Working Group:Sequence Features

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  • Display of Sequence Features on the website
    • And Transcription factors and Gene_product binds.
  • Stream out working flow
  • Sample papers curation
    • Prepare a paper list from each person
  • assign meaningful names to the public_name field, e.g. 'distal enhancer 1' instead of 'DE1'
    • gw3 - I disagree with this. We should use the name that is used to describe the region in the paper, rather than making up our own names. I have had to go back and re-annotate regions after Xiaodong found problems with my stuff several months after I had originally done it and I really needed to be able to unambiguously identify which region the paper was talking about by using the Public_name field and matching this up to the name of the region in the paper. Users may well need to do this as well if they are reading the paper and looking at the Features marking up the regions.

Pre-Jamboree prep

  • Suggestions for work
    • Curate some (5? 10?) papers from our lists and collate data as follows
      • How long did each paper take to curate
      • How many new objects did you add to WormBase
      • Where in the paper was the information (e.g. supplementary data, figure legends, within text)
      • Did you need to contact the author for more information
      • Did you come across data for other curators

The Jamboree 15-17th Sept 2014

  • Suggestions for work
    • Discuss result from above
    • Work through some papers which have already been curated and have different data types (e.g. promoter and gene regulation) to identify best curation practices.
    • browsing capabilities through WormMine?

Papers to curate

  • I have taken the Sequence Feature Papers from RT and assigned the four of us 10 papers each.
WBPaper00002925 Daniela
WBPaper00004568 Daniela
WBPaper00005842 Daniela
WBPaper00024328 Daniela
WBPaper00028802 Daniela
WBPaper00028915 Daniela
WBPaper00029140 Daniela
WBPaper00029255 Daniela
WBPaper00030829 Daniela
WBPaper00030933 Daniela
WBPaper00003929 Gary
WBPaper00005044 Gary
WBPaper00005971 Gary This has already been done by Gary: Feature WBsf718850
WBPaper00024440 Gary
WBPaper00028816 Gary
WBPaper00028986 Gary
WBPaper00029181 Gary
WBPaper00029327 Gary
WBPaper00030849 Gary
WBPaper00031355 Gary
WBPaper00004181 Mary Ann
WBPaper00005056 Mary Ann
WBPaper00006429 Mary Ann
WBPaper00024505 Mary Ann
WBPaper00028849 Mary Ann
WBPaper00029058 Mary Ann
WBPaper00029190 Mary Ann
WBPaper00029406 Mary Ann
WBPaper00030877 Mary Ann
WBPaper00031471 Mary Ann
WBPaper00004482 Xiaodong
WBPaper00005609 Xiaodong This has already been done by Gary: Feature WBsf038788 to WBsf019098
WBPaper00024189 Xiaodong
WBPaper00024981 Xiaodong
WBPaper00028910 Xiaodong
WBPaper00029109 Xiaodong
WBPaper00029229 Xiaodong
WBPaper00030809 Xiaodong
WBPaper00030931 Xiaodong
WBPaper00031565 Xiaodong
  • I suggest we curate 5 of our papers before the jamboree, taking notes as described above and any other things that arise during your curation.