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From: SourceForge.net <no...@so...> - 2011-03-31 10:40:32
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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 |
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From: SourceForge.net <no...@so...> - 2011-04-19 10:11:18
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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 |
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From: SourceForge.net <no...@so...> - 2011-04-19 12:19:18
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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 |
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From: SourceForge.net <no...@so...> - 2011-04-19 13:54:51
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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 13:54 Message: MOD tracker link for 'S-thiolated' request: https://sourceforge.net/tracker/?func=detail&aid=3289476&group_id=65472&atid=776607 ---------------------------------------------------------------------- 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 |
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From: SourceForge.net <no...@so...> - 2011-06-22 18:20:09
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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: 5 Private: No Submitted By: Valerie Wood (val_wood) >Assigned to: Midori Harris (gomidori) 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 13:54 Message: MOD tracker link for 'S-thiolated' request: https://sourceforge.net/tracker/?func=detail&aid=3289476&group_id=65472&atid=776607 ---------------------------------------------------------------------- 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-cysteinesulfinic 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 |
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From: SourceForge.net <no...@so...> - 2011-07-08 16:23:05
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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: Midori Harris (gomidori) 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: 2011-07-08 16:23 Message: now have mappings for S-thiolated and biotinylated (see MOD tracker links) if I don't hear anything in a few days about the MOD cleavage item, I'll assume we'll use a SO term and close this ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2011-04-19 13:54 Message: MOD tracker link for 'S-thiolated' request: https://sourceforge.net/tracker/?func=detail&aid=3289476&group_id=65472&atid=776607 ---------------------------------------------------------------------- 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 |
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From: SourceForge.net <no...@so...> - 2011-07-11 09:49:45
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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: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Midori Harris (gomidori) 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: 2011-07-11 09:49 Message: closing - Val has moved the cleavage annotations ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2011-07-08 16:23 Message: now have mappings for S-thiolated and biotinylated (see MOD tracker links) if I don't hear anything in a few days about the MOD cleavage item, I'll assume we'll use a SO term and close this ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2011-04-19 13:54 Message: MOD tracker link for 'S-thiolated' request: https://sourceforge.net/tracker/?func=detail&aid=3289476&group_id=65472&atid=776607 ---------------------------------------------------------------------- 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 |
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