Difference between revisions of "November 25, 2009 - Sequence Curation Flags"
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|- | |- | ||
! Flag name | ! Flag name | ||
− | ! Number of papers flagged ( | + | ! Number of papers flagged manually (from curation status form) |
+ | ! Flag email (from form) | ||
! Current approach | ! Current approach | ||
! Curator(s) | ! Curator(s) | ||
! Comments | ! Comments | ||
|- | |- | ||
− | + | ! 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 | |
− | + | ! | |
− | + | ! | |
− | + | ! | |
+ | ! | ||
|- | |- | ||
− | + | ! structure correction | |
− | + | ! 333 | |
− | + | ! worm-ticket, worm-bug | |
− | + | ! | |
− | + | ! | |
+ | ! 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 | |
− | + | ! 981 | |
− | + | ! genenames | |
− | + | ! | |
− | + | ! | |
+ | ! | ||
|- | |- | ||
− | + | ! new SNPs | |
− | + | ! 50 | |
− | + | ! tbieri | |
− | + | ! | |
− | + | ! | |
+ | ! | ||
|- | |- | ||
− | + | ! new mutant {alleles) | |
− | + | ! 1372 | |
− | + | ! Erich, Gary, Jolene | |
− | + | ! | |
− | + | ! | |
+ | ! | ||
|- | |- | ||
} | } |
Revision as of 15:55, 24 November 2009
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Contents
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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%).
Current status of each flag
}Flag name | Number of papers flagged manually (from curation status form) | Flag email (from form) | Current approach | Curator(s) | Comments | |
---|---|---|---|---|---|---|
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 | ||||
structure correction | 333 | worm-ticket, worm-bug | 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 | 981 | genenames | ||||
new SNPs | 50 | tbieri | ||||
new mutant {alleles) | 1372 | Erich, Gary, Jolene |