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[Pombase-chado] [ pombase-Chado-3590727 ] IC (and IEA?) filtering
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From: SourceForge.net <no...@so...> - 2012-12-03 11:16:08
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Chado item #3590727, was opened at 2012-11-28 08:02 Message generated for change (Comment added) made by gomidori You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Midori Harris (gomidori) Assigned to: Kim Rutherford (kim_rutherford) Summary: IC (and IEA?) filtering Initial Comment: In my investigations for the missing 'from' .problem (SF 3590723), I also noticed that the number of IC annotations that reach the GAF has varied over time by far more than can be explained by actual annotation changes. Examples: pombase-build-2012-10-19-v1-l1.gaf - 215 pombase-build-2012-11-05-v1-l1.gaf - 214 pombase-build-2012-11-18-v2-l1.gaf - 1126 pombase-build-2012-11-25-v2-l1.gaf - 1122 % grep -c 'evidence=IC' *contig finds about 1500 matches Val has also commented on the number of IEA annotations (6559 in the file committed to GOC). Is something up with filtering? Also see SF 3586386, which was about v28 and what shows up on pombase gene pages. https://sourceforge.net/tracker/?func=detail&aid=3586386&group_id=65526&atid=2096276 ---------------------------------------------------------------------- >Comment By: Midori Harris (gomidori) Date: 2012-12-03 03:16 Message: The 11-28-v2 GAF has just over 4700 IEAs, which Val says is about right. I don't know what to make of the IC count changes, but the current 1100-odd makes sense, so I'll call this fixed. ---------------------------------------------------------------------- Comment By: Kim Rutherford (kim_rutherford) Date: 2012-12-02 10:38 Message: The current IC count is 1127. I can't explain the change in count over time. As far as I can see there haven't been any code changes that code have made a difference. Is 6559 IEAs too high? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-11-28 09:04 Message: It could be because the filtering filters IC/TAS/NAS/IEA redundently with no precedence for any particular evidence code? I think there is an item about this on the chado tracker with low priority... (so we are seeing ICs replaced by IEAs?... but this wouldn't explain the increase in both, or the non-filtering reported in the other ticket ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096276&aid=3590727&group_id=65526 |