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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_April_2020|April]] | | [[WormBase-Caltech_Weekly_Calls_April_2020|April]] |
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| + | [[WormBase-Caltech_Weekly_Calls_May_2020|May]] |
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| + | [[WormBase-Caltech_Weekly_Calls_June_2020|June]] |
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− | == May 7, 2020 ==
| + | [[WormBase-Caltech_Weekly_Calls_July_2020|July]] |
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− | === Alliance COVID Page ===
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− | * Available on stage
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− | * Textpresso for Coronavirus up for testing
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− | === SimpleMine at Alliance ===
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− | * Still some confusion about what it is
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− | * Will try to help clarify on PI meeting on Friday
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− | === Development environment for Alliance work ===
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− | * Raymond and Juancarlos have been working on
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− | * Existing hardware is strained; set up virtual machine
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− | * Still some technical issues
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− | === Open Publishing Festival ===
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− | * Later this month
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− | * Micropublications involved
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− | * Organized by the Collaborative Knowledge Foundation
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− | * Will involve publishers of books, journals, etc.
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− | * Will have a MOD-focused event, would be good to have WB curators participate/attend
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− | * Open to all
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− | === Genotype class ===
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− | * Ranjana finished populating the Genotype OA with genotypes needed for disease curation
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− | * Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
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− | * There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
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− | * Would be good to be clear/transparent about which components were automatically inferred
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− | === WS277/278 ===
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− | * Pipelines are pushed back by about 14 days/2 weeks
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− | ==May 13, 2020==
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− | === SURF students ===
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− | * Welcome Fernando!
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− | * Will work on neuron function with respect to dauer formation
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− | === Progress Report ===
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− | * Review Google Doc from Paul to make sure you're latest updates are there
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− | * Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
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− | ===Genotype class===
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− | *Have 27 genotypes in the genotype OA, dumper and test .ace file ready
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− | *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
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− | *Disease OA annotations now converted to the newly created genotypes where needed
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− | *Need to work on disease dumper changes next
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− | === What genes should be linked to genotypes? ===
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− | * We have a "Gene" tag in the ?Genotype model for capturing relevant genes
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− | * What should we consider a "relevant gene"?
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− | * We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
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− | * 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(+)"?
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− | * For rearrangements, consider relevant any genes "inside" the rearrangement?
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− | * For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
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− | * 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
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− | === Volunteer Community Curators ===
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− | * Have had an additional 13 people volunteer
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− | * Single one-on-one tutorial for someone in Hong Kong this past Monday
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− | * Chris will hold a tutorial today and tomorrow for everyone else
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− | * Have received many new community annotations from volunteers (and authors), validation still pending
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− | === Open Publishing Festival ===
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− | * Ranjana will join as a panelist
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− | * Other MOD curators will also join
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− | * Festival calendar: https://openpublishingfest.org/calendar.html
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− | === Move to Chen building ===
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− | * Scheduled for late January 2021
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− | === First completely virtual GO meeting ===
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− | * Kimberly: went really well
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− | * Only met 4 hours per day, due to time zone differences
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− | * Had breakout sessions for focus groups
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− | === Alliance Literature Acquisition working group ===
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− | * Plan to come up with use cases for OntoMate and Textpresso
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− | **Ontomate link https://rgd.mcw.edu/QueryBuilder/
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− | * Kimberly plans to draw up most common use cases for Textpresso
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− | * Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
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− | == May 21, 2020 ==
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− | === Volunteer curators ===
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− | * Received surge of annotations earlier this week
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− | * All tutorials done for now; all but 3 recorded
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− | * Each tutorial is ~1 hour in length
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− | === AFP tutorial ===
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− | * AFP group working on tutorial/webinar
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− | * Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
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− | === Open Publishing Festival ===
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− | * Had micropublication session yesterday, went well
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− | * Had ~50 participants
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− | * Saved Zoom chats? Can get public ones, maybe not private ones
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− | == May 28, 2020 ==
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− | === Wormicloud === | + | ==August 6th, 2020== |
− | * 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/) | + | ===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 |