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]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
+
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
 
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
 
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
  
== August 2, 2018 ==
 
  
=== AFP ===
+
== May 7, 2020 ==
  
* The AFP pipeline is currently emailing authors from karen's e-mail address
+
=== Alliance COVID Page ===
* Use same e-mail account Chris is using for phenotype community curation requests or create a new account for AFP (gmail)
+
* Available on stage
* Can use outreach@wormbase.org for consistency
+
* Textpresso for Coronavirus up for testing
* May use the PMID in the subject line so e-mails will not be all in the same thread
 
* Todd and Chris have email credentials
 
** Chris will send to Valerio, Juancarlos, Daniela, and Kimberly
 
* Let Valerio and Juancarlos know what pipelines use AFP before they modify
 
* Do curators still want to receive emails when authors flag their data type?
 
** We will leave the alert emails as is for now
 
  
 +
=== SimpleMine at Alliance ===
 +
* Still some confusion about what it is
 +
* Will try to help clarify on PI meeting on Friday
  
== August 9, 2018 ==
+
=== Development environment for Alliance work ===
 +
* Raymond and Juancarlos have been working on
 +
* Existing hardware is strained; set up virtual machine
 +
* Still some technical issues
  
=== AFP ===
+
=== Open Publishing Festival ===
* Mei Zhen, SAB member suggested that we include disease models in the AFP form.  
+
* Later this month
* The AFP group will work with Ranjana to incorporate it. Ranjana will prepare a mock by next week.
+
* Micropublications involved
* We will then decide about using the existing afp_humdis tables or creating new ones.
+
* 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
  
=== Tazendra ===
+
=== 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
  
* Shall we move tazendra.caltech.edu to the cloud? Either WormBase cloud or Caltech cloud?
+
=== WS277/278 ===
 +
* Pipelines are pushed back by about 14 days/2 weeks
  
  
 +
==May 13, 2020==
  
== August 16, 2018 ==
+
=== SURF students ===
 +
* Welcome Fernando!
 +
* Will work on neuron function with respect to dauer formation
  
=== Tazendra ===
+
=== Progress Report ===
* Moving to cloud? To avoid local hardware issues?
+
* Review Google Doc from Paul to make sure you're latest updates are there
* Need to discuss with Juancarlos and Paul S.
+
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
* Need to consider logistics; put all of Tazendra functionality on cloud? Keep some things local?
 
** Postgres in cloud; forms local? Paper pipeline?
 
** Will consult with Textpresso
 
  
=== ICBO 2018 recap ===
+
===Genotype class===
* POTATO workshop (Phenotype Ontologies Traversing All The Organisms)
+
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
** Will work towards generating standardized logical definitions using Dead Simple OWL Design Patterns (DOSDP)
+
*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
*** <Quality> and inheres_in some <Entity> (and has_modifier some <Mod>)
+
*Disease OA annotations now converted to the newly created genotypes where needed
*** Exercise: Reconciling logical definitions for apparently equivalent phenotype terms across ontologies (e.g. MP vs. HP)
+
*Need to work on disease dumper changes next
** Can use Protege to edit the OWL ontology and ROBOT for automating generation of many terms and logical definitions in parallel
 
** Will try to align WPO to UPheno as best as we can; will depend (at least in part) heavily on alignment with Uberon for anatomy
 
** Some Uberon alignment challenges: e.g. Fruit fly "tibia" and human "tibia"; human "tibia" parent is "bone" but fly "tibia" is not a bone
 
** Will participate in Phenotype Ontology Developer's call, every 2 weeks on Tuesdays (9am Pacific, 12pm East coast, 5pm UK)
 
*** Next meeting September 4, 2018
 
** Crash course in Protege, ROBOT, Ontology Development Kit, using GitHub to help develop OWL ontologies
 
** PATO needs work
 
** Questions that arose:
 
*** What should the scope of an ontology term be? Context? Life stage? Conditions? Treatment?
 
*** Being weary of ontology term count explosion; what's the right balance?
 
*** When defining phenotype terms, should the cause be included or only the observation? Maybe causes as a subclass (and assuming the observation includes assessment of cause)
 
** Some distinction between human phenotype terms and model organism terms: phenotype of individual vs. population
 
* Xenbase is trying to develop a phenotype ontology (spoke with Troy Pell, developer)
 
** Asked about WPO and how we curate
 
* Lots of plant talks
 
* Many talks on performing quality checks on ontology development and ontology re-use
 
* Domain Informational Vocabulary Extraction (DIVE) tool
 
** Entity recognition/extraction
 
** Working with two plant journals
 
** Tries to identify co-occurrence patterns of words
 
** Web interface and curation tool
 
* Semantic similarity tools and evaluation of them
 
  
=== WormBase Phenotype Ontology working group ===
+
=== What genes should be linked to genotypes? ===
* Chris will send around Doodle poll
+
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
* Goal is to discuss creation of logical definitions and alignment of phenotypes for Alliance
+
* 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
  
