Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
Line 34: Line 34:
== 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 ===
* 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
== May 28, 2020 ==
=== Wormicloud ===
* Introducing a new tool for a graphical summary of queried papers, Please take a look and leave any comments on it. (http://textpressocentral.org:5010/)
=== Genes to Physical Map ===
* https://colab.research.google.com/drive/1e83jv94-eO_VQ7kKdJ36TgDDb4WRkFhM?usp=sharing
To run: Runtime->Run All. Change the list of gene names and run again.

Revision as of 15:38, 4 June 2020