WormBase-Caltech Weekly Calls March 2021

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March 4, 2021

Webinar Monday

  • Juancarlos can send a reminder email; he just needs the text for the body of the email message
  • Can we send the webinar reminder to WB staff? Cannot use staff@wormbase.org to register
  • Raymond will try to remember to forward to staff

Neural Network (NN) evaluation

  • Kimberly (and other curators) looking through NN results
  • Had previously prevented LOW scoring SVMs(?) from being sent to authors
  • We need an agreed upon protocol for evaluation
  • To avoid bias, we should randomly sample papers; usually will find negatives; how do we represent high, medium and low-scoring papers in the set without making curators review >> 100 papers?
  • Michael will come up with protocol and send around list of papers for each data type (in Google Doc)
  • Perhaps evaluation should happen on non-curated, newer papers


March 11, 2021

Spreadsheet for Data not in ACEDB

CeNGEN To Dos

  • Daniela, Wen, Valerio, Eduardo, Raymond met with CeNGEN
  • Want to add JBrowse track for promoters(?)
  • Three things:
    • CeNGEN will provide histograms that we can put on each gene page, similar to modENCODE plots (do they provide static images or data that we process and display as histograms?) Both are possible (Raymond)
    • Their tool can assess "enriched" genes by cell type (enriched vs. neurons or vs. all cell types; not just housekeeping genes); these can be sent to WB -> SObA and enrichment analysis
    • We will link to the CeNGEN homepage wherever appropriate
  • All else will depend on Eduardo's tools for single cell expression data
  • Raymond will be WB point person to communicate with CeNGEN
  • Display solutions can be used for Alliance single-cell data in general
  • May want to consider future use cases, e.g. mutant-vs-WT expression, chemical/drug-induced expression, etc.

Chen building access

  • You'll need an ID with RFID? (Yes, 20 year old IDs don't work)
  • help.caltech.edu -> request type Card Office
  • It will be ready and wait for you at the Reddoor cafe.


March 18, 2021

Caltech Alliance source?

  • Could some data (like paper class/data) go to the Alliance directly from Caltech? Could be quicker and more efficient (and allow special characters that are lost at the acedb layer)
  • Data would no longer be coming from the "Single Source of Truth" for WB data (i.e. ACEDB/Datomic)
  • WB paper data would be ahead of the ACEDB paper data
  • Kimberly will reach out to Magdalena et al. to propose

CITAce upload

  • Upload to Hinxton on April 19 (? Friday April 16th ?)
  • Upload to CITace for Wen on Friday before (April 9th) by end of the day

Alliance biological working groups priority

  • Keep working on harmonization and LinkML models for data types

LinkML data visualization

  • Is there a way to visualize data coming from LinkML models? Like in .ACE files?
  • There may be some software that can render that kind of visualization, but we need to see
  • Curators want a way to make sure the model and the data are correct before officially submitting
  • Adam plans to demonstrate a visualization of literature data next Tuesday at literature acquisition working group (this was in the context of having a UI for seeing what's stored in the persistent database without waiting for elastic search processing to pass it to the regular UI, currently Literature is not modeled off of the LinkML yet)

QC analysis for steps in Alliance ingest pipeline

  • Curators can get access to the FMS to look at uploaded files, processed files; need to know how to process JSON files
  • Curators can also access Neo, but need to know how to query
  • Would be good to have readable reports to provide numbers for overall data sets


March 25, 2021

How to access data at the Alliance

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