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
    • How can we automatically identify Sequence Feature papers.
  • 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
        • gw3 - I don't know in detail what data other curators require. It would be useful to know this so I can summarise data for others.

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?

Matters Arising

  • things noted - not necessarily to do with the topic in hand
    • There are many duplicates of Interaction objects in geneace, with or without two leading digits. Sometimes there is only the shorter form.

Papers to curate

  • I have taken the Sequence Feature Papers from RT and assigned the four of us 10 papers each.
  • Just in case there is any paper here that has already been curated for Interaction, I've added the number of Interaction objects linked to by the paper. If this is not helpful, feel free to remove it.
WBPaper00002925 Daniela Interaction: 8
WBPaper00004568 Daniela Interaction: 2
WBPaper00005842 Daniela
WBPaper00024328 Daniela Interaction: 4
WBPaper00028802 Daniela
WBPaper00028915 Daniela
WBPaper00029140 Daniela
WBPaper00029255 Daniela Interaction: 55
WBPaper00030829 Daniela Interaction: 5
WBPaper00030933 Daniela Interaction: 1
WBPaper00003929 Gary Interaction: 25
                Time: 4 hours
                New objects: none - 6 existing Features were corrected and updated. (WBsf019182, WBsf019181, WBsf019179, WBsf019177, WBsf019178, WBsf019180)
                Location of information: body text and in a figure in the supplemental table of the paper WBPaper00006376
                Other curator data: "lin-41 and lin-42 are negatively regulated by let-7"
                Comments: This is Gary Ruvkun's (Nature 2000) let-7 paper that started the miRNA field!
                Comments: This is being marked as a pair of 'binding_site' Features because this is miRNA not TF binding.
                See also: let-7, lin-41 binding WBPaper00006376 PubMed: 14729570 ( - This is the paper that defined the binding sites.
WBPaper00005044 Gary Interaction: 20
                Time: 3 hours
                New objects: made ire-1 binding site Feature (WBsf977530)
                Location of information: body of this paper and WBPaper00005036
                Other curator data: IRE-1 is a stress-activated endonuclease resident in the ER that is conserved in all known eukaryotes. IRE-1 mediated unconventional splicing of an intron from xbp-1 mRNA controls expression of the encoded transcription factor and is required for upregulation of most UPR target genes.
                See also: WBPaper00005036
WBPaper00005971 Gary Interaction: 16 This has already been done by Gary: Feature WBsf718850
WBPaper00024440 Gary Interaction: 1
WBPaper00028816 Gary
WBPaper00028986 Gary Interaction: 16
WBPaper00029181 Gary
WBPaper00029327 GaryInteraction: 33
WBPaper00030849 Gary
WBPaper00031355 Gary Interaction: 5
WBPaper00004181 Mary Ann Interaction: 8 
                No Features. Took 5 mins to read. 
WBPaper00005056 Mary Ann 
                Time: 35 mins
                New objects: 37 - not yet curated.
                Location of information: Mainly in fig. 1, but in body text. 
                Comments: TRTTKRY element in promoter region of T05E11.3, D2096.6, C44H4.1, ZK816.4, ceh-22, 
                          tph-1, M05B5.2, myo-2. Bound by pha-4 
WBPaper00006429 Mary Ann Interaction: 3
                Time: 1/2hr
                New objects: 1
                Location of information: In body of text and fig. 3B
                Comments: Alludes to GATA binding sites, but no experimental data. 
WBPaper00024505 Mary Ann
                New objects: 
                Location of information: 
WBPaper00028849 Mary Ann
                Time: 45 mins
                New objects: 1
                Location of information: In body of text and fig. 3B
WBPaper00029058 Mary Ann Interaction: 50
WBPaper00029190 Mary Ann
WBPaper00029406 Mary Ann Interaction: 145
WBPaper00030877 Mary Ann Interaction: 8
WBPaper00031471 Mary Ann
WBPaper00004482 Xiaodong Interaction: 2
WBPaper00005609 Xiaodong Interaction: 20 This has already been done by Margaret: Feature WBsf019097, WBsf038788, WBsf038789, WBsf038790, WBsf038791, WBsf038793, WBsf038794, WBsf019098, WBsf038792
WBPaper00024189 Xiaodong
WBPaper00024981 Xiaodong
WBPaper00028910 Xiaodong Interaction: 7
WBPaper00029109 Xiaodong
WBPaper00029229 Xiaodong Interaction: 3
WBPaper00030809 Xiaodong
WBPaper00030931 Xiaodong Interaction: 18
WBPaper00031565 Xiaodong Interaction: 1
  • 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.