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From: SourceForge.net <no...@so...> - 2013-04-30 10:20:20
|
Annotation issues item #3612224, was opened at 2013-04-29 12:09 Message generated for change (Comment added) made by asangrador You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3612224&group_id=36855 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: InterPro mapping Group: MGI Status: Open Resolution: None Priority: 5 Private: No Submitted By: Karen Christie (kchris) Assigned to: InterPro (interhelp) Summary: IPR001275, GO term mappings Initial Comment: Hi, Please consider removing the mapping for this InterPro domain to the GO term "sex differentiation". Mouse has 10-11 of these, 7 of which have been characterized experimentally and though many are involved in regulation of sex differentiation, for some of them, I do not think the existing evidence supports the contention that everything with IPR001275 is involved in "sex differentiation", specifically see Dmrt2 and Dmrta2 (aka Dmrt5). Dmrt2: http://www.informatics.jax.org/go/marker/MGI:1330307 Dmrta2: http://www.informatics.jax.org/go/marker/MGI:2653629 Also, it might be possible to update the existing MF mapping to "GO:0043565 sequence-specific DNA binding" to the more specific term "GO:0003700 - sequence-specific DNA binding transcription factor activity". thanks, Karen Current mappings: ---------------------------- Biological Process - GO:0006355 regulation of transcription, DNA-dependent - GO:0007548 sex differentiation Molecular Function - GO:0043565 sequence-specific DNA binding Cellular Component - GO:0005634 nucleus ---------------------------------------------------------------------- >Comment By: Amaia Sangrador (asangrador) Date: 2013-04-30 03:20 Message: I have removed the term "sex differentiation",as you suggested, as this may not apply to all the proteins with this domain (thanks for providing us this information). I haven't changed "sequence-specific DNA binding" to the more specific "sequence-specific DNA binding transcription factor activity" because when an entry represents a domain we try to refer the function to the domain instead of the whole protein, and this domain seems to be involved in DNA binding. But I have updated a family entry (IPR026607) that covers the same of proteins and added the term "sequence-specific DNA binding transcription factor activity", so this annotation won't be lost. The changes will appear in our next release. Thanks, Amaia ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3612224&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-30 10:12:34
|
Annotation issues item #3601979, was opened at 2013-01-24 02:55 Message generated for change (Settings changed) made by huntley You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 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: UniProt subcell2GO mapping Group: GOA >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: GOA project at EBI (goa-ebi) Summary: SP_SL:SL-0364 and pombe Initial Comment: Hi, We're picking up annotations to GO:0043595 for pombe spn6 and spn7, but the GO text definition and taxon restrictions indicate that this term is applicable only to prokaryotes. Either the UniProtKB-SubCell:SL-0364 term needs to be remapped, or it should be removed from these pombe proteins (and any other eukaryotic proteins). thanks, m ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-29 08:07 Message: Thank you! m ---------------------------------------------------------------------- Comment By: rach_huntley (huntley) Date: 2013-04-29 06:14 Message: Response from UniProt: I checked and updated entries Q09883 and O60165 and indeed the UniProt subcellular location seems inappropriate. I replaced the term "Spore wall, spore cortex" by "Forespore membrane; Peripheral membrane protein" which seems more appropriate (and not restricted to bacteria), according to PubMed: 20123972. The modifications will be publicly available at the next UniProt release. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-29 03:33 Message: OK, thanks for passing it on. I will be a happier bunny when I can stop deleting those annotations manually! m ---------------------------------------------------------------------- Comment By: rach_huntley (huntley) Date: 2013-04-29 01:06 Message: Hi Midori, Sorry, I just hadn't got around to this yet. The mapping looks OK so I have contacted UniProt to see if they can remove the location from the pombe proteins. I'll update when I know more. Rachael. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-11 03:19 Message: Has there been any action on this? The incorrect pombe annotations are still coming through. thanks, m ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-29 19:10:13
|
