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]]
  
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
== May 7, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
=== Alliance COVID Page ===
 +
* Available on stage
 +
* Textpresso for Coronavirus up for testing
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
+
=== SimpleMine at Alliance ===
 +
* Still some confusion about what it is
 +
* Will try to help clarify on PI meeting on Friday
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
=== 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_August_2019|August]]
+
=== 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_September_2019|September]]
+
=== 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
  
== October 3, 2019 ==
 
  
=== SObA comparison graphs ===
+
==May 13, 2020==
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
 
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
 
** [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 ===
+
=== SURF students ===
* 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"
+
* Welcome Fernando!
* 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"
+
* Will work on neuron function with respect to dauer formation
** [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 ===
+
=== Progress Report ===
* 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
+
* Review Google Doc from Paul to make sure you're latest updates are there
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
+
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
* Does anyone object to removing these entries throughout Postgres?
 
* Juancarlos will remove all the empty fields identified by his script
 
  
 +
===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 10, 2019 ==
+
=== 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
  
=== Biocuration 2020 ===
+
=== Volunteer Community Curators ===
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
+
* Have had an additional 13 people volunteer
* Dates: Sunday May 17th to Wednesday May 20th, 2020
+
* Single one-on-one tutorial for someone in Hong Kong this past Monday
* Will have 3rd POTATO workshop
+
* Chris will hold a tutorial today and tomorrow for everyone else
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
+
* Have received many new community annotations from volunteers (and authors), validation still pending
* 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
+
* Ranjana will join as a panelist
* [https://icbo2020.inf.unibz.it/ Meeting website]
+
* Other MOD curators will also join
* Held in Bozen-Bolzano, Italy
+
* Festival calendar: https://openpublishingfest.org/calendar.html
* 16 - 19 September 2020
 
  
=== SObA comparison tool ===
+
=== Move to Chen building ===
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
+
* Scheduled for late January 2021
  
=== Textpresso derived paper connections ===
+
=== First completely virtual GO meeting ===
* For example for strains and constructs, maybe anatomy terms?
+
* Kimberly: went really well
* May want to flag Textpresso predictions (as opposed to manually connected)
+
* Only met 4 hours per day, due to time zone differences
* Couple of options:
+
* Had breakout sessions for focus groups
** 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
 
  
 +
=== Alliance Literature Acquisition working group ===
 +
* Plan to come up with use cases for OntoMate and Textpresso
 +
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
  
== October 17, 2019 ==
+
* 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
  
=== Alliance All Hands Face-to-Face ===
 
* Flights: has everyone already booked? No, not yet
 
* Any coordination of flights from Pasadena/LA?
 
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
 
  
=== SObA Comparison Tool ===
+
== May 21, 2020 ==
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 
* Prototype discussed last week, updated with feedback from prior discussions
 
* Would this be a stand-alone tool discoverable under the Tools menu?
 
** Possibly; could be a gene page widget, but may be out of place
 
** Stand-alone tool probably makes more sense
 
* Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
 
  
=== SObA ===
+
=== Volunteer curators ===
* Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
+
* Received surge of annotations earlier this week
* For example, share GO SObA graph for other species
+
* All tutorials done for now; all but 3 recorded
* Will need to be dependent on a SOLR server with all species data
+
* Each tutorial is ~1 hour in length
** Raymond has run into problems trying to setup his own SOLR server
 
** Raymond asked Seth Carbon if we could us GO server, but he prefers not
 
** Appear to be software versioning issues, possible memory issues
 
  
=== GO meeting ===
+
=== AFP tutorial ===
* Kimberly can give update on recent updates to GO from the recent GO meeting
+
* AFP group working on tutorial/webinar
* Slides are shared online
+
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
  
=== "all stages Ce" life stage ===
+
=== Open Publishing Festival ===
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
+
* Had micropublication session yesterday, went well
* "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
+
* Had ~50 participants
* Should we:
+
* Saved Zoom chats? Can get public ones, maybe not private ones
** 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
 
*** Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
 
** 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
 
* Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
 

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