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 ===
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
* 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 ===
+
== September 3, 2020 ==
* Raymond and Juancarlos have been working on
 
* Existing hardware is strained; set up virtual machine
 
* Still some technical issues
 
  
=== Open Publishing Festival ===
+
=== WS279 Citace upload ===
* Later this month
+
* September 25
* Micropublications involved
+
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
* 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 ===
+
=== New AFP datatype for curation status form (CSF)? ===
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
+
* afp_othergenefunc (to capture gene function other than enzymatic activity)
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
+
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
* 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 ===
+
=== GO annotation for description ===
* Pipelines are pushed back by about 14 days/2 weeks
+
* 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)
  
==May 13, 2020==
+
=== 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
  
=== SURF students ===
 
* Welcome Fernando!
 
* Will work on neuron function with respect to dauer formation
 
  
=== Progress Report ===
+
== September 10, 2020 ==
* 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===
+
=== GO GAF Files ===
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
+
* WS278 GO GAF is using the new 2.2 file format
*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
+
* [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]
*Disease OA annotations now converted to the newly created genotypes where needed
+
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
*Need to work on disease dumper changes next
+
* 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
  
=== What genes should be linked to genotypes? ===
+
===Disease files on FTP===
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
+
*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)
* What should we consider a "relevant gene"?
+
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
* 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 ===
+
=== WormBase talk at Worcester Area Worm Meeting ===
* Have had an additional 13 people volunteer
+
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
* Single one-on-one tutorial for someone in Hong Kong this past Monday
+
* 30 minute slot; complementary to BAWM talk?
* Chris will hold a tutorial today and tomorrow for everyone else
+
* WormBase members can attend
* Have received many new community annotations from volunteers (and authors), validation still pending
 
  
=== Open Publishing Festival ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Ranjana will join as a panelist
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Other MOD curators will also join
+
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
* Festival calendar: https://openpublishingfest.org/calendar.html
+
* WormBase members can attend; Zoom link will be sent next Monday
  
=== Move to Chen building ===
+
=== Worm Anatomy Ontology Fixes ===
* Scheduled for late January 2021
+
* 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
  
=== First completely virtual GO meeting ===
+
=== Dead Variations in Postgres ===
* Kimberly: went really well
+
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
* Only met 4 hours per day, due to time zone differences
+
* Noticed that many transgene names were being included, which can result in false positives for the categories
* Had breakout sessions for focus groups
+
* 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
  
=== Alliance Literature Acquisition working group ===
+
=== WS279 Citace Upload ===
* Plan to come up with use cases for OntoMate and Textpresso
+
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
 
  
* 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
 
  
 +
== September 17, 2020 ==
  
== May 21, 2020 ==
+
=== Species errors in CITace ===
 +
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
  
=== Volunteer curators ===
+
=== Webinars ===
* Received surge of annotations earlier this week
+
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
* All tutorials done for now; all but 3 recorded
+
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
* Each tutorial is ~1 hour in length
+
* 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?
  
=== AFP tutorial ===
+
=== Transcription factors and regulatory networks ===
* AFP group working on tutorial/webinar
+
* Had another question about TFs, asking for common TFs for a list of genes
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
+
* 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
  
=== Open Publishing Festival ===
+
=== Alzheimer's disease portal ===
* Had micropublication session yesterday, went well
+
* Funding has been awarded for Alzheimer's research
* Had ~50 participants
+
* Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
* Saved Zoom chats? Can get public ones, maybe not private ones
+
* 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
  
== May 28, 2020 ==
+
=== 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
  
=== Wormicloud ===
+
=== Data mining tool comparison sheet ===
* 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/)
+
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
 +
* 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