Annotation issues item #3612224, was opened at 2013-04-29 12:09 Message generated for change (Settings changed) made by kchris You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3612224&group_id=36855 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: InterPro mapping Group: MGI Status: Open Resolution: None Priority: 5 Private: No Submitted By: Karen Christie (kchris) Assigned to: InterPro (interhelp) >Summary: IPR001275, GO term mappings Initial Comment: Hi, Please consider removing the mapping for this InterPro domain to the GO term "sex differentiation". Mouse has 10-11 of these, 7 of which have been characterized experimentally and though many are involved in regulation of sex differentiation, for some of them, I do not think the existing evidence supports the contention that everything with IPR001275 is involved in "sex differentiation", specifically see Dmrt2 and Dmrta2 (aka Dmrt5). Dmrt2: http://www.informatics.jax.org/go/marker/MGI:1330307 Dmrta2: http://www.informatics.jax.org/go/marker/MGI:2653629 Also, it might be possible to update the existing MF mapping to "GO:0043565 sequence-specific DNA binding" to the more specific term "GO:0003700 - sequence-specific DNA binding transcription factor activity". thanks, Karen Current mappings: ---------------------------- Biological Process - GO:0006355 regulation of transcription, DNA-dependent - GO:0007548 sex differentiation Molecular Function - GO:0043565 sequence-specific DNA binding Cellular Component - GO:0005634 nucleus ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3612224&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-29 19:09:22
|
Annotation issues item #3612224, was opened at 2013-04-29 12:09 Message generated for change (Tracker Item Submitted) made by kchris You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3612224&group_id=36855 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: InterPro mapping Group: MGI Status: Open Resolution: None Priority: 5 Private: No Submitted By: Karen Christie (kchris) Assigned to: InterPro (interhelp) Summary: IPR001275 Initial Comment: Hi, Please consider removing the mapping for this InterPro domain to the GO term "sex differentiation". Mouse has 10-11 of these, 7 of which have been characterized experimentally and though many are involved in regulation of sex differentiation, for some of them, I do not think the existing evidence supports the contention that everything with IPR001275 is involved in "sex differentiation", specifically see Dmrt2 and Dmrta2 (aka Dmrt5). Dmrt2: http://www.informatics.jax.org/go/marker/MGI:1330307 Dmrta2: http://www.informatics.jax.org/go/marker/MGI:2653629 Also, it might be possible to update the existing MF mapping to "GO:0043565 sequence-specific DNA binding" to the more specific term "GO:0003700 - sequence-specific DNA binding transcription factor activity". thanks, Karen Current mappings: ---------------------------- Biological Process - GO:0006355 regulation of transcription, DNA-dependent - GO:0007548 sex differentiation Molecular Function - GO:0043565 sequence-specific DNA binding Cellular Component - GO:0005634 nucleus ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3612224&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-29 15:07:34
|
Annotation issues item #3601979, was opened at 2013-01-24 02:55 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 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: UniProt subcell2GO mapping Group: GOA Status: Open Resolution: None Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: GOA project at EBI (goa-ebi) Summary: SP_SL:SL-0364 and pombe Initial Comment: Hi, We're picking up annotations to GO:0043595 for pombe spn6 and spn7, but the GO text definition and taxon restrictions indicate that this term is applicable only to prokaryotes. Either the UniProtKB-SubCell:SL-0364 term needs to be remapped, or it should be removed from these pombe proteins (and any other eukaryotic proteins). thanks, m ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2013-04-29 08:07 Message: Thank you! m ---------------------------------------------------------------------- Comment By: rach_huntley (huntley) Date: 2013-04-29 06:14 Message: Response from UniProt: I checked and updated entries Q09883 and O60165 and indeed the UniProt subcellular location seems inappropriate. I replaced the term "Spore wall, spore cortex" by "Forespore membrane; Peripheral membrane protein" which seems more appropriate (and not restricted to bacteria), according to PubMed: 20123972. The modifications will be publicly available at the next UniProt release. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-29 03:33 Message: OK, thanks for passing it on. I will be a happier bunny when I can stop deleting those annotations manually! m ---------------------------------------------------------------------- Comment By: rach_huntley (huntley) Date: 2013-04-29 01:06 Message: Hi Midori, Sorry, I just hadn't got around to this yet. The mapping looks OK so I have contacted UniProt to see if they can remove the location from the pombe proteins. I'll update when I know more. Rachael. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-11 03:19 Message: Has there been any action on this? The incorrect pombe annotations are still coming through. thanks, m ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-29 13:14:49
|
Annotation issues item #3601979, was opened at 2013-01-24 02:55 Message generated for change (Comment added) made by huntley You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 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: UniProt subcell2GO mapping Group: GOA Status: Open Resolution: None Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: GOA project at EBI (goa-ebi) Summary: SP_SL:SL-0364 and pombe Initial Comment: Hi, We're picking up annotations to GO:0043595 for pombe spn6 and spn7, but the GO text definition and taxon restrictions indicate that this term is applicable only to prokaryotes. Either the UniProtKB-SubCell:SL-0364 term needs to be remapped, or it should be removed from these pombe proteins (and any other eukaryotic proteins). thanks, m ---------------------------------------------------------------------- >Comment By: rach_huntley (huntley) Date: 2013-04-29 06:14 Message: Response from UniProt: I checked and updated entries Q09883 and O60165 and indeed the UniProt subcellular location seems inappropriate. I replaced the term "Spore wall, spore cortex" by "Forespore membrane; Peripheral membrane protein" which seems more appropriate (and not restricted to bacteria), according to PubMed: 20123972. The modifications will be publicly available at the next UniProt release. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-29 03:33 Message: OK, thanks for passing it on. I will be a happier bunny when I can stop deleting those annotations manually! m ---------------------------------------------------------------------- Comment By: rach_huntley (huntley) Date: 2013-04-29 01:06 Message: Hi Midori, Sorry, I just hadn't got around to this yet. The mapping looks OK so I have contacted UniProt to see if they can remove the location from the pombe proteins. I'll update when I know more. Rachael. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-11 03:19 Message: Has there been any action on this? The incorrect pombe annotations are still coming through. thanks, m ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-29 10:33:14
|
Annotation issues item #3601979, was opened at 2013-01-24 02:55 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 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: UniProt subcell2GO mapping Group: GOA Status: Open Resolution: None Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: GOA project at EBI (goa-ebi) Summary: SP_SL:SL-0364 and pombe Initial Comment: Hi, We're picking up annotations to GO:0043595 for pombe spn6 and spn7, but the GO text definition and taxon restrictions indicate that this term is applicable only to prokaryotes. Either the UniProtKB-SubCell:SL-0364 term needs to be remapped, or it should be removed from these pombe proteins (and any other eukaryotic proteins). thanks, m ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2013-04-29 03:33 Message: OK, thanks for passing it on. I will be a happier bunny when I can stop deleting those annotations manually! m ---------------------------------------------------------------------- Comment By: rach_huntley (huntley) Date: 2013-04-29 01:06 Message: Hi Midori, Sorry, I just hadn't got around to this yet. The mapping looks OK so I have contacted UniProt to see if they can remove the location from the pombe proteins. I'll update when I know more. Rachael. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-11 03:19 Message: Has there been any action on this? The incorrect pombe annotations are still coming through. thanks, m ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-29 08:06:55
|
Annotation issues item #3601979, was opened at 2013-01-24 02:55 Message generated for change (Comment added) made by huntley You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 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: UniProt subcell2GO mapping Group: GOA Status: Open Resolution: None Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: GOA project at EBI (goa-ebi) Summary: SP_SL:SL-0364 and pombe Initial Comment: Hi, We're picking up annotations to GO:0043595 for pombe spn6 and spn7, but the GO text definition and taxon restrictions indicate that this term is applicable only to prokaryotes. Either the UniProtKB-SubCell:SL-0364 term needs to be remapped, or it should be removed from these pombe proteins (and any other eukaryotic proteins). thanks, m ---------------------------------------------------------------------- >Comment By: rach_huntley (huntley) Date: 2013-04-29 01:06 Message: Hi Midori, Sorry, I just hadn't got around to this yet. The mapping looks OK so I have contacted UniProt to see if they can remove the location from the pombe proteins. I'll update when I know more. Rachael. ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2013-04-11 03:19 Message: Has there been any action on this? The incorrect pombe annotations are still coming through. thanks, m ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-23 09:46:52
