WormBase-Caltech Weekly Calls
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Contents
Previous Years
2021 Meetings
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 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