Difference between revisions of "WormBase-Caltech Weekly Calls"

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* 21 papers flagged as not having phenotypes
 
* 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
 
* 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
 +
 +
=== Micropublications ===
 +
* 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
 +
* Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
 +
 +
=== Undiagnosed Disease Network data ===
 +
* Andy Golden will meet with Ranjana and Chris at IWM to discuss
 +
* Andy asked about protocol pages at WormBase?
 +
* Paul: Bioprotocols and Protocols IO
 +
* Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)

Revision as of 18:55, 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

Micropublications

  • 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
  • Karen: Micropublications team will reach out to curators to help build submission forms for respective data types

Undiagnosed Disease Network data

  • Andy Golden will meet with Ranjana and Chris at IWM to discuss
  • Andy asked about protocol pages at WormBase?
  • Paul: Bioprotocols and Protocols IO
  • Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)