|
Annotation issues item #3611547, was opened at 2013-04-22 04:51 Message generated for change (Comment added) made by asangrador You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3611547&group_id=36855 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: InterPro mapping Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: RFoulger (rfoulger) Assigned to: InterPro (interhelp) Summary: Update GO mappings for Outer capsid protein (IPR009113) Initial Comment: In looking at the 'cell surface binding' terms, the GO mappings for IPR009113 can be updated: FROM: cell surface binding ; GO:0043498 TO: host cell surface binding ; GO:0046812 Also consider making the CC annotation more specific: FROM: GO:0019028 viral capsid TO: viral outer capsid ; GO:0039624 Let me know if you've any questions. Thanks, Becky ---------------------------------------------------------------------- >Comment By: Amaia Sangrador (asangrador) Date: 2013-04-23 02:46 Message: I have updated the GO terms as suggested. Thanks, Amaia ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3611547&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-22 11:51:11
|
Annotation issues item #3611547, was opened at 2013-04-22 04:51 Message generated for change (Tracker Item Submitted) made by rfoulger You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3611547&group_id=36855 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: InterPro mapping Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: RFoulger (rfoulger) Assigned to: InterPro (interhelp) Summary: Update GO mappings for Outer capsid protein (IPR009113) Initial Comment: In looking at the 'cell surface binding' terms, the GO mappings for IPR009113 can be updated: FROM: cell surface binding ; GO:0043498 TO: host cell surface binding ; GO:0046812 Also consider making the CC annotation more specific: FROM: GO:0019028 viral capsid TO: viral outer capsid ; GO:0039624 Let me know if you've any questions. Thanks, Becky ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3611547&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-15 12:28:36
|
Annotation issues item #3610745, was opened at 2013-04-13 04:05 Message generated for change (Comment added) made by asangrador You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3610745&group_id=36855 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: InterPro mapping Group: InterPro Status: Open Resolution: None Priority: 5 Private: No Submitted By: rach_huntley (huntley) Assigned to: InterPro (interhelp) Summary: InterPro mapping to UniProt:I3R230 Initial Comment: Hi, I received this through UniProt help, could you please copy me on any response since I need to resolve it also through the UniProt helpdesk. Thanks! Rachael. Hello Rachael, One of our users raised an issue which concerns the InterPro2GO mapping (see below). Could you transfer this message to the right person who will be able to answer to this user (fp...@bi...) ? Thanks a lot, Elisabeth -------- Original Message -------- Subject: [help #76238] [uuw] UniProtKB/TrEMBL I3R230 entry update request Date: Fri, 05 Apr 2013 13:29:21 +0200 From: Severine Duvaud via RT <sp...@ex...> Reply-To: sp...@ex... To: eli...@is... Fri Apr 05 13:29:21 2013: Request 76238 was acted upon. Transaction: Given to ecoudert by duvaud Queue: swiss-updates Subject: [uuw] UniProtKB/TrEMBL I3R230 entry update request Owner: ecoudert Requestors: fp...@bi... Status: new Ticket <URL: https://rt.isb-sib.ch//Ticket/Display.html?id=76238 > Initial request : ---------------------------------------------------------------- How did this function assignment happen? Unfortunately, I would like to question that the assignment is correct. Biological_process: coenzyme M biosynthetic process - there is no coenzyme M in halophilic archaea Inferred from electronic annotation. Source: InterPro - InterPro clearly states the following: "Homologues of ComB have been identified in all available cyanobacterial genome sequences and in genomes from phylogenetically diverse bacteria and archaea. However, many of these organisms lack homologues of other CoM biosynthetic genes" Thus, it seems invalid to copy the biological_process annotation from InterPro for organisms not having other coenzyme M biosynthesis genes. Name: Friedhelm Pfeiffer Subscribe: no Referred from: http://www.uniprot.org/uniprot/I3R230 Browser: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:19.0) Gecko/20100101 Firefox/19.0 ---------------------------------------------------------------------- >Comment By: Amaia Sangrador (asangrador) Date: 2013-04-15 05:28 Message: I have removed the coenzyme M biosynthetic process term from InterPro entry IPR005238, which was responsible for I3R230 annotation to this term. This entry was matching 7 Trembl proteins from halophilic archaea, including I3R230, as well as many bacterial and Methanoarchaeal proteins, and probably this is the reason why the small number of haloarchaeal matches was overlooked. Thanks for letting us know, Amaia ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3610745&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-13 11:05:29
