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]]
  
== April 2, 2020 ==
 
  
=== Community phenotype requests ===
 
* March 9-28
 
* 2,548 emails went out; 89 bounced; 6 resent; 13 backup; 2,478 successful emails
 
* 361 annotations overall
 
* 48 papers requested received curation (2% response rate)
 
* 53 distinct papers overall (5 papers without request)
 
* 53 distinct persons overall
 
  
=== Community curation volunteers ===
+
== May 7, 2020 ==
* Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
 
* 14 volunteers so far, all have been assigned a WBPerson ID
 
* Chris will set up a webinar tutorial in the coming week or two
 
  
=== AFP pipeline ===
+
=== Alliance COVID Page ===
* Will resend email requests to authors that haven't already responded
+
* Available on stage
* May also send out for older papers
+
* Textpresso for Coronavirus up for testing
* May work with people to help
 
* Does the old AFP form still work? It should
 
* If someone has a link to the old form, they won't get one for the new form
 
* Maybe could set up an automatic redirect from the old form to the new form
 
* Received many submissions recently (>20% response rate)
 
  
=== Ontology Annotator ===
+
=== SimpleMine at Alliance ===
* Need to work on Genotype OA dumper
+
* Still some confusion about what it is
* Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
+
* Will try to help clarify on PI meeting on Friday
* Ampersands (&) are also problematic for object names in the OA
 
** 20237  | Is[Pgcy-5::daf-2a::venus; Punc-122::mCherry]                          | 2014-10-08 10:32:45.874519-07
 
** 20239  | Ex[Pgcy-5::casy-1::venus; Pgcy-5::aman-2::mCherry; Punc-122::mCherry] | 2014-10-08 10:45:23.202362-07
 
** 20238  | Is[Pgcy-5::daf-2c::venus; Punc-122::mCherry]                          | 2014-10-08 10:38:19.859078-07
 
** 25249  | Ex[Prheb-1::rheb-1::GFP; unc-119(+]                                  | 2018-06-29 10:16:40.784295-07
 
** 16283  | [hlh-13::GFP;unc-119(+)]                                              | 2013-02-07 17:43:22.384819-08
 
** 26131  | Ex[pedc-3EDC-3::DsRed;pRF4]                                          | 2019-08-14 08:44:49.91063-07
 
  
=== Use Slack More ===
+
=== Development environment for Alliance work ===
* Slack is a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication
+
* 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
  
== April 9, 2020 ==
+
=== 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
  
=== Volunteer curators ===
+
=== WS277/278 ===
* Have sent out emails to schedule tutorials
+
* Pipelines are pushed back by about 14 days/2 weeks
* Chris had one tutorial with Michael Davies (Alyson Ashe's lab) yesterday
 
* One already scheduled for next Monday with Wilber and Stephanie from Paul's lab
 
* Two others already scheduled for next Tuesday with Lina Dahlberg and Colin Dolphin
 
  
===TAGC is virtual (4.22-25.2020)===
 
FYI in case you missed it
 
*You still have to register (it's free), if you hadn't before
 
https://genetics-gsa.org/tagc-2020/registration/
 
  
===summer students===
+
==May 13, 2020==
* Caltech SURF students (and other summer students worldwide) now are looking for projects
 
* Maybe they could curate for WormBase
 
* In addition to phenotype, they could curate:
 
** Allele/lesion sequence curation (using Allele Sequence form); maybe Paul Davis could make a tutorial video?
 
** Anatomy function, looking for novel info; opportunity to program/code
 
  
=== OA semicolon issue ===
+
=== SURF students ===
* Juancarlos has fixed the issues on sandbox
+
* Welcome Fernando!
* Curators should test on Mangolassi
+
* Will work on neuron function with respect to dauer formation
  
=== Textmining/automation ===
+
=== Progress Report ===
* Daniela will discuss with Christina Zorn from Xenbase
+
* Review Google Doc from Paul to make sure you're latest updates are there
* Will discuss SVM, AFP, Textpresso, etc.
+
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
  
