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From: SourceForge.net <no...@so...> - 2011-11-17 21:31:34
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Ensembl item #3253204, was opened at 2011-03-28 10:17 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3253204&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 3 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: "liftover" Initial Comment: We will need this eventually to load datasets, so it would be good to also have it available as a community resource as SGD do. Before this can happen I will need to document the changes and the versions. Val I am an increasingly number of queries about mapping datasets between versions of the genome. Today I found out about the UCSC data convertor "LiftOver" which can perform this operation relatively seamlessly if supplied with "chain files". After talking to the SGD curators and developers, it appears that the creation of the initial chain files it is a slightly painful procedure, but this process only needs to be done once. So, has any community spirited person created these files previously and would like to make themselves very popular with everybody by making them publicly available (or a bioinformatician who would like to have a stab at making them?). We can then ask if the UCSC site will host the files on their public "liftOver" utility here: http://genome.ucsc.edu/cgi-bin/hgLiftOver There are only 5 sequence versions with minor changes. http://www.sanger.ac.uk/Projects/S_pombe/sequence_updates.shtml (I can help sorting out the physical sequences for the different versions) If there is nobody out there who can do this, I will put it on my Todo list but be warned that it isn't likely to happen immediately....... Many Thanks, Val ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3253204&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-11-17 21:26:03
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Ensembl item #3369231, was opened at 2011-07-17 03:20 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369231&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: write out gff files Initial Comment: This may happen already? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:00 Message: let John Mates know ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369231&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-11-17 21:25:30
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Ensembl item #3288250, was opened at 2011-04-16 10:48 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3288250&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: UTR datasets Initial Comment: Make available ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-11-17 13:25 Message: Closed, this will happen as part of data hosting ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3288250&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-11-17 21:24:47
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Ensembl item #3288254, was opened at 2011-04-16 10:57 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3288254&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: wiki links Initial Comment: Add links to wiki pages if they are about pombe genes e.g. SPBC11B10.09 http://en.wikipedia.org/wiki/Cdk1 SPAC2F7.03c http://en.wikipedia.org/wiki/Pom1 ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-11-17 13:24 Message: Moved to jira ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3288254&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-11-17 21:22:42
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Ensembl item #3274271, was opened at 2011-04-04 08:21 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3274271&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: generate Stats page from Ensembl Initial Comment: Should be able to automatically generate (an improved version) of this from the Ensembl data once everything is imported.... http://www.sanger.ac.uk/Projects/S_pombe/genome_stats.shtml ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3274271&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-07-17 21:44:41
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Ensembl item #3288250, was opened at 2011-04-16 17:48 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3288250&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: UTR datasets Initial Comment: Make available ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3288250&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-07-17 21:32:38
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Ensembl item #3369242, was opened at 2011-07-17 10:36 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369242&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: overlapping protein sequence Initial Comment: VERY LOW PRIORITY AUTOGENERATE LIST OF OVERLAPPING PROTEIN SEQ see thread below No worries, I now reilase I can find these from artemis. So that we don't need to maintain this manually it would be useful if they were autogenerated. However, becasue we will have them all annotated, and this is very unlikely to change, it proably isn't worth you speding any time on ...ignore...there's lots more important stuff to do.... if it comes up again I'll request (I will think about other "warnings" which can be autogenerated adn you can do them all together when the more important stuff is done) Val On 26/06/2011 20:21, mcd...@eb... wrote: > Hi Val, > > (ps Kim, we are not sat next to each other) > >> I wondered if it is possible to extract a list of protein coding regions >> which overlap with each other from Chado or Ensembl? > This should be easy to include in the PomBase website as an extra page. > > We could get out the locations with some SQL if you wanted them now though > before getting this into the website. > > I'll raise this as a feature request for JIRA. > > Mark > ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-07-17 21:32 Message: from other item I want to annotate all of the protein coding genes which overlap with each other (as the overlaps are usually small, only a few amino acids), but it is useful to users to know. I think this is most of them: http://old.genedb.org/genedb/Curation?organism=pombe&action=search&search=warning%2C+protein+coding+overlap+with+adjacent+gene We can identify these in Artemis, and check that all are flagged (the new gene structures may have added or removed some) from trac ticket: https://sourceforge.net/apps/trac/pombase/ticket/3 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369242&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-07-17 21:29:57
