Difference between revisions of "WormBase-Caltech Weekly Calls"
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]] | [[WormBase-Caltech_Weekly_Calls_March_2020|March]] | ||
| + | [[WormBase-Caltech_Weekly_Calls_April_2020|April]] | ||
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| − | === | + | == May 7, 2020 == |
| − | |||
| − | |||
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| − | === | + | === 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 | ||
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| − | == | + | ==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 | + | *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 18:15, 28 May 2020
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2020 Meetings
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
To run: Runtime->Run All. Change the list of gene names and run again.
