November 25, 2009 - Sequence Curation Flags

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Review sequence-related first pass flags

http://tazendra.caltech.edu/~postgres/cgi-bin/curator_first_pass.cgi

Pipelines and options for flagging

SVMs

  • Curated papers are the best training set. Flagged papers can be used, if flagging was generally consistent.
  • Curation status form has lists, but not completely up-to-date.
  • Is there any way for curators to see a list of features for each SVM? May help with understanding false positives.
  • How to evaluate the results of the SVMs

Textpresso

  • pattern matching
  • category searches

Author flags

  • Curators need to tell Juancarlos they'd like to receive emails when authors flag a data type.
  • Caltech needs to supply list of papers flagged since September 2009.
  • Stats on return rates as of November 12, 2009 (supplied by Juancarlos):

Since Sept 1st, we have sent out 195 requests, and gotten back 72 results (36.9%).

Since Oct 1st, we have sent out 147 requests, and gotten back 52 results (35.3%).

Since Nov 1st, we have sent out 18 requests, and gotten back 7 results (38.9%).

Current status of each sequence-related flag

}
Flag name Number of papers flagged manually (from curation status form) Flag email (from first pass form) Getting author flags? Current approach Curator(s) Comments Current pipeline sufficient?
gene symbol 342 genenames, vanauken no-vanauken SVM (see comments) Kimberly, Mary Ann? Currently being combined with seqchange. Could possibly employ secondary screen with categories.
mapping data 194 genenames
sequence features 248 worm-bug, stlouis, xiaodong (xdwang)
mass spectrometry 65 gw3, worm-bug Textpresso categories Ruihua, Gary?
structure correction 333 worm-ticket, worm-bug tried SVM Gary, Paul Davis Ideally divided into four categories: a change in a gene's structure, the addition of an isoform, a change to one of the SL1/SL2 or polyA site features, a sequence correction in the N2 reference genome
sequence change 981 genenames SVM
new SNPs 50 tbieri
new mutant - alleles 1372 Erich, Gary, Jolene

Minutes, Action Items