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Ensembl item #3235234, was opened at 2011-03-22 18:41 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3235234&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: Mapping for Orfeome cross references Initial Comment: Ensembl may need mapping for this ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-07-17 21:29 Message: done ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3235234&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-07-17 21:29:13
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Ensembl item #3264611, was opened at 2011-03-31 16:42 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3264611&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: Go extenstions required Initial Comment: PMID ID with /from fields later, annotation extensions ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-07-17 21:29 Message: on jira ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3264611&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-07-17 11:00:24
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Ensembl item #3369231, was opened at 2011-07-17 10:20 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369231&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: write out gff files Initial Comment: This may happen already? ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-07-17 11:00 Message: let John Mates know ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369231&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-07-17 10:36:18
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Ensembl item #3369242, was opened at 2011-07-17 10:36 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369242&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: overlapping protein sequence Initial Comment: VERY LOW PRIORITY AUTOGENERATE LIST OF OVERLAPPING PROTEIN SEQ see thread below No worries, I now reilase I can find these from artemis. So that we don't need to maintain this manually it would be useful if they were autogenerated. However, becasue we will have them all annotated, and this is very unlikely to change, it proably isn't worth you speding any time on ...ignore...there's lots more important stuff to do.... if it comes up again I'll request (I will think about other "warnings" which can be autogenerated adn you can do them all together when the more important stuff is done) Val On 26/06/2011 20:21, mcd...@eb... wrote: > Hi Val, > > (ps Kim, we are not sat next to each other) > >> I wondered if it is possible to extract a list of protein coding regions >> which overlap with each other from Chado or Ensembl? > This should be easy to include in the PomBase website as an extra page. > > We could get out the locations with some SQL if you wanted them now though > before getting this into the website. > > I'll raise this as a feature request for JIRA. > > Mark > ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369242&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-07-17 10:20:23
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Ensembl item #3369231, was opened at 2011-07-17 10:20 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369231&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: write out gff files Initial Comment: This may happen already? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3369231&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-16 17:57:39
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Ensembl item #3288254, was opened at 2011-04-16 17:57 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3288254&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: wiki links Initial Comment: Add links to wiki pages if they are about pombe genes e.g. SPBC11B10.09 http://en.wikipedia.org/wiki/Cdk1 SPAC2F7.03c http://en.wikipedia.org/wiki/Pom1 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3288254&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 16:05:01
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Ensembl item #3274347, was opened at 2011-04-04 16:05 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3274347&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: flag gene name conflicts Initial Comment: need to document how ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3274347&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 15:33:27
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Ensembl item #3273979, was opened at 2011-04-04 12:34 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&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: 3 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: Making genomic regions more easily accessible Initial Comment: I have had a couple of queries recently about locating centromeres, and a couple of queries abaout locating the mating type locus. These aren't easy to locate in GeneDB you can get to the separately annotated mating type region contig here http://old.genedb.org/genedb/ContigMap?organism=pombe I am just about to make misc features with SO ID fro centromeres SO:0000577 We do have individual centromere repeats annotated (dg, de etc) using the EMBL feature type repeat regoin ....... these should also be converted to SO terms/IDs (not the only existing children of centromeres in SO appear to be related to S. cerevisiae point centromeres and are not applicable to other organisms with modular centromeres). ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-04-04 15:33 Message: Found this item on my old to do list which is related..... We will need to ask a centoromere expert about this. Maybe something we could do in Boston...... 96. centromere associated ntr centromere central core cnp1 mis6 bub1 (Saito 1997)/ centromere outer repeat region /centromere central core cut14 IDA ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-04 14:01 Message: Raise priority when PomBase released ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-04 14:00 Message: misc_features dbxref=SO:0000577 now added to each chromosome Still need to sort the repeats (low priority) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-04 12:35 Message: Centromere coordinates in current assembly: chromosome 1 3753687..3789421 chromosome 2 1602264..1644747 chromosome 3 1070904..1137003 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 15:22:41
