Difference between revisions of "WormBase-Caltech Weekly Calls"

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GoToMeeting link: https://www.gotomeet.me/wormbase1
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= 2020 Meetings =
 
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
== May 7, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
 
 
=== Alliance COVID Page ===
 
* Available on stage
 
* Textpresso for Coronavirus up for testing
 
  
=== SimpleMine at Alliance ===
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
* 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 ===
+
== September 3, 2020 ==
* 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 ===
+
=== WS279 Citace upload ===
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
+
* September 25
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
+
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
* 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 ===
+
=== New AFP datatype for curation status form (CSF)? ===
* Pipelines are pushed back by about 14 days/2 weeks
+
* afp_othergenefunc (to capture gene function other than enzymatic activity)
 +
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
  
 +
=== GO annotation for description ===
 +
* Kimberly will look into 'male tail tip developement' terms for description
  
==May 13, 2020==
+
=== Migrate wobr1 server to AWS ===
 +
* SOLR, WOBr, SObA, Enrichment analysis
 +
* Working with Sibyl on the process
 +
* Will try migrating wobr1 first, as a test case
 +
* May eventually move, for example, Tazendra
 +
** Will there be drawbacks to doing this?
 +
** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
 +
* Don't yet know the details of the costs, but we can try and keep track
 +
* We should move into WB or Alliance AWS instances (or Stanford)
  
=== SURF students ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Welcome Fernando!
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Will work on neuron function with respect to dauer formation
+
* Meeting will be virtual on Zoom
 +
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 +
* Send topic requests to Chris for the talk
 +
* Current topics:
 +
** Micropublications
 +
** Author First Pass
 +
** Automated Gene Descriptions
 +
** Community Curation
 +
** WB Query Tools
 +
* Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
 +
* If the organizers record the talk, we can post it on the blog and WB YouTube channel
  
=== 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
 
  
===Genotype class===
+
== September 10, 2020 ==
*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? ===
+
=== GO GAF Files ===
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
+
* WS278 GO GAF is using the new 2.2 file format
* What should we consider a "relevant gene"?
+
* [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md Specifications]
* We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
+
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
* 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(+)"?
+
* Implications for gene descriptions, but what about other tools, applications at WB?
* For rearrangements, consider relevant any genes "inside" the rearrangement?
+
* Some errors in the current WS278 GAF, but will get fixed soon
* For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
+
** Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed
* 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 ===
+
===Disease files on FTP===
* Have had an additional 13 people volunteer
+
*No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
* Single one-on-one tutorial for someone in Hong Kong this past Monday
+
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
* 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 ===
+
=== WormBase talk at Worcester Area Worm Meeting ===
* Ranjana will join as a panelist
+
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
* Other MOD curators will also join
+
* 30 minute slot; complementary to BAWM talk?
* Festival calendar: https://openpublishingfest.org/calendar.html
+
* WormBase members can attend
  
=== Move to Chen building ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Scheduled for late January 2021
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
 +
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 +
* WormBase members can attend; Zoom link will be sent next Monday
  
=== First completely virtual GO meeting ===
+
=== Worm Anatomy Ontology Fixes ===
* Kimberly: went really well
+
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
* Only met 4 hours per day, due to time zone differences
+
* Assessing the best way to address them
* Had breakout sessions for focus groups
+
* Would be good to be able to automate some edits; options:
 +
** Use OWL API (need someone proficient in coding with OWL API)
 +
** Convert to OBO, programmatically edit, convert back to OWL?
 +
** Use Cellfie plugin for Protege?
 +
** Should discuss with Nico once we have a sense as to what changes need to be made
  
=== Alliance Literature Acquisition working group ===
+
=== Dead Variations in Postgres ===
* Plan to come up with use cases for OntoMate and Textpresso
+
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
+
* Noticed that many transgene names were being included, which can result in false positives for the categories
 +
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
 +
* Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
 +
* May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
 +
* We could use pattern matching to filter out transgene names
 +
* Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories
  
* Kimberly plans to draw up most common use cases for Textpresso
+
=== WS279 Citace Upload ===
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
+
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
  
  
== May 21, 2020 ==
+
== September 17, 2020 ==
  
=== Volunteer curators ===
+
=== Species errors in CITace ===
* Received surge of annotations earlier this week
+
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
* All tutorials done for now; all but 3 recorded
 
* Each tutorial is ~1 hour in length
 
  
=== AFP tutorial ===
+
=== Webinars ===
* AFP group working on tutorial/webinar
+
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
+
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
 +
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
 +
* Chris and Wen can discuss how to setup
 +
* Should we have people register? Maybe
 +
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
  
=== Open Publishing Festival ===
+
=== Transcription factors and regulatory networks ===
* Had micropublication session yesterday, went well
+
* Had another question about TFs, asking for common TFs for a list of genes
* Had ~50 participants
+
* An issue is that the TF binding data we have is in disparate forms, trying to reconcile
* Saved Zoom chats? Can get public ones, maybe not private ones
+
* We have a ?Transcription_factor class; it would be good to update and integrate with other related data types
  
