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

What type of data is going into each flag?

Pipelines and options for flagging

Data may come into WormBase via various pipelines (e.g. Genbank, Knockout Consortia, user submissions) but for flagging data in published papers, here are the current pipelines:

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.
  • How to evaluate the results of the SVMs
    • Precision - Of the returned positives, how many are true positives?
    • Recall - Of the true positives, how many were returned? (need to look at negatives for particular data type)
    • What precision and recall values are acceptable?
  • Is there any way for curators to see a list of features for each SVM? May help with understanding false positives.


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 Flag information 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 newly cloned gene or new name for previously known gene 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 genetic mapping data 194 genenames
sequence features regulatory sequence features, includes promoters, enhancer, elements in mRNA 248 worm-bug, stlouis, xiaodong (xdwang)
mass spectrometry mass spec analysis 65 gw3, worm-bug Textpresso categories Ruihua, Gary?
structure correction gene structure corrections (see comments) 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 sequence of mutant alleles 981 genenames SVM
new SNPs new polymorphisms 50 tbieri
new mutant - alleles new phenotypes for new or existing (?) alleles 1372 Erich, Gary, Jolene

Minutes, Action Items