WormBase-Caltech Weekly Calls

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2013 Meetings

January

February

March 7, 2013

Grant

• Grant gets reviewed next week
• Should hear results in ~two weeks

Gene Concise Description form

• Ranjana, Kimberly working on form layout
• Easy to use form, simple drop down menus to select, e.g., Species
• Can users follow references for info?
• Citing references in concise descriptions has, in the past, greatly increased workload/time to write
• Prepopulated, precanned Textpresso info?
• Send out to targeted members of the community, get feedback; Who should we ask for other species?
• Curators could each try using form to make at least one concise descriptions, give feedback
• Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..."
• Can promote form at the International meeting

Galaxy Workshop

• Screencast videos capturing use of Galaxy available
• Chris will send around

Genetic Interaction Ontology

• Perhaps add "what is expected" info during curation?
• Good to have a comparison of curation with core set of common papers
  • Cross check for consistency of curation (at least terms should lay in same lineage, if not at same depth)

March 14, 2013

Cleaning up Citace Minus

• Stemming from Paul Davis' GitHub ticket pointing out small-scale data problems
• Bogus molecule objects (Chris will take care of)
• Homol_data from RNAi (and the housing RNAi objects) can be removed
• Ghost Expr_pattern objects, Wen taking care of (Xiaodong will remove from the Gene_regulation OA)
• Will need to create a better (more robust) pipeline (with SOPs) for converting, for example, object names to WBID#'s
  • Once a conversion has been made, we need to check Postgres and Citace (& Citace Minus) for consistency
  • Need to minimize the burden on Wen to perform quality and consistency checks
  • Curators need to clean up/fix their data before a big change
  • Scenarios to foramlize:
    • Whole-class name changing
    • Model changes
• Is there a list of classes and objects that are held in Citace Minus?
  • We will generate a flat-text list