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]]
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 +
[[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 =
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
 
[[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]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
 
 
  
== July 11th, 2019 ==
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
=== Alliance all hands meeting ===
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
* Raymond: would be interested in discussing ontologies and their usage in the Alliance
 
** Phenotype, anatomy ontologies, GO, etc.
 
** Ontology browsers, SObA
 
  
=== IWM workshop ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* Videos ready for upload
 
* Wen and Raymond now have access to outreach@wormbase.org account; will upload videos
 
  
=== Protocol videos ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase?
 
* Can make each video a Video Weblog so people can make comments, etc.
 
  
  
== July 25, 2019 ==
+
== June 4, 2020 ==
  
=== Anatomy ontology ===
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=== Citace (tentative) upload ===
* Raymond added back some deprecated cell group terms as obsolete terms
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 +
* Citace upload to Hinxton on Friday, July 10th
  
=== Life stage ontology ===
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=== Caltech reopening ===
* Who will take charge of it? Raymond or Chris?
+
* Paul looking to get plan approved
* OBO-to-ACE script is working
+
* People that want to come to campus need to watch training video
* OBO is working (?) in SObA and WOBr
+
* Masks available in Paul's lab
* Chris will take over life stage ontology; Daniela & Raymond will send Chris location of OBO-to-ACE script
+
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
* Chris will send release OBO to Raymond to test WOBr and SObA
+
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 +
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
=== Anatomy term acronyms ===
+
=== Nameserver ===
* Some anatomy terms: can the name be changed?
+
* Nameserver was down
** e.g. "DTC" is main label for "distal tip cell"
+
* CIT curators would still like to have a single form to interact with
** e.g. "HMC" is main label for "head mesodermal cell"
+
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
** e.g. "gon herm dtca" is main label for "anterior distal tip cell"
+
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
* Karen: would be good to still point out a "public name" or "common name"
+
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
** Chris: we may need to select a specific OWL annotation property to dump into OBO so our scripts can recognize them and populate ACEDB/Datomic; will look into; may require model change
+
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
=== Author first pass ===
+
=== Alliance SimpleMine ===
* Paul: spent about 30-40 minutes doing author first pass for a micropublication
+
* Any updates? 3.1 feature freeze is tomorrow
* Entities need to be listed 10+ times (fixed threshold) to be recognized, but micropubs won't usually have this many occurrences of terms
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* Need a better way to report allele details; curation of alleles can happen at Caltech or Hinxton; need to discuss
 
* Google summer of code: add to schedule so we can post requests/openings
 
* Karen: Could implement something like Apollo? Talk to Nathan?
 

Revision as of 00:09, 5 June 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

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call