Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
== February 6, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
=== Worcester Area Worm Meeting talk ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* 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 ==
+
== May 7, 2020 ==
  
=== Alliance Literature Group ===
+
=== Alliance COVID Page ===
* Held first meeting on Monday, February 10th
+
* Available on stage
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
+
* Textpresso for Coronavirus up for testing
* 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 ===
+
=== SimpleMine at Alliance ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
+
* Still some confusion about what it is
* Can aim to implement for WS277 but may have to wait until WS278
+
* Will try to help clarify on PI meeting on Friday
  
=== Genotype OA ===
+
=== Development environment for Alliance work ===
* Will put documentation [[Genotype|here]]
+
* Raymond and Juancarlos have been working on
 +
* Existing hardware is strained; set up virtual machine
 +
* Still some technical issues
  
=== WB All-Hands Meeting ===
+
=== Open Publishing Festival ===
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
+
* Later this month
* Any thoughts at this point?  Still need to discuss with Hinxton, Toronto.
+
* Micropublications involved
 +
* Organized by the Collaborative Knowledge Foundation
 +
* Will involve publishers of books, journals, etc.
 +
* Will have a MOD-focused event, would be good to have WB curators participate/attend
 +
* Open to all
  
 +
=== Genotype class ===
 +
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
 +
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
 +
* There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
 +
* Would be good to be clear/transparent about which components were automatically inferred
  
== February 20, 2020 ==
+
=== WS277/278 ===
 +
* Pipelines are pushed back by about 14 days/2 weeks
  
=== 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 ===
+
==May 13, 2020==
* 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?
+
=== SURF students ===
* We could make different species entries that specify the assembly version
+
* Welcome Fernando!
 +
* Will work on neuron function with respect to dauer formation
 +
 
 +
=== Progress Report ===
 +
* Review Google Doc from Paul to make sure you're latest updates are there
 +
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
 +
 
 +
===Genotype class===
 +
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
 +
*Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
 +
*Disease OA annotations now converted to the newly created genotypes where needed
 +
*Need to work on disease dumper changes next
 +
 
 +
=== What genes should be linked to genotypes? ===
 +
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
 +
* What should we consider a "relevant gene"?
 +
* We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
 +
* For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
 +
* For rearrangements, consider relevant any genes "inside" the rearrangement?
 +
* For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
 +
* In the future, we may want to consider genes that have been specifically annotated as having some functional consequence and informs that the gene is of functional relevance to the genotype
 +
 
 +
=== Volunteer Community Curators ===
 +
* Have had an additional 13 people volunteer
 +
* Single one-on-one tutorial for someone in Hong Kong this past Monday
 +
* Chris will hold a tutorial today and tomorrow for everyone else
 +
* Have received many new community annotations from volunteers (and authors), validation still pending
 +
 
 +
=== Open Publishing Festival ===
 +
* Ranjana will join as a panelist
 +
* Other MOD curators will also join
 +
* Festival calendar: https://openpublishingfest.org/calendar.html
 +
 
 +
=== Move to Chen building ===
 +
* Scheduled for late January 2021
 +
 
 +
=== First completely virtual GO meeting ===
 +
* Kimberly: went really well
 +
* Only met 4 hours per day, due to time zone differences
 +
* Had breakout sessions for focus groups
 +
 
 +
=== Alliance Literature Acquisition working group ===
 +
* Plan to come up with use cases for OntoMate and Textpresso
 +
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
 +
 
 +
* Kimberly plans to draw up most common use cases for Textpresso
 +
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
 +
 
 +
 
 +
== May 21, 2020 ==
 +
 
 +
=== Volunteer curators ===
 +
* Received surge of annotations earlier this week
 +
* All tutorials done for now; all but 3 recorded
 +
* Each tutorial is ~1 hour in length
 +
 
 +
=== AFP tutorial ===
 +
* AFP group working on tutorial/webinar
 +
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
 +
 
 +
=== Open Publishing Festival ===
 +
* Had micropublication session yesterday, went well
 +
* Had ~50 participants
 +
* Saved Zoom chats? Can get public ones, maybe not private ones

Latest revision as of 16:11, 21 May 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


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

2020 Meetings

January

February

March

April


May 7, 2020

Alliance COVID Page

  • Available on stage
  • Textpresso for Coronavirus up for testing

SimpleMine at Alliance

  • Still some confusion about what it is
  • Will try to help clarify on PI meeting on Friday

Development environment for Alliance work

  • Raymond and Juancarlos have been working on
  • Existing hardware is strained; set up virtual machine
  • Still some technical issues

Open Publishing Festival

  • Later this month
  • Micropublications involved
  • Organized by the Collaborative Knowledge Foundation
  • Will involve publishers of books, journals, etc.
  • Will have a MOD-focused event, would be good to have WB curators participate/attend
  • Open to all

Genotype class

  • Ranjana finished populating the Genotype OA with genotypes needed for disease curation
  • Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
  • There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
  • Would be good to be clear/transparent about which components were automatically inferred

WS277/278

  • Pipelines are pushed back by about 14 days/2 weeks


May 13, 2020

SURF students

  • Welcome Fernando!
  • Will work on neuron function with respect to dauer formation

Progress Report

Genotype class

  • Have 27 genotypes in the genotype OA, dumper and test .ace file ready
  • Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
  • Disease OA annotations now converted to the newly created genotypes where needed
  • Need to work on disease dumper changes next

What genes should be linked to genotypes?

  • We have a "Gene" tag in the ?Genotype model for capturing relevant genes
  • What should we consider a "relevant gene"?
  • We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
  • For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
  • For rearrangements, consider relevant any genes "inside" the rearrangement?
  • For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
  • In the future, we may want to consider genes that have been specifically annotated as having some functional consequence and informs that the gene is of functional relevance to the genotype

Volunteer Community Curators

  • Have had an additional 13 people volunteer
  • Single one-on-one tutorial for someone in Hong Kong this past Monday
  • Chris will hold a tutorial today and tomorrow for everyone else
  • Have received many new community annotations from volunteers (and authors), validation still pending

Open Publishing Festival

Move to Chen building

  • Scheduled for late January 2021

First completely virtual GO meeting

  • Kimberly: went really well
  • Only met 4 hours per day, due to time zone differences
  • Had breakout sessions for focus groups

Alliance Literature Acquisition working group


May 21, 2020

Volunteer curators

  • Received surge of annotations earlier this week
  • All tutorials done for now; all but 3 recorded
  • Each tutorial is ~1 hour in length

AFP tutorial

  • AFP group working on tutorial/webinar
  • Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)

Open Publishing Festival

  • Had micropublication session yesterday, went well
  • Had ~50 participants
  • Saved Zoom chats? Can get public ones, maybe not private ones