Ontology meeting 2017-07-14

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Conference Line


DavidH will present a quick workaround for making logical definitions and subclasses using terms with single quotes.

Other discussion: https://github.com/geneontology/go-ontology/projects/1

August Meeting Agenda


  • On call: Barbara, Chris, David H., David OS, Eric, Jim, Judy, Karen, Kimberly, Paul T., Tanya

Editing Single Quote-Containing Terms

  • Can set preferences to show term IDs, not names
  • Also a shortcut for setting this preference in view

Review August Ontology Meeting Schedule

  • Review OWL
  • Review relations
  • Review design patterns
  • Review imports
    • Most are straightforward except for ChEBI, which requires more data management
  • Dealing with build failures
    • Take screenshots when this happens for documentation
  • Tickets
    • Divide up backlog of tickets based on expertise, workload

Review github Tickets

  • Will try to find tickets that will help bring Barbara up-to-speed
  • Edit and release OBO-Edit files
    • OBO-Edit provides nice visuals
    • Resolution: use the daily release OBO file, instead of the editors OBO file
  • Need SOP for avoiding ID clashes when 1 editor has multiple branches awaiting merge
    • Protege should remember IDs between Protege session, if that option is selected in preferences in Auto-generated ID section of Setting ID ranges - this preference should be checked
    • Do we need checks for potential collisions?
    • To fix this, either hand edit the file, or abandon the working branch
    • We do want to implement a check that no ID should ever have more than one label, definition, etc.
  • Use of uberon classes for generic anatomical structures means taxon restrictions are too strict
    • Anatomical structure in UBERON starts with zygote, which excludes PomBase curators from using children that are a descendant of terms that map up to an anatomical structure term
    • Originally UBERON was designed for use with animals, but UBERON now also includes plants
    • May ultimately be better to map to CARO (Common Anatomy Reference Ontology) class for anatomical structure
  • Import new CHEBI term oxLDL (CHEBI_60151)
    • Chris will investigate further
  • ntr: process for D-erythroascorbic acid, biosynthesis
    • Placement of this new term - under vitamin? under co-factor?
    • The vitamin and co-factor portion of GO doesn't completely align with ChEBI roles
    • Should GO have things like drug, hormone, toxin, vitamin?
    • Should we obsolete 'vitamin' terms?
    • Will discuss and try to document what happens in August
  • Obsolete virus receptor activity ?
    • Paul T. proposed grouping term of 'highjacked molecular function' for terms like 'virus receptor activity'
    • Should the term be obsoleted? Can terms like this be isolated in a separate branch of the MF?