WormBase-Caltech Weekly Calls

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2021 Meetings





May 27, 2021

Single cell

  • Eduardo and Valerio will give an update on single cell analysis and visualization tools

May 13, 2021

Textpresso supplement

  • Due Monday
  • Michael working with Paul S

AWS credits

  • Michael and Valerio were awarded AWS credits, more than they can use
  • Maybe they can be repurposed
  • Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance

Automated gene descriptions

  • Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
  • Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
  • May be the focus of an Alliance supplement
  • We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)

IWM 2021 WB Workshop

  • Scheduled for June 22, 2021
  • Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
  • Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
  • Here is the submitted workshop schedule:
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A

May 20, 2021

Ontology updates in OA

  • ODK pipeline is not updating the "date" line in OBO artifacts and thus the ontology is not updating
  • Need to remove the "date" from the anatomy ontology OBO file header and let the OA script use the "data-version" line instead
  • Life stage still has "date"; Chris will investigate if there are update issues for life stage
  • Juancarlos has updated the GO URIs from Kimberly's suggestions; use monthly release URI or ~daily snapshot URIs?
    • Should probably go with daily snapshots for curation purposes (frequent updating for new/deprecated terms)

OA updates for UTF-8

  • Daniela and Juancarlos have updated OA dumpers (antibody, expression, picture, movie) accordingly
  • Others need to be updated:
    • Chris will help with Interaction OA, GeneReg OA, Phenotype OA, RNAi OA
    • Ranjana will help with Disease, Genotype and Concise OAs
    • Karen will help with Construct, Transgene, Topic, Molecule OAs
  • Anatomy function form (Valerio wrote) writes to Postgres; need some updates

Student Internship

  • Student will work with Raymond, Kimberly to do anatomy function & Noctua/GO-CAM curation on dauer development
  • To do anatomy function curation in Noctua, requirements will need to be written out and addressed
  • Can the anatomy function form write directly into Noctua (eventually)?

AI-readiness supplement

  • Valerio looking into AI-ready format input
  • Looking into applying to neural circuits

May 27, 2021

CeNGEN data

  • CeNGEN project wants to generate expression displays like our FPKM plots (made by Gary Williams)
  • Can we generate plots like these with this new data?