== August 23, 2018 ==
+
=== Open Publishing Festival ===
 +
* Ranjana will join as a panelist
 +
* Other MOD curators will also join
 +
* Festival calendar: https://openpublishingfest.org/calendar.html
  
=== Alliance tables ===
+
=== Move to Chen building ===
* Filtering/sorting priorities
+
* Scheduled for late January 2021
* Open question about which tables on the Alliance website should be prioritized for acquiring sorting and filtering functionality
 
  
=== Worm Phenotype Ontology working group ===
+
=== First completely virtual GO meeting ===
* Gary S., Karen, Kimberly, and Chris have responded to [https://doodle.com/poll/xzkxet8sb57enver#table Doodle poll]
+
* Kimberly: went really well
* Looks like 12pm Pacific (3pm Eastern) on Thursdays is the time that works for everyone
+
* Only met 4 hours per day, due to time zone differences
** May start late on days when WB CIT meeting goes past 12pm Pacific
+
* Had breakout sessions for focus groups
** May want to start a bit past 12pm to allow west coasters to get lunch, etc.?
 
* Goals:
 
** Work on logical definitions for WPO terms
 
** Consider any restructuring of WPO that would facilitate ontology alignment with other MODs and UPheno
 
** Could we eventually create a phenotype annotation tool (and term requester) that allows modular expressions of a phenotype observation to lookup existing terms or create new terms with logical definitions based on those modular elements?
 
  
=== Alliance anatomy ===
+
=== Alliance Literature Acquisition working group ===
* Data quartermasters and expression working group are looking to get updated anatomy-Uberon mappings
+
* Plan to come up with use cases for OntoMate and Textpresso
* How frequent are data updates at the Alliance? Seems to be every ~2 months
+
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
* Anatomy-Uberon mappings will affect phenotype ontology alignments
 
  
=== Automated Gene Descriptions ===
+
* Kimberly plans to draw up most common use cases for Textpresso
*Ranjana and Valerio working to finish the new pipeline for automated descriptions for WB, will aim to finish them for the next upload, WS268.
+
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
* Working on one of the last data types--tissue expression; will use the anatomy ontology to perform logical trimming for the annotation set of cell/anatomy types (for each gene) including neurons (as opposed to using a file for neuronal term groupings taken from Oliver Hobert paper in the old pipeline)
 
* Currently playing around with thresholds to see how the sentences look, will feedback any ontology related issues to Raymond
 
* Working on incorporating feedback from users for information-poor genes (defined as genes with no human orthology and no GO annotations). Will include other types of information suggested by Users such as human ortholog function and protein domains, etc.
 
* When no other data is available, will include expression cluster data. Users have complained that they don't find this data useful as it's non-specific and from large scale studies, so will give it the lowest priority for inclusion.
 
*Suggestion to exclude the writing and storing of the thousands of automated descriptions to the Postgres database; there is really no advantage in them being in Postgres. 
 
* At the time of generation of the automated descriptions the related .ace files can also be generated; though will need to include the 6000+ manual descriptions that live in Postgres.  So will need to rethink this part a bit, though skipping Postgres will reduce the number of manual steps in the pipleline and Postgres will have less data that needs to be uploaded and downloaded from future cloud storage.
 
  
== August 30, 2018 ==
 
  
=== EPIC dataset in the Alliance import ===
+
== May 21, 2020 ==
  
* the EPIC dataset has fine-grained anatomy-life stage annotations (e.g. single cell per minute)
+
=== Volunteer curators ===
* This generates thousands of annotations per gene (up to 30,000) for the 127 genes analyzed in the study
+
* Received surge of annotations earlier this week
* How to deal with this. In WB we do not display anatomy/life stage pairings but we display one list for anatomy terms and one for life stage. Also, we display the EPIC study in a separate panel on the gene page so that it does not ‘dilute’ small scale annotations (concerned raised by Oliver H at the time of the import).
+
* All tutorials done for now; all but 3 recorded
 +
* Each tutorial is ~1 hour in length
  
https://www.wormbase.org/species/c_elegans/gene/WBGene00015143#1--10
+
=== AFP tutorial ===
 +
* AFP group working on tutorial/webinar
 +
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
  
*Possible solution:
+
=== Open Publishing Festival ===
** throw away the pairing information. e.g. for WBGene00020093, there are paired 10713 annotations from expression pattern Expr10421. On WormBase, we have a panel for Expr10421 (on the page for WBGene00020093) that shows 413 life-stage associations and 112 anatomy associations, with no pairing information. 
+
* Had micropublication session yesterday, went well
***This approach will still give big tables (annotation in the hundreds) for the analyzed genes and the dilution problem will still be there. On the other hand, when the Alliance tables could be sorted/filtered this can be less of an issue
+
* Had ~50 participants
 +
* Saved Zoom chats? Can get public ones, maybe not private ones

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