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)

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.