WormBase-Caltech Weekly Calls

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2018 Meetings











November 1, 2018

Community phenotype requests

  • Sent out 1,000 request emails for community submissions of phenotypes on October 18 and October 20
  • As before, request focuses on a single paper, but we've now added extra papers at bottom of email message
  • We've also added a link for users to click on to indicate that the paper in question (focus paper) has no nematode phenotypes
  • 21 emails bounced
  • 56 papers received annotations, 44 from direct requests, 12 not directly requested
  • 9 of 12 not directly requested were appended requests to email message
  • 277 annotations submitted (raw) via the form (some more submitted as Excel spreadsheets)
    • 247 allele/transgene phenotype annotations
    • 30 RNAi phenotype annotations
  • 48 distinct community curators


  • Todd working on a spell.wormbase.org site for doing worm SPELL analyses
  • Should be faster, more stable

Predicted protein-protein interactions

  • Jae has requested data set
  • Total data set 20GB (how much is C. elegans?)
  • Haven't heard back from author recently
  • How much do we want this data? Should reach out a couple more times (once every ~two weeks)

November 8, 2018

Author First Pass

  • Do curators want to be notified by e-mail when authors flag their datatype in the AFP form?
  • Shall we add in the Curation status form Datatypes that are not currently in it (e.g. Time and site of action)
  • How would we like to handle Methods papers? These may have reagents and some bona fide experimental results, but are not our 'typical' experimental papers. Possibly add a new 'methods' flag?
  • Do we need to still maintain the cfp form? If we can keep the data tables and still see the flags in the curation status form, do we need the cfp form?

Expression Pattern Model

  • there would be value in having a separate ?Expr_annotation class, like we did for ?GO_annotation. It might look something like this (details not completely thought through):
Class ?Expr_annotation
   Life_stage ?Life_stage XREF Expr_pattern #Qualifier
   Not_in_Life_stage ?Life_stage #Qualifier
   Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
   Not_in_Anatomy_term ?Anatomy_term #Qualifier
   GO_CC ?GO_term XREF Expr_pattern
   GO_BP ?GO_term XREF Expr_pattern
   Cell ?Cell
   Cell_group ?Cell_group

#Qualifer Certain

An Expr_pattern can then have a list of ?Expr_annotations, each grouping together all properties of a single observation.