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_January_2020|January]]
 
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
== February 6, 2020 ==
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 
 
=== Worcester Area Worm Meeting talk ===
 
* Confirmed for December 2020 or February 2021
 
 
 
=== Alaska software ===
 
* Code developed and maintained by Joseph, but not long term solution
 
* Raymond and Eduardo talked about taking it over
 
* Why have a web application vs. a command-line application?
 
** Wanted to make it easy, but also to capture meta data for WB
 
* Should/will find out from Joseph about how hard it is to maintain the software
 
* Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
 
* Expression working group working with Brian Oliver to have GEO take in more structured meta data
 
* Array Express tried requiring more structured meta data, but authors stopped submitting
 
* May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
 
 
 
 
 
== February 13, 2020 ==
 
 
 
=== Alliance Literature Group ===
 
* Held first meeting on Monday, February 10th
 
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
 
* Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
 
* Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
 
 
 
=== ?Genotype class model ===
 
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
 
* Can aim to implement for WS277 but may have to wait until WS278
 
 
 
=== Genotype OA ===
 
* Will put documentation [[Genotype|here]]
 
 
 
=== WB All-Hands Meeting ===
 
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
 
* Any thoughts at this point?  Still need to discuss with Hinxton, Toronto.
 
 
 
 
 
== February 20, 2020 ==
 
 
 
=== Genotype ===
 
* We will equate superficially similar/identical genotypes for now
 
* What if labs sequence strains later and find out more?
 
* Labs will have to report strains and their sequence and we back-curate accordingly
 
  
=== VC2010 assembly genes ===
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
 
* How to best handle these "extra" genes?
 
* We could make different species entries that specify the assembly version
 
  
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
== February 27, 2020 ==
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
=== WB Project meeting ===
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* Early May (~May 7th, 8th)
 
  
=== Genotype ===
 
* [[Genotype|Genotype Wiki page]] updated
 
* Will start building Genotype OA
 
  
=== Outreach inbox ===
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==August 6th, 2020==
* 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
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===Experimental conditions data flow into Alliance===
* Many are bounced emails messages
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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)
* Do we want a common place to track bad/bouncing email addresses? We need to distinguish addresses that bounce for policy/SPAM reasons versus those that are likely outdated or no longer in use.
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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

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