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pombase-curation-tasks
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From: SourceForge.net <no...@so...> - 2012-11-02 14:48:18
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Curation tasks item #3582683, was opened at 2012-11-02 07:48 Message generated for change (Tracker Item Submitted) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Valerie Wood (val_wood) Summary: paralogs Initial Comment: Nazia said that on GeneDB paralogs of a gene used to be listed. She said this was true for SPBCPT2R1.01c but this info has disappeared from both pombase and genedb (I can't see it in Artemis either but she said it was CV 'similar to' possibly). Sounds quite useful, where did it go? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-02 15:14:38
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Curation tasks item #3582683, was opened at 2012-11-02 07:48 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Valerie Wood (val_wood) Summary: paralogs Initial Comment: Nazia said that on GeneDB paralogs of a gene used to be listed. She said this was true for SPBCPT2R1.01c but this info has disappeared from both pombase and genedb (I can't see it in Artemis either but she said it was CV 'similar to' possibly). Sounds quite useful, where did it go? ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-11-02 08:14 Message: hmmm, yes, there are a bunch of "similar to" cv terms in chado, but with nothing annotated to them: http://curation.pombase.org/pombe/search/type/cvterm?numrows=100&page=1&search-term=similar*&model=chado&submit=search I can't remember what we said we were doing with these ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-03 14:35:14
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Curation tasks item #3582683, was opened at 2012-11-02 07:48 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Valerie Wood (val_wood) Summary: paralogs Initial Comment: Nazia said that on GeneDB paralogs of a gene used to be listed. She said this was true for SPBCPT2R1.01c but this info has disappeared from both pombase and genedb (I can't see it in Artemis either but she said it was CV 'similar to' possibly). Sounds quite useful, where did it go? ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-11-03 07:35 Message: Yep the info is stored, will need to chat to Kim as we need to extract some info from the ortholog data for example SPBC12D12.04c YBL105C SPAC17G8.14c YBL105C is not explictly annotated as paralog, which is why I haven't hurried to display (basically it is incomplete), but easy to do. I'll raise the priority after I have fixed the N-C/term issues with the pombe cerevisiae ortholog table. The SF item is this one on the chado tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3399011&group_id=65526&atid=2096276 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-02 08:14 Message: hmmm, yes, there are a bunch of "similar to" cv terms in chado, but with nothing annotated to them: http://curation.pombase.org/pombe/search/type/cvterm?numrows=100&page=1&search-term=similar*&model=chado&submit=search I can't remember what we said we were doing with these ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-11-04 09:06:19
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Curation tasks item #3582683, was opened at 2012-11-02 07:48 Message generated for change (Comment added) made by antonialock You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Closed >Resolution: Duplicate Priority: 5 Private: No Submitted By: Antonia Lock (antonialock) Assigned to: Valerie Wood (val_wood) Summary: paralogs Initial Comment: Nazia said that on GeneDB paralogs of a gene used to be listed. She said this was true for SPBCPT2R1.01c but this info has disappeared from both pombase and genedb (I can't see it in Artemis either but she said it was CV 'similar to' possibly). Sounds quite useful, where did it go? ---------------------------------------------------------------------- >Comment By: Antonia Lock (antonialock) Date: 2012-11-04 01:06 Message: ah ok. I'll close thix then as it is duplicate ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-03 07:35 Message: Yep the info is stored, will need to chat to Kim as we need to extract some info from the ortholog data for example SPBC12D12.04c YBL105C SPAC17G8.14c YBL105C is not explictly annotated as paralog, which is why I haven't hurried to display (basically it is incomplete), but easy to do. I'll raise the priority after I have fixed the N-C/term issues with the pombe cerevisiae ortholog table. The SF item is this one on the chado tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3399011&group_id=65526&atid=2096276 ---------------------------------------------------------------------- Comment By: Midori Harris (gomidori) Date: 2012-11-02 08:14 Message: hmmm, yes, there are a bunch of "similar to" cv terms in chado, but with nothing annotated to them: http://curation.pombase.org/pombe/search/type/cvterm?numrows=100&page=1&search-term=similar*&model=chado&submit=search I can't remember what we said we were doing with these ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096421&aid=3582683&group_id=65526 |
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