|
Annotation issues item #3610745, was opened at 2013-04-13 04:05 Message generated for change (Tracker Item Submitted) made by huntley You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3610745&group_id=36855 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: InterPro mapping Group: InterPro Status: Open Resolution: None Priority: 5 Private: No Submitted By: rach_huntley (huntley) Assigned to: InterPro (interhelp) Summary: InterPro mapping to UniProt:I3R230 Initial Comment: Hi, I received this through UniProt help, could you please copy me on any response since I need to resolve it also through the UniProt helpdesk. Thanks! Rachael. Hello Rachael, One of our users raised an issue which concerns the InterPro2GO mapping (see below). Could you transfer this message to the right person who will be able to answer to this user (fp...@bi...) ? Thanks a lot, Elisabeth -------- Original Message -------- Subject: [help #76238] [uuw] UniProtKB/TrEMBL I3R230 entry update request Date: Fri, 05 Apr 2013 13:29:21 +0200 From: Severine Duvaud via RT <sp...@ex...> Reply-To: sp...@ex... To: eli...@is... Fri Apr 05 13:29:21 2013: Request 76238 was acted upon. Transaction: Given to ecoudert by duvaud Queue: swiss-updates Subject: [uuw] UniProtKB/TrEMBL I3R230 entry update request Owner: ecoudert Requestors: fp...@bi... Status: new Ticket <URL: https://rt.isb-sib.ch//Ticket/Display.html?id=76238 > Initial request : ---------------------------------------------------------------- How did this function assignment happen? Unfortunately, I would like to question that the assignment is correct. Biological_process: coenzyme M biosynthetic process - there is no coenzyme M in halophilic archaea Inferred from electronic annotation. Source: InterPro - InterPro clearly states the following: "Homologues of ComB have been identified in all available cyanobacterial genome sequences and in genomes from phylogenetically diverse bacteria and archaea. However, many of these organisms lack homologues of other CoM biosynthetic genes" Thus, it seems invalid to copy the biological_process annotation from InterPro for organisms not having other coenzyme M biosynthesis genes. Name: Friedhelm Pfeiffer Subscribe: no Referred from: http://www.uniprot.org/uniprot/I3R230 Browser: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:19.0) Gecko/20100101 Firefox/19.0 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3610745&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-11 10:19:33
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Annotation issues item #3601979, was opened at 2013-01-24 02:55 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 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: UniProt subcell2GO mapping Group: GOA Status: Open Resolution: None Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: GOA project at EBI (goa-ebi) Summary: SP_SL:SL-0364 and pombe Initial Comment: Hi, We're picking up annotations to GO:0043595 for pombe spn6 and spn7, but the GO text definition and taxon restrictions indicate that this term is applicable only to prokaryotes. Either the UniProtKB-SubCell:SL-0364 term needs to be remapped, or it should be removed from these pombe proteins (and any other eukaryotic proteins). thanks, m ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2013-04-11 03:19 Message: Has there been any action on this? The incorrect pombe annotations are still coming through. thanks, m ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3601979&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-04-02 17:23:55
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Annotation issues item #3591070, was opened at 2012-11-29 07:39 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3591070&group_id=36855 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: Matrix Group: None Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: IPR009018 mapping Initial Comment: is mapping to negative regulation of translational elongation but is SRP-dependent cotranslational protein targeting to membrane (Its mutation may affect the ragte of translation, but I don't think this is shown to be regulatory?) ---------------------------------------------------------------------- Comment By: Amaia Sangrador (asangrador) Date: 2012-12-04 02:25 Message: I have removed the term "negative regulation of translational elongation". I think this was originally added because in eukaryotes the SRP interaction with the nascent RNA retards translation elongation until SRP targets the complex to the translocation channel. But I agree that this is not regulation of translation elongation. Regards, Amaia ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3591070&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-03-18 10:43:56
