November 25, 2009 - Sequence Curation Flags

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Participants

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.

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 flag

}
Flag name Number of papers flagged (manual) Current approach Curator(s) Comments
gene symbol Currently being combined with seqchange.
mapping data
sequence features
mass spectrometry
structure correction Could be divided into several 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
new SNPs
new mutant {alleles)

Minutes, Action Items