Difference between revisions of "WormBase-Caltech Weekly Calls"

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GoToMeeting link: https://www.gotomeet.me/wormbase1
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= 2020 Meetings =
 
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
== April 2, 2020 ==
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 
 
=== 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 [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing 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 ===
 
* Slack is a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication
 
 
 
 
 
== April 9, 2020 ==
 
 
 
=== Volunteer curators ===
 
* Have sent out emails to schedule tutorials
 
* Chris had one tutorial with Michael Davies (Alyson Ashe's lab) yesterday
 
* One already scheduled for next Monday with Wilber and Stephanie from Paul's lab
 
* Two others already scheduled for next Tuesday with Lina Dahlberg and Colin Dolphin
 
 
 
===TAGC is virtual (4.22-25.2020)===
 
FYI in case you missed it
 
*You still have to register (it's free), if you hadn't before
 
https://genetics-gsa.org/tagc-2020/registration/
 
 
 
===summer students===
 
* Caltech SURF students (and other summer students worldwide) now are looking for projects
 
* Maybe they could curate for WormBase
 
* In addition to phenotype, they could curate:
 
** Allele/lesion sequence curation (using Allele Sequence form); maybe Paul Davis could make a tutorial video?
 
** Anatomy function, looking for novel info; opportunity to program/code
 
 
 
=== OA semicolon issue ===
 
* Juancarlos has fixed the issues on sandbox
 
* Curators should test on Mangolassi
 
 
 
=== Textmining/automation ===
 
* Daniela will discuss with Christina Zorn from Xenbase
 
* Will discuss SVM, AFP, Textpresso, etc.
 
  
=== Retracted WBPapers ===
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
* Jae & Kimberly put in GitHub ticket to make retractions clear on WormBase site
 
* https://github.com/WormBase/website/issues/7637
 
* Can we systematically detect retractions? Yes
 
* What about finding papers that cite retractions? Maybe, but likely tricky
 
  
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
== April 16, 2020 ==
 
  
=== Community Phenotype Curation Tutorials ===
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==August 6th, 2020==
* Chris has run 6 tutorials, recorded 4
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===Experimental conditions data flow into Alliance===
* MPG files saved on DropBox; ask Chris for access
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*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
* Plan to edit videos to make tutorial video to post on WB YouTube channel
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*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
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*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
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*So for data flow into Alliance:
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**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
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**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
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* How do we handle genetic sex? Part of condition?
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** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
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** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex

Revision as of 16:36, 6 August 2020

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2020 Meetings

January

February

March

April

May

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July


August 6th, 2020

Experimental conditions data flow into Alliance

  • Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
  • We use the WB Molecule CV for Inducers and Modifiers in disease annotation
  • Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
  • So for data flow into Alliance:
    • In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
    • Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
  • How do we handle genetic sex? Part of condition?
    • Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
    • Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex