WormBase-Caltech Weekly Calls

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Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


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


2019 Meetings

January

February

March

April

May

June

July


August 1, 2019

Life stage public names missing in WS271

  • Did we ever get a patch in for this?
  • WormMine only has WBls IDs (no public name) for almost all life stages
  • Wen will resend the patch file

2020 WB NAR paper

  • Who's contributing?
    • Raymond, Chris, Ranjana, Valerio, Daniela, Kimberly
  • Topics
    • Automated descriptions
    • Ontology tools (SObA)
    • Community curation
    • Author first pass

2019 IWM Workshop videos

  • On YouTube, but not public yet
  • Chris will make them public and send links to Ranjana for the blog post


August 15, 2019

GO Alliance slim terms

  • We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance
  • May need to watch out for terms that don't apply to worms
  • Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?)

Phenotype ontology patternization


August 22, 2019

Obsolete ontology terms in Postgres

Community phenotype requests

  • Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019
  • 2,627 emails/papers requested
  • 112 emails bounced; 4 resent to new addresses
  • 205 Phenotype OA community annotations; 55 RNAi OA annotations, from 47 papers, by 42 distinct community curators (so far)
  • Also, 3 worksheets submitted, for 4 papers
  • 35 papers flagged as not having phenotypes
  • 86 papers with responses (3% response; still early)
  • Need to coordinate with the AFP request pipeline

GO slim terms

  • SObA highlights Alliance slim terms, but doesn't correspond to ribbon
  • Want to use same slim terms used for ribbons
  • Add slim terms into ACEDB? One option
  • Ribbon order of slim terms is an issue
  • Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
  • Will have to manually synchronize with Alliance if Alliance changes its ribbon