Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
 +
= 2020 Meetings =
 +
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
= 2018 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
== May 7, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
=== Alliance COVID Page ===
 +
* Available on stage
 +
* Textpresso for Coronavirus up for testing
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
=== SimpleMine at Alliance ===
 +
* Still some confusion about what it is
 +
* Will try to help clarify on PI meeting on Friday
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
=== Development environment for Alliance work ===
 +
* Raymond and Juancarlos have been working on
 +
* Existing hardware is strained; set up virtual machine
 +
* Still some technical issues
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
+
=== WS277/278 ===
 +
* Pipelines are pushed back by about 14 days/2 weeks
  
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
 
  
 +
==May 13, 2020==
  
== October 4, 2018 ==
+
=== SURF students ===
 +
* Welcome Fernando!
 +
* Will work on neuron function with respect to dauer formation
  
=== SimpleMine ===
+
=== Progress Report ===
* Automated descriptions will be removed from Postgres/OA
+
* Review Google Doc from Paul to make sure you're latest updates are there
* SimpleMine needed to update where it pulls the automated descriptions from
+
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
* Will add expression cluster and automated description columns output (in addition to concise description)
 
* Added RNAseq FPKM download function for 9 species: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/fpkmmine.cgi
 
* Added SimpleMine-like topic search: http://tazendra.caltech.edu/%7Eazurebrd/cgi-bin/forms/spellmine.cgi
 
* Should put the new tools under the WormBase Tools menu
 
  
 +
===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
  
== October 11, 2018 ==
+
=== 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
  
=== Ready for new round of phenotype requests ===
+
=== Volunteer Community Curators ===
* Some users are getting confused about the name & email prepopulation based on IP address
+
* Have had an additional 13 people volunteer
** May want to stop autopopulating name and email or autopopulate based on email recipient only (encode in URL sent in email)
+
* Single one-on-one tutorial for someone in Hong Kong this past Monday
** Could we use cookies? Possibly, but may only help if a computer is shared but the browser isn't
+
* Chris will hold a tutorial today and tomorrow for everyone else
* Current autocomplete expects exact match to person primary name; e.g. "Scott Emmons" will not match the official name "Scott Wilson Emmons"
+
* Have received many new community annotations from volunteers (and authors), validation still pending
** Maybe we could improve search matching; algorithm from Cecilia/Juancarlos? Elastic search by Valerio?
 
** Can we capture incomplete sessions? We may be able to learn from them. May be flooded by robot visits? Is it worth going through all the logs/sessions? Info is there if we want to look at it.
 
* Will go ahead and send emails for only new set of papers (won't resend requests for papers that had emails sent in June/July)
 
* Maybe go back to papers that already had a request sent at the 6 month time point
 
* Include other papers in need of curation at bottom of email; possibly, would it turn off users?
 
  
=== Worm Phenotype Ontology ===
+
=== Open Publishing Festival ===
* WPO has a new home on GitHub
+
* Ranjana will join as a panelist
** https://github.com/obophenotype/c-elegans-phenotype-ontology
+
* Other MOD curators will also join
* Edits should only be made to the edit file
+
* Festival calendar: https://openpublishingfest.org/calendar.html
** https://github.com/obophenotype/c-elegans-phenotype-ontology/blob/master/src/ontology/wbphenotype-edit.owl
 
* Anyone interested in contributing to the WPO should contact Chris for update pipeline info
 
* Need to make sure that all users of the WPO have the updated link information
 
  
=== Provide provenance in query tools ===
+
=== Move to Chen building ===
* Prompted by user question/request
+
* Scheduled for late January 2021
* Specifically in WOBr, Anatomy pages
 
* WOBr provides genes annotated to term; should provide provenance of each gene and its annotations
 
* Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
 
* Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page
 
  
=== WOBr disease associations ===
+
=== First completely virtual GO meeting ===
* Ranjana wondering if WOBr is using updated disease-gene associations
+
* Kimberly: went really well
* Gene association file (for disease) being generated by script; likely need to update where the data is coming from
+
* Only met 4 hours per day, due to time zone differences
* Ranjana will discuss with Raymond and Kevin
+
* Had breakout sessions for focus groups
  
=== New WormMine superuser ===
+
=== Alliance Literature Acquisition working group ===
* Now all template queries are owned by a new superuser
+
* Plan to come up with use cases for OntoMate and Textpresso
* If people are interested in adding or editing templates talk to Chris or Paulo for superuser access
+
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
* We were running into login, template ownership, and consistency issues
 
  
=== Next upload Nov 16 ===
+
* Kimberly plans to draw up most common use cases for Textpresso
* WS269 citace upload Tuesday, November 13
+
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
* Can we add upload dates to Google calendar for WormBase?
 
  
  
== October 18, 2018 ==
+
== May 21, 2020 ==
  
=== Upload for WS269===
+
=== Volunteer curators ===
* To Hinxton Nov 16
+
* Received surge of annotations earlier this week
* Citace upload to Wen Nov 13
+
* All tutorials done for now; all but 3 recorded
 +
* Each tutorial is ~1 hour in length
  
=== Data provenance in WOBr tools ===
+
=== AFP tutorial ===
* Juancarlos and Raymond have been working on
+
* AFP group working on tutorial/webinar
* Awaiting pull request
+
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
* Can test: juancarlos.wormbase.org
 
** Go to WOBr and test anatomy ontology
 
** Now WOBr gene count results show data objects from which the associations come (Expr_pattern and Expression_cluster objects)
 
  
=== New SPELL server ===
+
=== Open Publishing Festival ===
* New server on Amazon (modifying server SGD uses)
+
* Had micropublication session yesterday, went well
* Raymond, Wen, and Todd working on
+
* Had ~50 participants
* Currently only have an SGD mirror running
+
* Saved Zoom chats? Can get public ones, maybe not private ones
* Wen will swap the data later today
 
* WormBase header link (to WormBase) or only link to Alliance site? We want a unified site for Alliance
 
* Each MOD would still support their own server for their data (MOD-specific grants support each server, for now)
 
  
=== Alliance expression data ===
 
* Anatomy-LifeStage pair required for Alliance expression annotations
 
* Since many expression pattern annotations don't have both, the missing entity would default to ontology root term
 
* Need to link anatomy root term to Uberon for ribbon display; root term annotations fall under the "Other" category in the ribbon slim
 
* Create "Anatomical_part" term to serve as the default "Other"/root term?
 
* All life-stage-only annotations will fall into anatomy "Other" and flood the list; should these be filtered out?
 
  
 +
== May 28, 2020 ==
  
== October 25, 2018 ==
+
=== 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/)
  
=== WormBase SPELL on Amazon Web Service ===
+
=== Genes to Physical Map ===
* http://34.224.93.60/ is running WormBase SPELL on WS267, based on the SPELL code supported by SGD.
+
* 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.

Latest revision as of 18:15, 28 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


May 28, 2020

Wormicloud

Genes to Physical Map

To run: Runtime->Run All. Change the list of gene names and run again.