Difference between revisions of "November 25, 2009 - Sequence Curation Flags"
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|- | |- | ||
! Flag name | ! Flag name | ||
+ | ! Flag information | ||
! Number of papers flagged manually (from curation status form) | ! Number of papers flagged manually (from curation status form) | ||
! Flag email (from first pass form) | ! Flag email (from first pass form) | ||
Line 61: | Line 62: | ||
|- | |- | ||
! gene symbol | ! gene symbol | ||
+ | ! newly cloned gene or new name for previously known gene | ||
! 342 | ! 342 | ||
! genenames, vanauken | ! genenames, vanauken | ||
Line 70: | Line 72: | ||
|- | |- | ||
! mapping data | ! mapping data | ||
+ | ! genetic mapping data | ||
! 194 | ! 194 | ||
! genenames | ! genenames | ||
Line 79: | Line 82: | ||
|- | |- | ||
! sequence features | ! sequence features | ||
+ | ! regulatory sequence features, includes promoters, enhancer, elements in mRNA | ||
! 248 | ! 248 | ||
! worm-bug, stlouis, xiaodong (xdwang) | ! worm-bug, stlouis, xiaodong (xdwang) | ||
Line 89: | Line 93: | ||
|- | |- | ||
! mass spectrometry | ! mass spectrometry | ||
+ | ! mass spec analysis | ||
! 65 | ! 65 | ||
! gw3, worm-bug | ! gw3, worm-bug | ||
Line 99: | Line 104: | ||
|- | |- | ||
! structure correction | ! structure correction | ||
+ | ! gene structure corrections (see comments) | ||
! 333 | ! 333 | ||
! worm-ticket, worm-bug | ! worm-ticket, worm-bug | ||
Line 108: | Line 114: | ||
|- | |- | ||
! sequence change | ! sequence change | ||
+ | ! sequence of mutant alleles | ||
! 981 | ! 981 | ||
! genenames | ! genenames | ||
Line 117: | Line 124: | ||
|- | |- | ||
! new SNPs | ! new SNPs | ||
+ | ! new polymorphisms | ||
! 50 | ! 50 | ||
! tbieri | ! tbieri | ||
Line 126: | Line 134: | ||
|- | |- | ||
! new mutant - alleles | ! new mutant - alleles | ||
+ | ! new phenotypes for new or existing (?) alleles | ||
! 1372 | ! 1372 | ||
! Erich, Gary, Jolene | ! Erich, Gary, Jolene |
Revision as of 11:51, 25 November 2009
Back to Caltech documentation
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
What type of data is going into each flag?
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.
- 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
- 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%).
}
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 |