Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
== March 5, 2020 ==
 
  
=== WormBase curation ===
+
== April 2, 2020 ==
* Tim Schedl: WB needs to do more curation for phenotype and variation
 
* Doing community curation, but not fast enough
 
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 
  
=== Alaksa ===
+
=== Community phenotype requests ===
* Joesph may be able to meet with Raymond
+
* March 9-28
* How can the tool be maintained? If it can't it needs to be pulled
+
* 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
  
=== Single cell expression tool ===
+
=== Community curation volunteers ===
* Tool is here: http://de.wormcells.com/
+
* Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
* What do we need to consider for pulling into WormBase?
+
* 14 volunteers so far, all have been assigned a WBPerson ID
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
+
* Chris will set up a webinar tutorial in the coming week or two
** Would want it to be in sync with WormBase releases
 
** May not need to reprocess with every release with current (small-ish) data set
 
* Fully integrated tool versus an embedded tool?
 
  
=== Name service updates ===
+
=== AFP pipeline ===
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
+
* Will resend email requests to authors that haven't already responded
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
+
* 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
  
== March 12, 2020 ==
+
=== Use Slack More ===
 
 
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
 
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
 
* Valerio would like to add these to Postgres to keep a more central repository of them
 
* Chris would still like to be able to readily update/edit the content of those lists
 

Revision as of 17:06, 2 April 2020

Previous Years

2009 Meetings

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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