WormBase-Caltech Weekly Calls

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January


February 2, 2017

Methods in Molecular Biology chapter

  • Chris and Mary Ann will be in touch with individuals about section writing
  • Karen: FlyBase chapter has a small section on pathways; do we want/need a small section?
    • As long as we stick to the "how to" focus, we can write as much as needed
  • Raymond: We should try to write so that the content remains pertinent for a while

Pharyngeal phenotype terms

  • Karen needs pharyngeal pumping phenotype terms for NemaMetrix micropublications
  • NemaMetrix experiments often involve serotonin-induced pharyngeal pumping
  • Karen asking Raymond to help with pharyngeal phenotype term organization
  • Raymond: Not very familiar with the existing usage of the terms and phenotype ontology structure wrt pharyngeal terms
  • Authors will submit phenotype data as part of the micropublication process
  • Proposal for phenotype ontology going forward: create terms with logical definitions (OWL statements)
  • We will start exploring more usage of logical definitions for phenotypes
  • Will start meeting Thursday afternoons, starting next week (Feb 9), 1:30pm Pacific

SObA graph for GO

  • Juancarlos & Raymond making progress
  • Added toggling for different roots of GO
  • Difficult to navigate graph when lots of terms (e.g. tax-4)
  • What can be done to improve the display?
  • Filtering out IEA annotations; currently only for phenotype annotations; will expand to all IEA annotations
  • Kimberly generating GO slim, 15-20 terms for each branch of GO, possible to use in ribbon display
  • Could we distinguish between is_a, part_of, and regulates relationships?
  • To simplify graph, could we further minimize the display of higher level/indirect nodes?
  • Would we want parallel paths to root be trimmed?