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_February_2020|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
== March 5, 2020 ==
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
=== WormBase curation ===
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
* 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 ===
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* Joesph may be able to meet with Raymond
 
* How can the tool be maintained? If it can't it needs to be pulled
 
  
=== Single cell expression tool ===
 
* Tool is here: http://de.wormcells.com/
 
* What do we need to consider for pulling into WormBase?
 
* 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)?
 
** 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 ===
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==August 6th, 2020==
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
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===Experimental conditions data flow into Alliance===
* 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
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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)
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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

Previous Years

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2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

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