WormBase-Caltech Weekly Calls November 2018

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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? http://tazendra.caltech.edu/~postgres/cgi-bin/curator_first_pass.cgi
    • The CFP form can be retired
  • Add back in the AFP from ‘this is a review paper, I am not flagging 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

November 15, 2018


  • New WormBase release linked to the new SPELL website (https://spell.wormbase.org)
  • Will watch for a few days
  • Maybe should make an announcement for our users (for those that have it bookmarked)

Broken Disease links

WOBr disease data

  • WOBr currently looking at stale disease data; needs to be updated
  • We also want to accommodate strain disease models; will take some work to get it into WOBr
  • Ranjana will work with Raymond

RNAi targeting of non-coding genes

  • WBPaper00053279 has example of RNAi knockdown of let-7 miRNA
  • Authors report using 99bp dsRNA targeting the pri-miRNA
  • Maybe survey RNAi labs to see if this is likely real, makes sense?
  • If it's real, we need to update RNAi mapping pipeline to include non-coding gene targets

OBO to OWL transitions

  • New GitHub repository for phenotype ontology
  • OBO format becoming defunct; OBO Edit not being maintained
  • We likely need to move from OBO to OWL
  • Now we have .owl and .obo files (obo generated from owl)
  • Can we (do we need to) update Postgres and query tools to use OWL files instead of OBO?
  • We can try a pilot on phenotype OWL file to see how much effort would be required for transition

Protege tutorial

  • Chris went to Stanford Protege tutorial
  • Chris can give local WB tutorial on Protege, maybe in January
  • Chris will send around documentation and tutorial docs

Updating phenotype ontology links