=== Retracted WBPapers ===
+
===Genotype class===
* Jae & Kimberly put in GitHub ticket to make retractions clear on WormBase site
+
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
* https://github.com/WormBase/website/issues/7637
+
*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
* Can we systematically detect retractions? Yes
+
*Disease OA annotations now converted to the newly created genotypes where needed
* What about finding papers that cite retractions? Maybe, but likely tricky
+
*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
  
== April 16, 2020 ==
+
=== 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
  
=== Community Phenotype Curation Tutorials ===
+
=== Open Publishing Festival ===
* Chris has run 6 tutorials, recorded 4
+
* Ranjana will join as a panelist
* MPG files saved on DropBox; ask Chris for access
+
* Other MOD curators will also join
* Plan to edit videos to make tutorial video to post on WB YouTube channel
+
* Festival calendar: https://openpublishingfest.org/calendar.html
  
=== Author First Pass ===
+
=== Move to Chen building ===
* May run a webinar and use Zoom to record
+
* Scheduled for late January 2021
* May make a short tutorial video
 
* Jae: Is there documentation for terminology used in the form?
 
  
=== Zoom accounts ===
+
=== First completely virtual GO meeting ===
* People can try to use Caltech Zoom account
+
* 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/
  
== April 23, 2020 ==
+
* 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
  
=== Community Phenotype Curation Tutorials ===
 
* Chris has finished first round of tutorials; 8 tutorials, 6 video recordings
 
* There are ~8 new volunteers; will setup tutorials for them soon
 
  
=== ECO code implementation ===
+
== May 21, 2020 ==
* ?ECO_term to replace ?GO_code in ACEDB models
 
* GAF files with three-letter codes can still be generated by mapping
 
  
=== Simplemine for Alliance ===
+
=== Volunteer curators ===
* Wen has presented proposal to Search group
+
* Received surge of annotations earlier this week
* Plan is to have a link to the Alliance Simplemine prototype from the Alliance web page
+
* All tutorials done for now; all but 3 recorded
 +
* Each tutorial is ~1 hour in length
  
=== Venn diagram tool ===
+
=== AFP tutorial ===
* Conceived by Jae, implemented by Sibyl
+
* AFP group working on tutorial/webinar
* Currently used for interactions data
+
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
* Could use for other data types like phenotype (e.g. comparing RNAi vs. allele phenotype)
+
 
* Could also use for Expression data, e.g. comparing results from different methods
+
=== Open Publishing Festival ===
* Could maybe use for disease data
+
* Had micropublication session yesterday, went well
 +
* Had ~50 participants
 +
* Saved Zoom chats? Can get public ones, maybe not private ones
  
=== AFP tutorial ===
 
* Daniela, Kimberly, Valerio will run through the AFP form with Nikita from Gupta lab tomorrow
 
* May record in the future to make a tutorial video
 
* Daniela may (re-)start curating markers for relevant expression patterns
 
* Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
 
  
=== Expression markers ===
+
== May 28, 2020 ==
* SURF student projects: Identifying good expression markers? Maybe, but may require more curation experience
 
* Wen looked at expression cluster data; hard to find good, very specific (i.e. neuron) markers
 
* Daniela may (re-)start curating markers for relevant expression patterns
 
* Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
 
* Already have an "Expression markers" widget on anatomy term pages
 
* Could combinations of genes (e.g. cGal) act as markers?
 
  
== April 30, 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/)
  
=== Adding ?ECO_term class for WS278 ===
+
=== Genes to Physical Map ===
* [https://wiki.wormbase.org/index.php/Evidence_Code_Ontology#.3FECO_term_Model ?ECO_term model]
+
* https://colab.research.google.com/drive/1e83jv94-eO_VQ7kKdJ36TgDDb4WRkFhM?usp=sharing
*Confirm proposed changes to class models that will use this tag:
+
To run: Runtime->Run All. Change the list of gene names and run again.
** ?GO_annotation
 
** ?Phenotype
 
** ?Disease_model_annotation
 

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.