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Ensembl item #3253204, was opened at 2011-03-28 17:17 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3253204&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: 3 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: "liftover" Initial Comment: We will need this eventually to load datasets, so it would be good to also have it available as a community resource as SGD do. Before this can happen I will need to document the changes and the versions. Val I am an increasingly number of queries about mapping datasets between versions of the genome. Today I found out about the UCSC data convertor "LiftOver" which can perform this operation relatively seamlessly if supplied with "chain files". After talking to the SGD curators and developers, it appears that the creation of the initial chain files it is a slightly painful procedure, but this process only needs to be done once. So, has any community spirited person created these files previously and would like to make themselves very popular with everybody by making them publicly available (or a bioinformatician who would like to have a stab at making them?). We can then ask if the UCSC site will host the files on their public "liftOver" utility here: http://genome.ucsc.edu/cgi-bin/hgLiftOver There are only 5 sequence versions with minor changes. http://www.sanger.ac.uk/Projects/S_pombe/sequence_updates.shtml (I can help sorting out the physical sequences for the different versions) If there is nobody out there who can do this, I will put it on my Todo list but be warned that it isn't likely to happen immediately....... Many Thanks, Val ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3253204&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 15:21:46
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Ensembl item #3274271, was opened at 2011-04-04 15:21 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3274271&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: generate Stats page from Ensembl Initial Comment: Should be able to automatically generate (an improved version) of this from the Ensembl data once everything is imported.... http://www.sanger.ac.uk/Projects/S_pombe/genome_stats.shtml ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3274271&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 14:01:01
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Ensembl item #3273979, was opened at 2011-04-04 12:34 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&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: 3 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: Making genomic regions more easily accessible Initial Comment: I have had a couple of queries recently about locating centromeres, and a couple of queries abaout locating the mating type locus. These aren't easy to locate in GeneDB you can get to the separately annotated mating type region contig here http://old.genedb.org/genedb/ContigMap?organism=pombe I am just about to make misc features with SO ID fro centromeres SO:0000577 We do have individual centromere repeats annotated (dg, de etc) using the EMBL feature type repeat regoin ....... these should also be converted to SO terms/IDs (not the only existing children of centromeres in SO appear to be related to S. cerevisiae point centromeres and are not applicable to other organisms with modular centromeres). ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-04-04 14:01 Message: Raise priority when PomBase released ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-04 14:00 Message: misc_features dbxref=SO:0000577 now added to each chromosome Still need to sort the repeats (low priority) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-04 12:35 Message: Centromere coordinates in current assembly: chromosome 1 3753687..3789421 chromosome 2 1602264..1644747 chromosome 3 1070904..1137003 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 14:00:34
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Ensembl item #3273979, was opened at 2011-04-04 12:34 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&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: 3 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: Making genomic regions more easily accessible Initial Comment: I have had a couple of queries recently about locating centromeres, and a couple of queries abaout locating the mating type locus. These aren't easy to locate in GeneDB you can get to the separately annotated mating type region contig here http://old.genedb.org/genedb/ContigMap?organism=pombe I am just about to make misc features with SO ID fro centromeres SO:0000577 We do have individual centromere repeats annotated (dg, de etc) using the EMBL feature type repeat regoin ....... these should also be converted to SO terms/IDs (not the only existing children of centromeres in SO appear to be related to S. cerevisiae point centromeres and are not applicable to other organisms with modular centromeres). ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-04 14:00 Message: misc_features dbxref=SO:0000577 now added to each chromosome Still need to sort the repeats (low priority) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-04 12:35 Message: Centromere coordinates in current assembly: chromosome 1 3753687..3789421 chromosome 2 1602264..1644747 chromosome 3 1070904..1137003 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 14:00:25
