L and IR-R regions, or the homology boxes). Finally, would it be possible to add a note somewhere directing people to the mating type contig? I hope this is useful - let me know if I can help with anything else Juan ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-04-04 21:45 Message: These were follow up question, no response need to follow up again, I made mat1-m the primary name for SPBC1711.01 and mat3-m the primary name for SPBC27G7.17 is that correct? I will add the features Xavi annotated to the main genome seq. This will take a bit of time, so I will do it in a couple of months when I do all of the pending sequence changes. Do you think we should have links to the mating type contig from the genes in the region in the main sequence? I don't think there is currently an easy way to do this with GeneDB. I can make sure that it happens later. I could add a link from the project page and the genedb front page. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3274373&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-04 16:18:56
|
Curation tasks item #3274373, was opened at 2011-04-04 16:18 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=3274373&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: mating type region update Initial Comment: Need to follow this up at some point. MAy need to check further with Juan... Yes, what Xavi did is perfect. He's put together mat2 and mat3 with adjacent regions (which should be present in all h90 strains). In h90 cells, mat1 would switch between having a p cassette or a m cassette. In 972 h- there is a deletion of mat2-p. However, in some h+ strains there is a deletion of mat3-M, but more frequently there are mutations that prevent the switching from P to M, although mat2-P is still there. Therefore, one would have to assemble a different region for each strain. I think the configuration of the different h+ and h- strains is described in the very old pombe book. Anyway, most of the time people don't even know which h+ or h- allele they have. I think it would help to annotate mat1-m and mat3-m as such in the main contig (rather than calling them matmi_1 and _2 - or at least add a note), so that people know which one they are looking at. Also, it would help to annotate the features of the mating type region that Xavi put in his contig and that are present in 972 (like the IR-L and IR-R regions, or the homology boxes). Finally, would it be possible to add a note somewhere directing people to the mating type contig? I hope this is useful - let me know if I can help with anything else Juan ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3274373&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-04 15:42:22
|
Curation tasks item #3274303, was opened at 2011-04-04 15:42 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=3274303&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: Community curation/ BioGRID Initial Comment: Still need to submit some of the the Biogrid curation from the commuity curation pilot ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3274303&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-04-04 12:17:55
|
Curation tasks item #3273960, was opened at 2011-04-04 12:17 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=3273960&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: horizontal transfer Initial Comment: curate horizontal transfer events from Broad paper ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3273960&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-03-31 16:48:51
|
Curation tasks item #3232443, was opened at 2011-03-21 16:09 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3232443&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None >Priority: 7 Private: No Submitted By: Midori Harris (gomidori) >Assigned to: Kim Rutherford (kim_rutherford) Summary: Host Contig files locally Initial Comment: We need to host the contig files somewhere where myself Midori and Antonia will be able to edit them in Artemis simultaneously..... val from trac ticket: https://sourceforge.net/apps/trac/pombase/ticket/25 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-03-31 16:48 Message: Moved up priority. Will need so we can all annotate in Artemis ..... Should think about doing this in about a month if possible...(latest before Antonia starts) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3232443&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-03-31 11:13:06
|
Curation tasks item #3263560, was opened at 2011-03-31 11:13 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=3263560&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 cellualr protein localization annotations Initial Comment: Need to follow up this at some point (and figure out how stored in Chado) ----- email Yep I have a bunch of these stored another way cellular protein localization GO term and IGI with SPACxxxx qualifier=localization_dependency is semantically equivalent The problem with this syntax is that it should really be evidence code IMP because although 2 genes are involved only one is mutated. When I first started doing this the annotation extension column did not exist and this was the only way I could capture the target easily. It is possible I have some of these as annotation_extension(localization_target(SPACxxxx) too On 27/01/2011 19:58, Kim Rutherford wrote: > "term=localization target Wee1; db_xref=PMID:19474789; date=20090826" ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263560&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-03-31 10:47:08
|
Curation tasks item #3263461, was opened at 2011-03-31 10:47 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=3263461&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 syntax checks to implement Initial Comment: IC should always have "from" IPI should always have "with" IGI should always have "with" GO ID should exist in ontology db_xref should only contain PMID:xxx OR GO_REF:xxx or GOC:unpublished GO term should not use synonym ID ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263461&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-03-31 10:40:32
|
Curation tasks item #3263423, was opened at 2011-03-31 10:31 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263423&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: modification ontology related Initial Comment: Need to 1. Decide which evidence codes are required IDA + 2. Write some text for the curation tool 3. Work out which terms the existing modifications map to (maybe the common ones could be mentioned in the help text) 4. ? ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-03-31 10:40 Message: 4. When done bounce over to curation tool tracker! ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263423&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-03-31 10:31:53
|
Curation tasks item #3263423, was opened at 2011-03-31 10:31 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=3263423&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: modification ontology frelated Initial Comment: Need to 1. Decide which evidence codes are required IDA + 2. Write some text for the curation tool 3. Work out which terms the existing modifications map to (maybe the common ones could be mentioned in the help text) 4. ? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3263423&group_id=65526 |
From: SourceForge.net <no...@so...> - 2011-03-22 18:43:17
|
Curation tasks item #3235241, was opened at 2011-03-22 18:43 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=3235241&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: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: deletion project updates Initial Comment: Follow this up with Kwang and Jacky ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3235241&group_id=65526 |