Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
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GoToMeeting link: https://www.gotomeet.me/wormbase1
 
 
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
 
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
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= 2020 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
== August 2, 2018 ==
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
=== AFP ===
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
* The AFP pipeline is currently emailing authors from karen's e-mail address
 
* Use same e-mail account Chris is using for phenotype community curation requests or create a new account for AFP (gmail)
 
* Can use outreach@wormbase.org for consistency
 
* May use the PMID in the subject line so e-mails will not be all in the same thread
 
* Todd and Chris have email credentials
 
** Chris will send to Valerio, Juancarlos, Daniela, and Kimberly
 
* Let Valerio and Juancarlos know what pipelines use AFP before they modify
 
* Do curators still want to receive emails when authors flag their data type?
 
** We will leave the alert emails as is for now
 
  
 +
== April 2, 2020 ==
  
== August 9, 2018 ==
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=== Community phenotype requests ===
 +
* March 9-28
 +
* 2,548 emails went out; 89 bounced; 6 resent; 13 backup; 2,478 successful emails
 +
* 361 annotations overall
 +
* 48 papers requested received curation (2% response rate)
 +
* 53 distinct papers overall (5 papers without request)
 +
* 53 distinct persons overall
  
=== AFP ===
+
=== Community curation volunteers ===
* Mai Zhen, SAB member suggested that we include disease models in the AFP form.  
+
* Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
* The AFP group will work with Ranjana to incorporate it. Ranjana will prepare a mock by next week.
+
* 14 volunteers so far, all have been assigned a WBPerson ID
* We will then decide if using the existing afp_humdis tables or if creating new ones.
+
* Chris will set up a webinar tutorial in the coming week or two
  
 +
=== AFP pipeline ===
 +
* Will resend email requests to authors that haven't already responded
 +
* May also send out for older papers
 +
* May work with people to help
 +
* Does the old AFP form still work? It should
 +
* If someone has a link to the old form, they won't get one for the new form
 +
* Maybe could set up an automatic redirect from the old form to the new form
 +
* Received many submissions recently (>20% response rate)
  
=== Tazendra ===
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=== Ontology Annotator ===
 +
* Need to work on Genotype OA dumper
 +
* Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
 +
* Ampersands (&) are also problematic for object names in the OA
 +
** 20237  | Is[Pgcy-5::daf-2a::venus; Punc-122::mCherry]                          | 2014-10-08 10:32:45.874519-07
 +
** 20239  | Ex[Pgcy-5::casy-1::venus; Pgcy-5::aman-2::mCherry; Punc-122::mCherry] | 2014-10-08 10:45:23.202362-07
 +
** 20238  | Is[Pgcy-5::daf-2c::venus; Punc-122::mCherry]                          | 2014-10-08 10:38:19.859078-07
 +
** 25249  | Ex[Prheb-1::rheb-1::GFP; unc-119(+]                                  | 2018-06-29 10:16:40.784295-07
 +
** 16283  | [hlh-13::GFP;unc-119(+)]                                              | 2013-02-07 17:43:22.384819-08
 +
** 26131  | Ex[pedc-3EDC-3::DsRed;pRF4]                                          | 2019-08-14 08:44:49.91063-07
  
* Shall we move tazendra.caltech.edu to the cloud? Either WormBase cloud or Caltech cloud?
+
=== Use Slack More ===

Latest revision as of 17:06, 2 April 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 2, 2020

Community phenotype requests

  • March 9-28
  • 2,548 emails went out; 89 bounced; 6 resent; 13 backup; 2,478 successful emails
  • 361 annotations overall
  • 48 papers requested received curation (2% response rate)
  • 53 distinct papers overall (5 papers without request)
  • 53 distinct persons overall

Community curation volunteers

  • Tracking volunteers here
  • 14 volunteers so far, all have been assigned a WBPerson ID
  • Chris will set up a webinar tutorial in the coming week or two

AFP pipeline

  • Will resend email requests to authors that haven't already responded
  • May also send out for older papers
  • May work with people to help
  • Does the old AFP form still work? It should
  • If someone has a link to the old form, they won't get one for the new form
  • Maybe could set up an automatic redirect from the old form to the new form
  • Received many submissions recently (>20% response rate)

Ontology Annotator

  • Need to work on Genotype OA dumper
  • Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
  • Ampersands (&) are also problematic for object names in the OA
    • 20237 | Is[Pgcy-5::daf-2a::venus; Punc-122::mCherry] | 2014-10-08 10:32:45.874519-07
    • 20239 | Ex[Pgcy-5::casy-1::venus; Pgcy-5::aman-2::mCherry; Punc-122::mCherry] | 2014-10-08 10:45:23.202362-07
    • 20238 | Is[Pgcy-5::daf-2c::venus; Punc-122::mCherry] | 2014-10-08 10:38:19.859078-07
    • 25249 | Ex[Prheb-1::rheb-1::GFP; unc-119(+] | 2018-06-29 10:16:40.784295-07
    • 16283 | [hlh-13::GFP;unc-119(+)] | 2013-02-07 17:43:22.384819-08
    • 26131 | Ex[pedc-3EDC-3::DsRed;pRF4] | 2019-08-14 08:44:49.91063-07

Use Slack More