Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 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]]
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
== May 7, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
=== Alliance COVID Page ===
 +
* Available on stage
 +
* Textpresso for Coronavirus up for testing
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
=== SimpleMine at Alliance ===
 +
* Still some confusion about what it is
 +
* Will try to help clarify on PI meeting on Friday
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
=== 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_May_2019|May]]
+
=== 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_June_2019|June]]
+
=== 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_July_2019|July]]
+
=== WS277/278 ===
 +
* Pipelines are pushed back by about 14 days/2 weeks
  
  
== August 1, 2019 ==
+
==May 13, 2020==
  
=== Life stage public names missing in WS271 ===
+
=== SURF students ===
* Did we ever get a patch in for this?
+
* Welcome Fernando!
* WormMine only has WBls IDs (no public name) for almost all life stages
+
* Will work on neuron function with respect to dauer formation
* Wen will resend the patch file
 
  
=== 2020 WB NAR paper ===
+
=== Progress Report ===
* Who's contributing?
+
* Review Google Doc from Paul to make sure you're latest updates are there
** Raymond, Chris, Ranjana, Valerio, Daniela, Kimberly
+
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
* Topics
 
** Automated descriptions
 
** Ontology tools (SObA)
 
** Community curation
 
** Author first pass
 
  
=== 2019 IWM Workshop videos ===
+
===Genotype class===
* On YouTube, but not public yet
+
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
* Chris will make them public and send links to Ranjana for the blog post
+
*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
  
== August 15, 2019 ==
+
=== 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
  
=== GO Alliance slim terms ===
+
=== Open Publishing Festival ===
* We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance
+
* Ranjana will join as a panelist
* May need to watch out for terms that don't apply to worms
+
* Other MOD curators will also join
* Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?)
+
* Festival calendar: https://openpublishingfest.org/calendar.html
  
=== Phenotype ontology patternization ===
+
=== Move to Chen building ===
* Now have 676 terms patternized (27% of 2,506 terms total)
+
* Scheduled for late January 2021
* Have reviewed the class hierarchy, collecting list of unexpected class subsumptions
 
* Issues to address collected here: https://docs.google.com/document/d/1IWtQbEQ-elM-U5SQyU4VfIH3vdJp6taVMGViIjGyVks/edit?usp=sharing
 
  
 +
=== 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
  
== August 22, 2019 ==
+
=== Alliance Literature Acquisition working group ===
 +
* Plan to come up with use cases for OntoMate and Textpresso
 +
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
  
=== Obsolete ontology terms in Postgres ===
+
* Kimberly plans to draw up most common use cases for Textpresso
* There are currently 172 GO annotations in the GO OA, 94 in Expr OA, and 54 in Pic OA referring to obsolete GO terms
+
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
** https://docs.google.com/spreadsheets/d/14iG3-s0GrZ3_W87iOjD6tZiQiUJklRRjgs6ARFWi9E4/edit?usp=sharing
 
* We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres
 
  
=== Community phenotype requests ===
 
* Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019
 
* 2,627 emails/papers requested
 
* 112 emails bounced; 4 resent to new addresses
 
* 205 Phenotype OA community annotations; 55 RNAi OA annotations, from 47 papers, by 42 distinct community curators (so far)
 
* Also, 3 worksheets submitted, for 4 papers
 
* 35 papers flagged as not having phenotypes
 
* 86 papers with responses (3% response; still early)
 
* Need to coordinate with the AFP request pipeline
 
  
=== GO slim terms ===
+
== May 21, 2020 ==
* SObA highlights Alliance slim terms, but doesn't correspond to ribbon
 
* Want to use same slim terms used for ribbons
 
* Add slim terms into ACEDB? One option
 
* Ribbon order of slim terms is an issue
 
* Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
 
* Will have to manually synchronize with Alliance if Alliance changes its ribbon
 
  
== August 29, 2019 ==
+
=== 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
  
=== Caltech use of Hinxton name service ===
+
=== AFP tutorial ===
* Name service :
+
* AFP group working on tutorial/webinar
** https://names.wormbase.org/gene
+
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
* API documentation :
 
** https://names.wormbase.org/api-docs/index.html#!
 
* Sibyl is wondering :
 
** "it would be nice to know when and how curators use the name service. And does any script managed by Caltech write data into the name services?"
 
** "what needs to be done to adopt the new name service. For example, what concern do you or the curators have about adopting the new name service, what kind of tests will allow the curators to trust that the new name service is working correctly, what changes to the new name service is needed for Caltech to be able to use it."
 
* Daniela, Chris, Karen are the only Caltech curators who use it.
 
* Daniela's workflow is :
 
** Look up variation through OA
 
** Look up variation through name service (what's the URL for that ?)
 
** Create object through name service, then enter information
 
** Create temporary entry for OA through Caltech postgres services
 
* Juancarlos has emailed Sibyl + Matt + Caltech with what we know so far.  Karen and Chris, please reply if you have other name service uses beyond what Daniela does.
 
* Name service google/wormbase login doesn't work right now for Caltech curators, Matt's been asked to add people.
 
  
===Anatomy term names===
+
=== Open Publishing Festival ===
* While going through the concise descriptions text Daniela have noted down some terms that could benefit from having a more descriptive name.
+
* Had micropublication session yesterday, went well
** e.g.: Pn.p hermaphrodite -> Pn.p hermaphrodite vulval precursor cell. e.g. P3.p hermaphrodite (WBbt:0008112) -> P3.p hermaphrodite vulval precursor cell
+
* Had ~50 participants
List of other potential terms:
+
* Saved Zoom chats? Can get public ones, maybe not private ones
<pre>
 
AB -> embryonic founder cell AB
 
EMS -> embryonic founder cell EMS -> should the definition of EMS be changed from ‘Embryonic cell’ to ‘Embryonic founder cell’? See WormAtlas founder cell definition.
 
C -> embryonic founder cell C
 
D ->  embryonic founder cell D
 
E ->  embryonic founder cell E
 
MS -> embryonic founder cell MS
 
Psub1 -> embryonic founder cell Psub1 (or simply embryonic founder cell P1)
 
Psub2 -> embryonic founder cell Psub2
 
Psub3 -> embryonic founder cell Psub3
 
Psub4 -> germline founder cell Psub4
 
G1 -> Postembryonic blast cell G1
 
G2 -> Postembryonic blast cell G2
 
</pre>
 

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