November 25, 2009 - Sequence Curation Flags
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Revision as of 16:04, 24 November 2009 by Vanaukenk (talk | contribs) (→Current status of each sequence-related flag)
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Contents
Call Information
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participant access code: 822114
Location: wherever you are
Participants
http://tazendra.caltech.edu/~postgres/cgi-bin/curator_first_pass.cgi
Pipelines and options for flagging
- 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.
- 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%).
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Flag name | Number of papers flagged manually (from curation status form) | Flag email (from first pass form) | Current approach | Curator(s) | Comments | Current pipeline sufficient? | |
---|---|---|---|---|---|---|---|
gene symbol | 342 | genenames, 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 | 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 |