Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
== March 5, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
=== WormBase curation ===
 
* Tim Schedl: WB needs to do more curation for phenotype and variation
 
* Doing community curation, but not fast enough
 
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 
  
=== Alaksa ===
 
* Joesph may be able to meet with Raymond
 
* How can the tool be maintained? If it can't it needs to be pulled
 
  
=== Single cell expression tool ===
+
== May 7, 2020 ==
* Tool is here: http://de.wormcells.com/
 
* What do we need to consider for pulling into WormBase?
 
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
 
** Would want it to be in sync with WormBase releases
 
** May not need to reprocess with every release with current (small-ish) data set
 
* Fully integrated tool versus an embedded tool?
 
  
=== Name service updates ===
+
=== Alliance COVID Page ===
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
+
* Available on stage
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
+
* 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
  
== March 12, 2020 ==
+
=== Development environment for Alliance work ===
 +
* Raymond and Juancarlos have been working on
 +
* Existing hardware is strained; set up virtual machine
 +
* Still some technical issues
  
=== Cancelled meetings ===
+
=== Open Publishing Festival ===
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
+
* Later this month
* We should start doing online advertisement for micropublications with webinars
+
* 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
  
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
+
=== Genotype class ===
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
+
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
* Valerio would like to add these to Postgres to keep a more central repository of them
+
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
* Chris would still like to be able to readily update/edit the content of those lists
+
* 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
  
* Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
+
=== WS277/278 ===
 +
* Pipelines are pushed back by about 14 days/2 weeks
  
=== Updates on Alaska ===
 
  
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
+
==May 13, 2020==
The future plan is to move the platform to Google colab to reduce maintainance work.
 
  
==Nameservice discussion==
+
=== SURF students ===
*Getting a token has worked for Chris and Ranjana
+
* Welcome Fernando!
*Karen and Daniela need to get tokens
+
* Will work on neuron function with respect to dauer formation
  
==Noctua GO-CAM updates==
+
=== Progress Report ===
*Noctua is a production tool available for annotations right now
+
* Review Google Doc from Paul to make sure you're latest updates are there
*Create as many interconnected models and make available for curators is the ongoing goal
+
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
*Reactome models are in the process of being imported
 
*Real time validation messages as curation is being done, is being worked on
 
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
 
  
 +
===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
  
== March 19, 2020 ==
+
=== 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
  
=== Citace Upload ===
+
=== Volunteer Community Curators ===
* Tuesday, March 31st
+
* 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
  
=== Latest ACEDB ===
+
=== Open Publishing Festival ===
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
+
* Ranjana will join as a panelist
 +
* Other MOD curators will also join
 +
* Festival calendar: https://openpublishingfest.org/calendar.html
  
=== Storing email addresses/persons to omit from requests ===
+
=== Move to Chen building ===
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
+
* Scheduled for late January 2021
  
=== Mailing lists ===
+
=== First completely virtual GO meeting ===
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
+
* 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/
  
==March 26th==
+
* Kimberly plans to draw up most common use cases for Textpresso
===Community curation===
+
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
 
* Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
 
* Blog about phenotype form to make people generally aware
 
  
=== AFP for older papers ===
+
 
* Discussed recently
+
== May 21, 2020 ==
* Many (all?) Old papers have already gone through the old AFP pipeline
+
 
* Need to check what has already been curated
+
=== 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