WormBase-Caltech Weekly Calls

From WormBaseWiki
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

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?
    • Raymond, Ranjana, Gary, Jae and Karen ok to have a monthly digest. Chris, Wen no email
    • Will check in with Gary W and see if he wants to be notified for RNAseq data flagging
    • Should ask April what she wants to do
  • Shall we add in the Curation status form Datatypes that are not currently in it (e.g. Time and site of action)
    • Yes, Add site and time 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?
    • Worth flagging methods papers. Will send methods papers to authors for 6 months and then evaluate how useful it is
  • 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?
    • The CFP form can be retired
  • Add back in the AFP from ‘this is a review paper, I am not curating this’

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.

Daniela will work on a model for an ?Expression_annotation class. The change can be gradual. We can Add the ?Expression_annotation class and still dump anatomy, life stage and GO in the old tags. Down the line those tags will be deprecated and fully replaced by the ?Expression_annotation tags

?Cell and ?Cell group could go away