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 ==
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[[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 ===
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
* 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 example: https://wormbase.org/resources/wbprocess/WBbiopr:00000001#09--10
 
  
=== WS276 Citace upload ===
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Hinxton upload Jan 31, 2020
 
* Citace upload on Tuesday, Jan 28, 2020
 
  
=== Author First Pass paper ===
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
* 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 ===
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* 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 ===
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* Have a backlog; Paul D is assigned but has been overwhelmed
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== September 2, 2021 ==
* Have asserted this as a priority
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* We have the allele-sequence form; where does it go? Hinxton
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
* Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
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Needed for
* Need to integrate curation with the Variant Effect Predictor (VEP) pipeline
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*AFP community curation
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*microPublication author tracking for all species
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*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
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 +
Problems:
 +
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
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*need to do this outside of Alliance
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 +
Action
 +
*Paul talks to zfin about interest in person pages
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*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
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*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
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 +
Will do
 +
*create biolink model based on current WB postgres/Caltech model
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*Adam will add tables when we have them
 +
 
 +
2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
 +
 
 +
== September 16, 2021 ==
 +
 
 +
1. CeNGEN enriched genes per cell type data targeted for WS283.
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 +
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.

Latest revision as of 16:04, 16 September 2021

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September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.