Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
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= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
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==August 6th, 2020==
 
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===Experimental conditions data flow into Alliance===
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
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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
== December 5, 2019 ==
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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)
=== New interaction Venn diagram tool ===
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**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
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* How do we handle genetic sex? Part of condition?
* Venn diagram shows how various interactors have multiple interaction types with a common focus gene
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** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
* For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
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** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
* Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
 
* Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
 
* Request: could there be a toggle to include/exclude high-throughput interactions?
 
* Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
 
* Request: Change the wording "Browse selection" to something like "View/analyze gene list"
 
* Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?
 
 
 
 
 
=== New round of phenotype requests ===
 
* GMail really throttling email sending
 
* Chris will reach out to Google/GMail to see if we can:
 
** A) get a clear explanation about what their restrictions are and how they work and
 
** B) see if we can get a paid plan to help expedite the email process (see how much cost)
 
 
 
=== Aligning interaction data with GO and GO-CAM ===
 
* The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
 
* Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
 
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
 
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
 
* Chris and Kimberly will meet to discuss further
 
 
 
=== Short SObA talk at Alliance meeting ===
 
* Raymond prepared to give short talk on SObA to the Alliance group
 
 
 
=== Single cell data visualization tool ===
 
* Eduardo will present to Paul's lab meeting tomorrow
 
* Will discuss at Alliance expression working group pre-meeting
 

Latest revision as of 16:36, 6 August 2020

Previous Years

2009 Meetings

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