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 =
+
[[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_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
== May 2, 2019 ==
 
  
=== SObA for all ontologies ===
+
== June 4, 2020 ==
* http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
 
* SObA graph search for all ontologies
 
* Juancarlos and Raymond looking for feedback; let them know
 
* Would be good to make it clear to users what the edges/arrows mean; what relations are included for inference? Can we include blurb in the legend?
 
** Raymond: thinking of putting blurb on a separate documentation page
 
* Can we track who is using this tool (and others)? SObA is hosted by WormBase so we'd have to ask Todd (Google analytics); SimpleMine is Caltech hosted so we'd need to look at Tazendra logs to see who (and how many people) are using the tool (cannot rule out bots etc.)
 
  
=== IWM swag - screen cloth ===
+
=== Citace (tentative) upload ===
* Need to finalize design
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Put Dick & Jane cartoon in one corner, tools in another corner, WB logo, Alliance logo
+
* Citace upload to Hinxton on Friday, July 10th
* Daniel can take care of ordering and printing, but needs someone to choose the design
 
  
=== Phenotype ontology patternization ===
+
=== Caltech reopening ===
* Chris working on patternizing phenotype terms to standardize logical definitions for classes of terms
+
* Paul looking to get plan approved
* This is part of the ongoing effort to align phenotype ontologies across the organisms
+
* People that want to come to campus need to watch training video
* Paul S: It's important for community submitted phenotypes (and the use of the form) to make sure the ontology makes sense and is readily browsable
+
* Masks available in Paul's lab
* Does "dumpy" mean the same thing to everyone? Is there a way to assess discrepancies in term definitions among members of the community?
+
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
* Does someone annotate to Egl or vulvaless?
+
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
* How do we help community curators decide the correct term?
+
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
* Could we develop a smart annotation aid/tool/helper? Use images, examples, etc.
+
* 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
  
== May 9, 2019 ==
+
=== Alliance SimpleMine ===
=== SObA for all ontologies ===
+
* Any updates? 3.1 feature freeze is tomorrow
* Revised version http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* Changed legend labelling, added linkouts
 
* To implement on Gene pages. One vs. Five widgets?
 
* Would be good to provide documentation on what the inferences mean; can we provide an indication of what relations a particular SObA edge could be comprised of?
 
* Let's release to the website, but gather feedback from (naive) users to see what documentation we needv
 

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