Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to: navigation, search
m (June 13, 2019)
m (June 13, 2019)
Line 96: Line 96:
 
* Concern was expressed about how to handle a really high throughput of submissions:
 
* Concern was expressed about how to handle a really high throughput of submissions:
 
** Daniela: Working towards automating as much of the processing pipeline as possible
 
** Daniela: Working towards automating as much of the processing pipeline as possible
** Raymond: The throughput will be handled appropriately depending on demand
+
** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
 +
** Not getting lots of submissions yet, probably won't be inundated in the near future
 +
** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions

Revision as of 18:43, 13 June 2019

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 6, 2019

New SObA graphs

  • May put graphs within existing widgets, but don't need to rush to get that ready for IWM

Phenotype association file format

  • May be best to leave the format as is
  • There are problems; paper IDs keep switching columns
  • Would need to revisit the reasoning for why we do it that way
  • When will the Alliance produce a similar/replacement file? Not sure

Phenotype requests

  • Sent out 1140 emails on May 30
  • Since have received 374 annotations from 54 papers (42 requested, 12 additional)
  • 21 papers flagged as not having phenotypes
  • Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week


June 13, 2019

IWM

  • Coordinating transportation of swag boxes to Pauley Pavilion
  • Workshop on Saturday June 22, from 1pm to 2:30pm
  • Saturday morning micropublication breakfast 7:30 - 8:30am
  • Workshop
    • Presenters: it may be best to present as use cases rather than a research project
    • Chris will cover SimpleMine for Wen
    • Chris: won't do live demo; only screenshots, maybe some video
  • Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
  • Paul's talk
    • Cover Alliance
    • New features
      • SObA (for new data)
      • Complete for protein-protein interactions
      • RNASeq tools
      • Updated automated gene concise descriptions?
    • Phenotype community curation
      • Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
    • Author First Pass
    • Micropublication

SGD SAB

  • Paul attended
  • Alliance publicity was discussed
  • SAB likes the Alliance orthology features
  • Working on topics: displaying papers and data
  • Pathways: discussion about best approach
  • Metabolic engineering
  • Meta data about RNASeq data
    • SPELL tool, basically only tool of its kind available; need new tools
  • Species-specific proteins: how best to find them? HMMs (Jackhammer)?

Concise descriptions

  • Progress being made within the Alliance to update the automated concise gene descriptions
  • We will still accept manually written descriptions and display them in parallel with automated descriptions

Micropubs

  • If people are requesting manually written gene descriptions, they could submit a microreview
  • Concern was expressed about how to handle a really high throughput of submissions:
    • Daniela: Working towards automating as much of the processing pipeline as possible
    • Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
    • Not getting lots of submissions yet, probably won't be inundated in the near future
    • Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions