Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
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= 2021 Meetings =
  
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
== January 9, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
=== Phenotype Curation Requests ===
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
* 1,229 emails sent Dec 3-6, 2019
 
* Received 194 annotations from 40 papers and from 37 distinct community curators
 
** 37 papers requested, 3 additional papers annotated
 
** 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
 
** 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
 
* 43 bounced emails
 
** 2 resent to new addresses
 
** 5 have backup email addresses (also sent)
 
  
=== Worm Area Meetings ===
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
* Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
 
* Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)
 
  
=== Reference widget Textpresso linkouts ===
 
* Now live on WormBase, WS274
 
* [https://github.com/WormBase/website/issues/7347 GitHub ticket]
 
* Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes
 
* Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10
 
* Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10
 
* Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10
 
* Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10
 
** Known issue: searching on synonyms in addition to public name; Sibyl will fix
 
* Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10
 
** Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix
 
* Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10
 
** Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell
 
* Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10
 
* Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10
 
** Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym
 
  
 +
== May 13, 2021 ==
  
=== WS276 Citace upload ===
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=== Textpresso supplement ===
* Hinxton upload Jan 31, 2020
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* Due Monday
* Citace upload on Tuesday, Jan 28, 2020
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* Michael working with Paul S
  
=== Author First Pass paper ===
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=== AWS credits ===
* AFP resent to Database
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* Michael and Valerio were awarded AWS credits, more than they can use
* Automated descriptions about to be sent
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* Maybe they can be repurposed
* SObA, write for micropub? One micropub on SObA and another on comparative SObA
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* Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance
  
=== Noctua/GO-CAM ===
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=== Automated gene descriptions ===
* New version of the Noctua form released next week
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* Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
* Imports from WormBase?
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* Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
** Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
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* May be the focus of an Alliance supplement
** Need to work on annotation history on back end
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* We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)
** May have face-to-face meeting in Pasadena
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 +
=== IWM 2021 WB Workshop ===
 +
* Scheduled for June 22, 2021
 +
* Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
 +
* Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
 +
* Here is the submitted workshop schedule:
 +
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
 +
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
 +
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
 +
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
 +
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A

Latest revision as of 18:31, 13 May 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April


May 13, 2021

Textpresso supplement

  • Due Monday
  • Michael working with Paul S

AWS credits

  • Michael and Valerio were awarded AWS credits, more than they can use
  • Maybe they can be repurposed
  • Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance

Automated gene descriptions

  • Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
  • Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
  • May be the focus of an Alliance supplement
  • We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)

IWM 2021 WB Workshop

  • Scheduled for June 22, 2021
  • Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
  • Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
  • Here is the submitted workshop schedule:
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A