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_March_2019|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 
 
 
 
 
== August 1, 2019 ==
 
 
 
=== Life stage public names missing in WS271 ===
 
* Did we ever get a patch in for this?
 
* WormMine only has WBls IDs (no public name) for almost all life stages
 
* Wen will resend the patch file
 
 
 
=== 2020 WB NAR paper ===
 
* Who's contributing?
 
** Raymond, Chris, Ranjana, Valerio, Daniela, Kimberly
 
* Topics
 
** Automated descriptions
 
** Ontology tools (SObA)
 
** Community curation
 
** Author first pass
 
 
 
=== 2019 IWM Workshop videos ===
 
* On YouTube, but not public yet
 
* Chris will make them public and send links to Ranjana for the blog post
 
 
 
  
== August 15, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
=== GO Alliance slim terms ===
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
* We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance
 
* May need to watch out for terms that don't apply to worms
 
* Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?)
 
  
=== Phenotype ontology patternization ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* Now have 676 terms patternized (27% of 2,506 terms total)
 
* Have reviewed the class hierarchy, collecting list of unexpected class subsumptions
 
* Issues to address collected here: https://docs.google.com/document/d/1IWtQbEQ-elM-U5SQyU4VfIH3vdJp6taVMGViIjGyVks/edit?usp=sharing
 
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
== August 22, 2019 ==
 
  
=== Obsolete ontology terms in Postgres ===
+
== June 4, 2020 ==
* There are currently 172 GO annotations in the GO OA, 94 in Expr OA, and 54 in Pic OA referring to obsolete GO terms
 
** https://docs.google.com/spreadsheets/d/14iG3-s0GrZ3_W87iOjD6tZiQiUJklRRjgs6ARFWi9E4/edit?usp=sharing
 
* We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres
 
  
=== Community phenotype requests ===
+
=== Citace (tentative) upload ===
* Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* 2,627 emails/papers requested
+
* Citace upload to Hinxton on Friday, July 10th
* 112 emails bounced; 4 resent to new addresses
 
* 205 Phenotype OA community annotations; 55 RNAi OA annotations, from 47 papers, by 42 distinct community curators (so far)
 
* Also, 3 worksheets submitted, for 4 papers
 
* 35 papers flagged as not having phenotypes
 
* 86 papers with responses (3% response; still early)
 
* Need to coordinate with the AFP request pipeline
 
  
=== GO slim terms ===
+
=== Caltech reopening ===
* SObA highlights Alliance slim terms, but doesn't correspond to ribbon
+
* Paul looking to get plan approved
* Want to use same slim terms used for ribbons
+
* People that want to come to campus need to watch training video
* Add slim terms into ACEDB? One option
+
* Masks available in Paul's lab
* Ribbon order of slim terms is an issue
+
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
* Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
+
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
* Will have to manually synchronize with Alliance if Alliance changes its ribbon
+
* 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
  
== August 29, 2019 ==
+
=== 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
  
=== Caltech use of Hinxton name service ===
+
=== Alliance SimpleMine ===
* Name service API :
+
* Any updates? 3.1 feature freeze is tomorrow
** https://names.wormbase.org/gene
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* API documentation :
 
** https://names.wormbase.org/api-docs/index.html#!
 
* Sibyl is wondering :
 
** "it would be nice to know when and how curators use the name service. And does any script managed by Caltech write data into the name services?"
 
** "what needs to be done to adopt the new name service. For example, what concern do you or the curators have about adopting the new name service, what kind of tests will allow the curators to trust that the new name service is working correctly, what changes to the new name service is needed for Caltech to be able to use it."
 

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