Difference between revisions of "WormBase-Caltech Weekly Calls"

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* Maybe go back to papers that already had a request sent at the 6 month time point
 
* Maybe go back to papers that already had a request sent at the 6 month time point
 
* Include other papers in need of curation at bottom of email; possibly, would it turn off users?
 
* Include other papers in need of curation at bottom of email; possibly, would it turn off users?
 
  
 
=== Worm Phenotype Ontology ===
 
=== Worm Phenotype Ontology ===
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* Anyone interested in contributing to the WPO should contact Chris for update pipeline info
 
* Anyone interested in contributing to the WPO should contact Chris for update pipeline info
 
* Need to make sure that all users of the WPO have the updated link information
 
* Need to make sure that all users of the WPO have the updated link information
 
  
 
=== Provide provenance in query tools ===
 
=== Provide provenance in query tools ===
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* Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
 
* Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
 
* Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page
 
* Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page
 
  
 
=== WOBr disease associations ===
 
=== WOBr disease associations ===
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* Gene association file (for disease) being generated by script; likely need to update where the data is coming from
 
* Gene association file (for disease) being generated by script; likely need to update where the data is coming from
 
* Ranjana will discuss with Raymond and Kevin
 
* Ranjana will discuss with Raymond and Kevin
 
  
 
=== New WormMine superuser ===
 
=== New WormMine superuser ===
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* If people are interested in adding or editing templates talk to Chris or Paulo for superuser access
 
* If people are interested in adding or editing templates talk to Chris or Paulo for superuser access
 
* We were running into login, template ownership, and consistency issues
 
* We were running into login, template ownership, and consistency issues
 
  
 
=== Next upload Nov 16 ===
 
=== Next upload Nov 16 ===
 
* WS269 citace upload Tuesday, November 13
 
* WS269 citace upload Tuesday, November 13
 
* Can we add upload dates to Google calendar for WormBase?
 
* Can we add upload dates to Google calendar for WormBase?

Revision as of 13:33, 12 October 2018

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1


2018 Meetings

January

February

March

April

May

June

July

August

September


October 4, 2018

SimpleMine


October 11, 2018

Ready for new round of phenotype requests

  • Some users are getting confused about the name & email prepopulation based on IP address
    • May want to stop autopopulating name and email or autopopulate based on email recipient only (encode in URL sent in email)
    • Could we use cookies? Possibly, but may only help if a computer is shared but the browser isn't
  • Current autocomplete expects exact match to person primary name; e.g. "Scott Emmons" will not match the official name "Scott Wilson Emmons"
    • Maybe we could improve search matching; algorithm from Cecilia/Juancarlos? Elastic search by Valerio?
    • Can we capture incomplete sessions? We may be able to learn from them. May be flooded by robot visits? Is it worth going through all the logs/sessions? Info is there if we want to look at it.
  • Will go ahead and send emails for only new set of papers (won't resend requests for papers that had emails sent in June/July)
  • Maybe go back to papers that already had a request sent at the 6 month time point
  • Include other papers in need of curation at bottom of email; possibly, would it turn off users?

Worm Phenotype Ontology

Provide provenance in query tools

  • Prompted by user question/request
  • Specifically in WOBr, Anatomy pages
  • WOBr provides genes annotated to term; should provide provenance of each gene and its annotations
  • Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
  • Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page

WOBr disease associations

  • Ranjana wondering if WOBr is using updated disease-gene associations
  • Gene association file (for disease) being generated by script; likely need to update where the data is coming from
  • Ranjana will discuss with Raymond and Kevin

New WormMine superuser

  • Now all template queries are owned by a new superuser
  • If people are interested in adding or editing templates talk to Chris or Paulo for superuser access
  • We were running into login, template ownership, and consistency issues

Next upload Nov 16

  • WS269 citace upload Tuesday, November 13
  • Can we add upload dates to Google calendar for WormBase?