 +
=== Alzheimer's disease portal ===
 +
* Funding has been awarded for Alzheimer's research
 +
* Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
 +
* Paul S: Alliance SAB tomorrow; we'll see what the SAB says
 +
* Can look at other resources like RGD disease portals and Reactome disease-related pathway models
 +
* Ruth Lovering is doing some work in this regard
  
== May 28, 2020 ==
+
=== GO meeting ===
 +
* All are welcome to attend
 +
* Will discuss GAF format changes, etc.
 +
* Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
 +
** Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss
  
=== Wormicloud ===
+
=== New GAF 2.2 file ===
* 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/)
+
* Kimberly has reviewed and sent feedback to Michael P
 +
* Valerio would like to stay in the loop to test the new files
  
=== Genes to Physical Map ===
+
=== Data mining tool comparison sheet ===
* https://colab.research.google.com/drive/1e83jv94-eO_VQ7kKdJ36TgDDb4WRkFhM?usp=sharing
+
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
To run: Runtime->Run All. Change the list of gene names and run again.
+
* Needs an update
 +
* Could we make this available to users? A link in the Tools menu?
 +
* Is this useful to users? Would they understand it? Maybe be better as a curator resource
 +
* Could this be micropublished?
 +
** Possible; may want to consider a series of publications with videos of webinars, etc.

Latest revision as of 16:39, 17 September 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

August


September 3, 2020

WS279 Citace upload

  • September 25
  • Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific

New AFP datatype for curation status form (CSF)?

  • afp_othergenefunc (to capture gene function other than enzymatic activity)
  • Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later

GO annotation for description

  • Kimberly will look into 'male tail tip developement' terms for description

Migrate wobr1 server to AWS

  • SOLR, WOBr, SObA, Enrichment analysis
  • Working with Sibyl on the process
  • Will try migrating wobr1 first, as a test case
  • May eventually move, for example, Tazendra
    • Will there be drawbacks to doing this?
    • Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
  • Don't yet know the details of the costs, but we can try and keep track
  • We should move into WB or Alliance AWS instances (or Stanford)

WormBase talk at Boston Area Worm Meeting

  • https://www.umassmed.edu/ambroslab/meetings/bawm/
  • Meeting will be virtual on Zoom
  • Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
  • Send topic requests to Chris for the talk
  • Current topics:
    • Micropublications
    • Author First Pass
    • Automated Gene Descriptions
    • Community Curation
    • WB Query Tools
  • Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
  • If the organizers record the talk, we can post it on the blog and WB YouTube channel


September 10, 2020

GO GAF Files

  • WS278 GO GAF is using the new 2.2 file format
  • Specifications
  • GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
  • Implications for gene descriptions, but what about other tools, applications at WB?
  • Some errors in the current WS278 GAF, but will get fixed soon
    • Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed

Disease files on FTP

  • No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
  • Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??

WormBase talk at Worcester Area Worm Meeting

  • Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
  • 30 minute slot; complementary to BAWM talk?
  • WormBase members can attend

WormBase talk at Boston Area Worm Meeting

Worm Anatomy Ontology Fixes

  • Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
  • Assessing the best way to address them
  • Would be good to be able to automate some edits; options:
    • Use OWL API (need someone proficient in coding with OWL API)
    • Convert to OBO, programmatically edit, convert back to OWL?
    • Use Cellfie plugin for Protege?
    • Should discuss with Nico once we have a sense as to what changes need to be made

Dead Variations in Postgres

  • Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
  • Noticed that many transgene names were being included, which can result in false positives for the categories
  • Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
  • Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
  • May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
  • We could use pattern matching to filter out transgene names
  • Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories

WS279 Citace Upload

  • Local Caltech upload to Spica, Tuesday September 22, 10am Pacific


September 17, 2020

Species errors in CITace

  • Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction

Webinars

  • We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
  • Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
  • Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
  • Chris and Wen can discuss how to setup
  • Should we have people register? Maybe
  • AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?

Transcription factors and regulatory networks

  • Had another question about TFs, asking for common TFs for a list of genes
  • An issue is that the TF binding data we have is in disparate forms, trying to reconcile
  • We have a ?Transcription_factor class; it would be good to update and integrate with other related data types

Alzheimer's disease portal

  • Funding has been awarded for Alzheimer's research
  • Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
  • Paul S: Alliance SAB tomorrow; we'll see what the SAB says
  • Can look at other resources like RGD disease portals and Reactome disease-related pathway models
  • Ruth Lovering is doing some work in this regard

GO meeting

  • All are welcome to attend
  • Will discuss GAF format changes, etc.
  • Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
    • Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss

New GAF 2.2 file

  • Kimberly has reviewed and sent feedback to Michael P
  • Valerio would like to stay in the loop to test the new files

Data mining tool comparison sheet