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]]
 +
 +
 +
 +
== 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
  
= 2019 Meetings =
+
=== 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_January_2019|January]]
+
=== WS277/278 ===
 +
* Pipelines are pushed back by about 14 days/2 weeks
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
==May 13, 2020==
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
=== SURF students ===
 +
* Welcome Fernando!
 +
* Will work on neuron function with respect to dauer formation
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
+
===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
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
=== 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
  
== October 3, 2019 ==
+
=== 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
  
=== SObA comparison graphs ===
+
=== Alliance Literature Acquisition working group ===
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
+
* Plan to come up with use cases for OntoMate and Textpresso
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
+
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
 
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 
* What information does a user most care about?
 
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 
* In either case users need a good legend and/or documentation
 
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
 
  
=== Germ line discussion ===
+
* Kimberly plans to draw up most common use cases for Textpresso
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
+
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
 
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
 
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
 
  
=== Script to remove blank entries from Postgres ===
 
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
 
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
 
* Does anyone object to removing these entries throughout Postgres?
 
* Juancarlos will remove all the empty fields identified by his script
 
  
 +
== May 21, 2020 ==
  
== October 10, 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
  
=== Biocuration 2020 ===
+
=== AFP tutorial ===
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
+
* AFP group working on tutorial/webinar
* Dates: Sunday May 17th to Wednesday May 20th, 2020
+
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
* Will have 3rd POTATO workshop
 
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
 
* Key Dates
 
** October 31, 2019 - Paper Submission Deadline
 
** January 24, 2020 - Abstract  and Workshop Submission Deadline
 
** March 6, 2020 - Notification of Acceptance
 
** April 6, 2020 - Early Bird Registration Ends
 
** May 8, 2020 - Registration Deadline
 
* Academic ISB Member, early bird registration fee is $250
 
* Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
 
  
=== ICBO 2020 ===
+
=== Open Publishing Festival ===
* International Conference on Biomedical Ontologies
+
* Had micropublication session yesterday, went well
* [https://icbo2020.inf.unibz.it/ Meeting website]
+
* Had ~50 participants
* Held in Bozen-Bolzano, Italy
+
* Saved Zoom chats? Can get public ones, maybe not private ones
* 16 - 19 September 2020
 
  
=== SObA comparison tool ===
 
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
 
  
=== Textpresso derived paper connections ===
+
== May 28, 2020 ==
* For example for strains and constructs, maybe anatomy terms?
 
* May want to flag Textpresso predictions (as opposed to manually connected)
 
* Couple of options:
 
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
 
** 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
 
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
 
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
 
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
 
* Transgene pipeline:
 
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
 
** Another script, captures Ex transgenes as well, automatically connects to construct objects
 
** WB only displays verified papers; unverified (predicted) associations are not dumped
 
* Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
 
* Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
 
* Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
 
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
 
  
 +
=== 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/)
  
== October 17, 2019 ==
+
=== 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.

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.