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 ==
 
  
=== GO Alliance slim terms ===
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
* 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_March_2020|March]]
* 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_April_2020|April]]
  
== August 22, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
=== Obsolete ontology terms in Postgres ===
 
* 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 ===
+
== June 4, 2020 ==
* Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019
 
* 2,627 emails/papers requested
 
* 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 ===
+
=== Citace (tentative) upload ===
* SObA highlights Alliance slim terms, but doesn't correspond to ribbon
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Want to use same slim terms used for ribbons
+
* Citace upload to Hinxton on Friday, July 10th
* Add slim terms into ACEDB? One option
 
* Ribbon order of slim terms is an issue
 
* Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
 
* Will have to manually synchronize with Alliance if Alliance changes its ribbon
 
  
== August 29, 2019 ==
+
=== 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
  
=== Caltech use of Hinxton name service ===
+
=== Nameserver ===
* Name service :
+
* Nameserver was down
** https://names.wormbase.org/gene
+
* CIT curators would still like to have a single form to interact with
* API documentation :
+
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
** https://names.wormbase.org/api-docs/index.html#!
+
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
* Sibyl is wondering :
+
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
** "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?"
+
* Hinxton is pulling in CGC strains, how often?
** "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."
+
* Caltech could possibly get a block of IDs
* Daniela, Chris, Karen are the only Caltech curators who use it.
 
* Daniela's workflow is :
 
** Look up variation through OA
 
** Look up variation through name service (what's the URL for that ?)
 
** Create object through name service, then enter information
 
** Create temporary entry for OA through Caltech postgres services
 
* Juancarlos has emailed Sibyl + Matt + Caltech with what we know so far.  Karen and Chris, please reply if you have other name service uses beyond what Daniela does.
 
* Name service google/wormbase login doesn't work right now for Caltech curators, Matt's been asked to add people.
 
  
===Anatomy term names===
+
=== Alliance SimpleMine ===
* While going through the concise descriptions text Daniela have noted down some terms that could benefit from having a more descriptive name.
+
* Any updates? 3.1 feature freeze is tomorrow
** e.g.: Pn.p hermaphrodite -> Pn.p hermaphrodite vulval precursor cell. e.g. P3.p hermaphrodite (WBbt:0008112) -> P3.p hermaphrodite vulval precursor cell
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
List of other potential terms:
 
<pre>
 
AB -> embryonic founder cell AB
 
EMS -> embryonic founder cell EMS -> should the definition of EMS be changed from ‘Embryonic cell’ to ‘Embryonic founder cell’? See WormAtlas founder cell definition.
 
C -> embryonic founder cell C
 
D ->  embryonic founder cell D
 
E ->  embryonic founder cell E
 
MS -> embryonic founder cell MS
 
Psub1 -> embryonic founder cell Psub1 (or simply embryonic founder cell P1)
 
Psub2 -> embryonic founder cell Psub2
 
Psub3 -> embryonic founder cell Psub3
 
Psub4 -> germline founder cell Psub4
 
G1 -> Postembryonic blast cell G1
 
G2 -> Postembryonic blast cell G2
 
</pre>
 

Revision as of 00:09, 5 June 2020

Previous Years

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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