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)
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|-
 
|-
 
! gene symbol
 
! gene symbol
 +
! newly cloned gene or new name for previously known gene
 
! 342
 
! 342
 
! genenames, vanauken
 
! genenames, vanauken
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|-
 
|-
 
! mapping data
 
! mapping data
 +
! genetic mapping data
 
! 194
 
! 194
 
! genenames
 
! genenames
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|-
 
|-
 
! 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)
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|-
 
! mass spectrometry
 
! mass spectrometry
 +
! mass spec analysis
 
! 65
 
! 65
 
! gw3, worm-bug
 
! gw3, worm-bug
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|-
 
! structure correction
 
! structure correction
 +
! gene structure corrections (see comments)
 
! 333
 
! 333
 
! worm-ticket, worm-bug
 
! worm-ticket, worm-bug
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|-
 
|-
 
! sequence change
 
! sequence change
 +
! sequence of mutant alleles
 
! 981
 
! 981
 
! genenames
 
! genenames
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|-
 
! new SNPs
 
! new SNPs
 +
! new polymorphisms
 
! 50
 
! 50
 
! tbieri
 
! tbieri
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! 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

Call information

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Location: wherever you are

Participants

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

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.
  • 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

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

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