WormBase-Caltech Weekly Calls March 2019

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March 7, 2019

IWM workshop

  • Still haven't heard back from organizers yet

IWM swag

  • Think of ideas for the meeting


  • Local upload to Spica is Tuesday, March 12th, 10am Pacific

Trustworthy data repositories workshop

  • Chris will go to NIH, April 8 and 9
  • To discuss trustworthiness standards for data repositories

March 21, 2019

IWM 2019 workshop


  • Start with gene page, that's when you have a single gene --Kimberly
  • Then go on to data mining, for multiple genes--SimpleMine, WormMine, Parasite BioMart etc --Wen and Chris
  • Then you can also visualize data with these tools-WoBR, SoBA, etc
  • If you are interested in other species, find cross-species data at the Alliance --Ranjana
  • Help us curate your data! End with community curation-New Author First pass form, community curation forms--Daniela

I think we have a good flow here, can keep thinking about this. Ranjana will shorten abstract and submit final list first week of April.

IWM 2019 swag ideas

  • WormBase sticker
    • Micropub folks have done stickers, in Paul's office, take a look
    • Daniela will look into this, pricing and time
  • Gary's ideas:
    • Screen cleaning cloths with community curation theme on them, he will send around the picture
    • Water bottles for the top community curators
    • Fidget spinners, with the WB picture in the middle
    • Gary will talk to Daniel to see if he can help with finding sellers/prices

We could do them all , a mixture, depending on the budget, need to ask Paul S. what the budget is for IWM swag

March 28, 2019

Textpresso Central vs Old Textpresso site

  • A search for "SimpleMine" got 1 paper in TPC, 5 papers in the old site.
  • A search for "alg-5" in TPC got 6 hits but the first two were redundant. The result missed pmid29927939 that was found by the old site.
  • A search for allele "ev673" in TPC returns no results, but expected paper (PMID:24004945 / WBPaper00044133) returned in old site.
  • TPC is undergoing an update to the paper pipeline
  • Individual issues should be entered in GitHub tracker
  • Duplicates result from XML vs PDF documents (should probably be merged somehow), as well as supplementals

Protein-protein interactions up-to-date

  • We should post an announcement to the community
  • Could ask for feedback if any authors are aware of anything missing

Micropublication tutorials

  • Can Wen mention (at small RNA meeting) that micropub representatives can do site visits to discuss micropubs?

Allele display on gene pages

  • Some have expressed that the display could be better
  • We will need some specific feedback
  • We had made several changes to isolate phenotypic alleles from non-phenotypic alleles

IWM swag

  • Screen cloths/cleaners? preferred option; order ~2,000
  • Stickers also? maybe not
  • Shot glasses (40-50 remaining)? Specific prizes for top community curators?
  • Left over WB bags (not high quality; maybe don't bother)

Help desk enrichment analysis

  • David (now postdoc at MIT) helped respond to user question; will eventually need to maintain without David
  • Should migrate enrichment analysis to Alliance (although ontologies not aligned yet)
  • Design requires decisions for tuning; some may not be obvious to users
  • Could allow curator or user to tune parameters? What are the statistical arguments?
  • We could try to simplify the current maintenance to make it easier to manage parameters in-house

Collaborators tool

  • Would be good to take advantage of WB person/author data to pull out list of collaborators for a given person/author
  • Should that be time/data interval restricted/specified? Just be inclusive and user/author can edit/trim as needed
  • Pedigree vs. collaborators analysis?