Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
 +
= 2020 Meetings =
  
= 2019 Meetings =
+
== January 9, 2020 ==
 
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
=== Phenotype Curation Requests ===
 +
* 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)
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
+
=== Worm Area Meetings ===
 +
* 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)
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
=== 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
 +
* Rearrangement example: https://wormbase.org/species/all/rearrangement/sDp3#03--10
 +
* Molecule example: https://wormbase.org/resources/molecule/WBMol:00003650#03--10
 +
* Process examples:
 +
** https://wormbase.org/resources/wbprocess/WBbiopr:00000001#09--10
 +
** https://wormbase.org/resources/wbprocess/WBbiopr:00000079#09--10
 +
* Michael has improved phrase search and combined supplemental documents with main paper documents; should roll out soon
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
=== WS276 Citace upload ===
 +
* Hinxton upload Jan 31, 2020
 +
* Citace upload on Tuesday, Jan 28, 2020
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
=== Author First Pass paper ===
 +
* AFP resent to Database
 +
* Automated descriptions about to be sent
 +
* SObA, write for micropub? One micropub on SObA and another on comparative SObA
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
+
=== Noctua/GO-CAM ===
 +
* New version of the Noctua form released next week
 +
* Imports from WormBase?
 +
** Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
 +
** Need to work on annotation history on back end
 +
** May have face-to-face meeting in Pasadena
  
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
+
=== Variation curation ===
 +
* Have a backlog; Paul D is assigned but has been overwhelmed
 +
* Have asserted this as a priority
 +
* We have the allele-sequence form; where does it go? Hinxton
 +
* Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
 +
* Need to integrate curation with the Variant Effect Predictor (VEP) pipeline
  
[[WormBase-Caltech_Weekly_Calls_December_2019|December]]
+
=== Topic meetings ===
 +
* Asia (Taipei) meeting, Paul S going
 +
* Aging meeting, Wen could go?
 +
* TAGC in April, Chris going

Revision as of 19:27, 9 January 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


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

2020 Meetings

January 9, 2020

Phenotype Curation Requests

  • 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

  • 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

WS276 Citace upload

  • Hinxton upload Jan 31, 2020
  • Citace upload on Tuesday, Jan 28, 2020

Author First Pass paper

  • AFP resent to Database
  • Automated descriptions about to be sent
  • SObA, write for micropub? One micropub on SObA and another on comparative SObA

Noctua/GO-CAM

  • New version of the Noctua form released next week
  • Imports from WormBase?
    • Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
    • Need to work on annotation history on back end
    • May have face-to-face meeting in Pasadena

Variation curation

  • Have a backlog; Paul D is assigned but has been overwhelmed
  • Have asserted this as a priority
  • We have the allele-sequence form; where does it go? Hinxton
  • Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
  • Need to integrate curation with the Variant Effect Predictor (VEP) pipeline

Topic meetings

  • Asia (Taipei) meeting, Paul S going
  • Aging meeting, Wen could go?
  • TAGC in April, Chris going