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Annotation issues item #3608366, was opened at 2013-03-18 03:02 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3608366&group_id=36855 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: SPKW dicer Initial Comment: Dicer (pombe, possibly others) is mapped to GO:0004386 helicase activity IEA UniProtKB:KW-0347 But it isn't a helicase, its a ribonuclease. Thanks Val ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2013-03-18 03:43 Message: ignore, it proably does have helicase activity also ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3608366&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-03-18 10:02:51
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Annotation issues item #3608366, was opened at 2013-03-18 03:02 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3608366&group_id=36855 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: SPKW dicer Initial Comment: Dicer (pombe, possibly others) is mapped to GO:0004386 helicase activity IEA UniProtKB:KW-0347 But it isn't a helicase, its a ribonuclease. Thanks Val ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3608366&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-03-13 12:39:33
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Annotation issues item #3607789, was opened at 2013-03-12 09:15 Message generated for change (Comment added) made by huntley You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3607789&group_id=36855 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: InterPro mapping Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Prudence (prudencemutowo) Assigned to: InterPro (interhelp) Summary: Some InterPro entries-taxon violations Initial Comment: Please find below some InterPro entries whose GO mappings are violating taxon constraints as discussed today 12 March 2013 IPR012908 - has 1128 bacteria proteins vs 730 eukaryotic ones GO:0031227 intrinsic to endoplasmic reticulum membrane ‘restricted to eukaryotes’ IPR012052 - with 612 bacterial proteins (out of 615 total). This had GO:0050906 detection of stimulus involved in sensory perception which has a taxon constraint 'only in Eukaryota' IPR007379 -1575 bacterial proteins vs 557 eukaryotic ones, mapped to GO:0005744 which has taxon constraint only in eukaryota IPR014822 - f 765 viral proteins , is mapped to GO:0019034 viral replication complex -has the taxon constraint only in eukaryota IPR012799 -1398 bacterial proteins vs 1 eukaryotic one, is mapped to GO:0016507mitochondrial fatty acid beta-oxidation multienzyme complex which has a taxon constraint only _in_eukaryota IPR007803 Has 1157 bacterial proteins (out of 1500) , is mapped to GO:0030176 integral to endoplasmic reticulum membrane which has a taxon constraint only in eukaryota (for the endoplasmic reticulum part) regards Prudence ---------------------------------------------------------------------- >Comment By: rach_huntley (huntley) Date: 2013-03-13 05:39 Message: Tony and I were discussing the possibility of using the taxon constraints as a filter to remove any bad annotations, e.g. if there is a IPRO2GO mapping that makes 50% good annotations and 50% bad annotations, then we can use the taxon rules to remove the bad annotations and leave the good ones, instead of deleting the whole mapping. We need to look into the viability of this a bit more once we have the updated InterPro violations next week, so you might want to hold off on removing any mappings until we get back to you. Thanks, Rachael. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3607789&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-03-12 16:15:40
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Annotation issues item #3607789, was opened at 2013-03-12 09:15 Message generated for change (Tracker Item Submitted) made by prudencemutowo You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3607789&group_id=36855 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: InterPro mapping Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Prudence (prudencemutowo) Assigned to: InterPro (interhelp) Summary: Some InterPro entries-taxon violations Initial Comment: Please find below some InterPro entries whose GO mappings are violating taxon constraints as discussed today 12 March 2013 IPR012908 - has 1128 bacteria proteins vs 730 eukaryotic ones GO:0031227 intrinsic to endoplasmic reticulum membrane ‘restricted to eukaryotes’ IPR012052 - with 612 bacterial proteins (out of 615 total). This had GO:0050906 detection of stimulus involved in sensory perception which has a taxon constraint 'only in Eukaryota' IPR007379 -1575 bacterial proteins vs 557 eukaryotic ones, mapped to GO:0005744 which has taxon constraint only in eukaryota IPR014822 - f 765 viral proteins , is mapped to GO:0019034 viral replication complex -has the taxon constraint only in eukaryota IPR012799 -1398 bacterial proteins vs 1 eukaryotic one, is mapped to GO:0016507mitochondrial fatty acid beta-oxidation multienzyme complex which has a taxon constraint only _in_eukaryota IPR007803 Has 1157 bacterial proteins (out of 1500) , is mapped to GO:0030176 integral to endoplasmic reticulum membrane which has a taxon constraint only in eukaryota (for the endoplasmic reticulum part) regards Prudence ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3607789&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-02-22 10:49:04
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Annotation issues item #3605418, was opened at 2013-02-20 04:52 Message generated for change (Settings changed) made by asangrador You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3605418&group_id=36855 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: InterPro mapping Group: InterPro >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: rach_huntley (huntley) Assigned to: InterPro (interhelp) Summary: InterPro mappings to x-part terms Initial Comment: Hello, UniProt-GOA have just put in a sanity check to alert us to annotations that use the cellular component 'x-part' terms. It was agreed by GO Consortium before Christmas that these terms should not be directly annotated to because, logically, the x-part terms are equivalent to their x counterparts for the purposes of standard GO annotation. I've copied a list of the 'x-part' terms that InterPro have mappings for. You should be able to just move them up to the parent component term, e.g. 'virion part' annotations can move up to 'virion'. virion part (13087 annotations) bacterial-type flagellum part (6866) Golgi apparatus part (950) host cell part (174) Thanks, Rachael. ---------------------------------------------------------------------- Comment By: Amaia Sangrador (asangrador) Date: 2013-02-22 02:48 Message: Thanks for letting us know. I have already removed all the 'x-part' annotations. Amaia ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3605418&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-02-22 10:48:43
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Annotation issues item #3605418, was opened at 2013-02-20 04:52 Message generated for change (Comment added) made by asangrador You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3605418&group_id=36855 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: InterPro mapping Group: InterPro Status: Open Resolution: None Priority: 5 Private: No Submitted By: rach_huntley (huntley) Assigned to: InterPro (interhelp) Summary: InterPro mappings to x-part terms Initial Comment: Hello, UniProt-GOA have just put in a sanity check to alert us to annotations that use the cellular component 'x-part' terms. It was agreed by GO Consortium before Christmas that these terms should not be directly annotated to because, logically, the x-part terms are equivalent to their x counterparts for the purposes of standard GO annotation. I've copied a list of the 'x-part' terms that InterPro have mappings for. You should be able to just move them up to the parent component term, e.g. 'virion part' annotations can move up to 'virion'. virion part (13087 annotations) bacterial-type flagellum part (6866) Golgi apparatus part (950) host cell part (174) Thanks, Rachael. ---------------------------------------------------------------------- >Comment By: Amaia Sangrador (asangrador) Date: 2013-02-22 02:48 Message: Thanks for letting us know. I have already removed all the 'x-part' annotations. Amaia ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3605418&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-02-20 13:37:16
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Annotation issues item #3605424, was opened at 2013-02-20 05:37 Message generated for change (Tracker Item Submitted) made by paolaroncaglia You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3605424&group_id=36855 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: Paola Roncaglia (paolaroncaglia) Assigned to: Nobody/Anonymous (nobody) Summary: Annot. to GO:0010421 hydrogen peroxide-mediated programmed Initial Comment: Hello, Stemming from the apoptosis project, some edits have been done in the more general 'programmed cell death' node as well. In particular, I'm looking at GO:0010421 hydrogen peroxide-mediated programmed cell death. A new is_a parent term has just been created and added to it ('programmed cell death in response to reactive oxygen species'), and also an is_a link to existing 'cellular response to hydrogen peroxide'. Now looking at the manual annotations, one from UniProt looks incorrect: F2JXJ3 based on PMID:18502869: this is a bacterial protein and the paper abstract reads: 'The marine bacterium Pseudoalteromonas tunicata produces an antibacterial and autolytic protein, AlpP, which causes death of a subpopulation of cells during biofilm formation...'. Therefore this process shouldn't be annotated to a type of (programmed) cell death, but rather to 'killing of cells of other organism' or similar, I think. Many thanks, Paola ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3605424&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-02-20 12:52:19
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Annotation issues item #3605418, was opened at 2013-02-20 04:52 Message generated for change (Tracker Item Submitted) made by huntley You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3605418&group_id=36855 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: InterPro mapping Group: InterPro Status: Open Resolution: None Priority: 5 Private: No Submitted By: rach_huntley (huntley) Assigned to: InterPro (interhelp) Summary: InterPro mappings to x-part terms Initial Comment: Hello, UniProt-GOA have just put in a sanity check to alert us to annotations that use the cellular component 'x-part' terms. It was agreed by GO Consortium before Christmas that these terms should not be directly annotated to because, logically, the x-part terms are equivalent to their x counterparts for the purposes of standard GO annotation. I've copied a list of the 'x-part' terms that InterPro have mappings for. You should be able to just move them up to the parent component term, e.g. 'virion part' annotations can move up to 'virion'. virion part (13087 annotations) bacterial-type flagellum part (6866) Golgi apparatus part (950) host cell part (174) Thanks, Rachael. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3605418&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-02-14 10:39:49
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Annotation issues item #3604229, was opened at 2013-02-12 02:43 Message generated for change (Settings changed) made by amitchell1 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3604229&group_id=36855 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: InterPro mapping Group: FlyBase >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: susantweedie (stweedie) Assigned to: InterPro (interhelp) Summary: IPR000300 process mapping Initial Comment: I might be missing something but it seems odd that IPR000300 is named as a phosphatase (Inositol polyphosphate-related phosphatase) but mapped to a phosphorylation process term (phosphatidylinositol phosphorylation) should it be a dephosphorylation term? ---------------------------------------------------------------------- Comment By: alex mitchell (amitchell1) Date: 2013-02-13 01:47 Message: Hi Susan, That's a mistake on our part. I will fix it. The correction will be visible in InterPro release 42.0. Alex ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3604229&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-02-14 10:39:15
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Annotation issues item #3604642, was opened at 2013-02-14 00:05 Message generated for change (Settings changed) made by amitchell1 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3604642&group_id=36855 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: IPR012953 not necesarily regulation of cell cycle Initial Comment: BOP1, N-terminal domain (IPR012953) Has a mapping to regulation of cell cycle from 16362343 A cDNA clone encoding a putative Bop1 homologous protein was identified in Giardia lamblia. Since Bop1 is a nucleolar protein involved in rRNA processing, thereby controlling the cell cycle, but not all of rRNA processing is involved in cell cycle regulation (although some may be), ribosome biogenesis is more closely aligned to growth than to cell cycle. I don't see any evidence that this is involved in cell cycle. val ---------------------------------------------------------------------- Comment By: alex mitchell (amitchell1) Date: 2013-02-14 02:38 Message: Hi Val, Thanks for this - I've removed the contentious GO term. Alex ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3604642&group_id=36855 |
From: SourceForge.net <no...@so...> - 2013-02-14 10:38:55
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Annotation issues item #3604642, was opened at 2013-02-14 00:05 Message generated for change (Comment added) made by amitchell1 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3604642&group_id=36855 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: IPR012953 not necesarily regulation of cell cycle Initial Comment: BOP1, N-terminal domain (IPR012953) Has a mapping to regulation of cell cycle from 16362343 A cDNA clone encoding a putative Bop1 homologous protein was identified in Giardia lamblia. Since Bop1 is a nucleolar protein involved in rRNA processing, thereby controlling the cell cycle, but not all of rRNA processing is involved in cell cycle regulation (although some may be), ribosome biogenesis is more closely aligned to growth than to cell cycle. I don't see any evidence that this is involved in cell cycle. val ---------------------------------------------------------------------- >Comment By: alex mitchell (amitchell1) Date: 2013-02-14 02:38 Message: Hi Val, Thanks for this - I've removed the contentious GO term. Alex ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3604642&group_id=36855 |