Difference between revisions of "WormBase-Caltech Weekly Calls"

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== October 18, 2018 ==
== October 18, 2018 ==
=== Upload ===
=== Upload for WS269===
* To Hinxton Nov 16
* To Hinxton Nov 16
* Citace upload to Wen Nov 13
* Citace upload to Wen Nov 13

Revision as of 17:56, 18 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










October 4, 2018


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?

October 18, 2018

Upload for WS269

  • To Hinxton Nov 16
  • Citace upload to Wen Nov 13

Data provenance in WOBr tools

  • Juancarlos and Raymond have been working on
  • Awaiting pull request
  • Can test: juancarlos.wormbase.org
    • Go to WOBr and test anatomy ontology
    • Now WOBr gene count results show data objects from which the associations come (Expr_pattern and Expression_cluster objects)

New SPELL server

  • New server on Amazon (modifying server SGD uses)
  • Raymond, Wen, and Todd working on
  • Currently only have an SGD mirror running
  • Wen will swap the data later today
  • WormBase header link (to WormBase) or only link to Alliance site? We want a unified site for Alliance
  • Each MOD would still support their own server for their data (MOD-specific grants support each server, for now)

Alliance expression data

  • Anatomy-LifeStage pair required for Alliance expression annotations
  • Since many expression pattern annotations don't have both, the missing entity would default to ontology root term
  • Need to link anatomy root term to Uberon for ribbon display; root term annotations fall under the "Other" category in the ribbon slim
  • Create "Anatomical_part" term to serve as the default "Other"/root term?
  • All life-stage-only annotations will fall into anatomy "Other" and flood the list; should these be filtered out?