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Ensembl item #3273979, was opened at 2011-04-04 12:34 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None >Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: Making genomic regions more easily accessible Initial Comment: I have had a couple of queries recently about locating centromeres, and a couple of queries abaout locating the mating type locus. These aren't easy to locate in GeneDB you can get to the separately annotated mating type region contig here http://old.genedb.org/genedb/ContigMap?organism=pombe I am just about to make misc features with SO ID fro centromeres SO:0000577 We do have individual centromere repeats annotated (dg, de etc) using the EMBL feature type repeat regoin ....... these should also be converted to SO terms/IDs (not the only existing children of centromeres in SO appear to be related to S. cerevisiae point centromeres and are not applicable to other organisms with modular centromeres). ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-04-04 14:00 Message: misc_features dbxref=SO:0000577 now added to each chromosome Still need to sort the repeats (low priority) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-04 12:35 Message: Centromere coordinates in current assembly: chromosome 1 3753687..3789421 chromosome 2 1602264..1644747 chromosome 3 1070904..1137003 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 12:35:23
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Ensembl item #3273979, was opened at 2011-04-04 12:34 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&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: Making genomic regions more easily accessible Initial Comment: I have had a couple of queries recently about locating centromeres, and a couple of queries abaout locating the mating type locus. These aren't easy to locate in GeneDB you can get to the separately annotated mating type region contig here http://old.genedb.org/genedb/ContigMap?organism=pombe I am just about to make misc features with SO ID fro centromeres SO:0000577 We do have individual centromere repeats annotated (dg, de etc) using the EMBL feature type repeat regoin ....... these should also be converted to SO terms/IDs (not the only existing children of centromeres in SO appear to be related to S. cerevisiae point centromeres and are not applicable to other organisms with modular centromeres). ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2011-04-04 12:35 Message: Centromere coordinates in current assembly: chromosome 1 3753687..3789421 chromosome 2 1602264..1644747 chromosome 3 1070904..1137003 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-04-04 12:34:41
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Ensembl item #3273979, was opened at 2011-04-04 12:34 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&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: Making genomic regions more easily accessible Initial Comment: I have had a couple of queries recently about locating centromeres, and a couple of queries abaout locating the mating type locus. These aren't easy to locate in GeneDB you can get to the separately annotated mating type region contig here http://old.genedb.org/genedb/ContigMap?organism=pombe I am just about to make misc features with SO ID fro centromeres SO:0000577 We do have individual centromere repeats annotated (dg, de etc) using the EMBL feature type repeat regoin ....... these should also be converted to SO terms/IDs (not the only existing children of centromeres in SO appear to be related to S. cerevisiae point centromeres and are not applicable to other organisms with modular centromeres). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3273979&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-03-31 16:42:04
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Ensembl item #3264611, was opened at 2011-03-31 16:42 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3264611&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: Go extenstions required Initial Comment: PMID ID with /from fields later, annotation extensions ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3264611&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-03-28 17:17:09
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Ensembl item #3253204, was opened at 2011-03-28 17:17 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3253204&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: "liftover" Initial Comment: We will need this eventually to load datasets, so it would be good to also have it available as a community resource as SGD do. Before this can happen I will need to document the changes and the versions. Val I am an increasingly number of queries about mapping datasets between versions of the genome. Today I found out about the UCSC data convertor "LiftOver" which can perform this operation relatively seamlessly if supplied with "chain files". After talking to the SGD curators and developers, it appears that the creation of the initial chain files it is a slightly painful procedure, but this process only needs to be done once. So, has any community spirited person created these files previously and would like to make themselves very popular with everybody by making them publicly available (or a bioinformatician who would like to have a stab at making them?). We can then ask if the UCSC site will host the files on their public "liftOver" utility here: http://genome.ucsc.edu/cgi-bin/hgLiftOver There are only 5 sequence versions with minor changes. http://www.sanger.ac.uk/Projects/S_pombe/sequence_updates.shtml (I can help sorting out the physical sequences for the different versions) If there is nobody out there who can do this, I will put it on my Todo list but be warned that it isn't likely to happen immediately....... Many Thanks, Val ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3253204&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2011-03-22 18:55:24
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Ensembl item #3235234, was opened at 2011-03-22 18:41 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3235234&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: Mapping for Orfeome cross references Initial Comment: Ensembl may need mapping for this ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096426&aid=3235234&group_id=65526 |