Ontology meeting 2019-03-11

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Conference Line

See calendar for details



GOC Meeting Cambridge

  • GOC meeting - Cambridge, UK April 11th - 12th (right after ISB meeting)
    • has_primary_input/output report---David
    • reactome import into GO-CAM--- Ben, Peter
    • Rhea alignment--- Harold
    • MF refactor Pascale
    • Spatial relations plan--- David or Kimberly
    • Check existing agenda for other items

Discussion topics

  • Getting rid of regulates_o_part_of -> regulates
  • The plan going forward:
    • Jim has created the file with about 3000 lines. David is continuing to review these. He has done about 2500 of the 3000 lines. I suspect that this will lead to a lot of changes in annotation with respect to slimming. Is there any way we can bounce this off of Val before we release it? In many cases there won't be much we can do because at a class level, removal of the chain will be valid, even though for some of the instances of gene products annotated to the regulation terms, the chain will be true. For example, we will remove the positive regulation of x-receptor activity --> positive regulation of x receptor signaling because at the class level, the ligand does not positively regulate the pathway even though it does positively regulate the receptor. However, there may be other gene products that sensitize the receptor to ligand and therefore do regulate the pathway. As I go through these, I am realizing that there are a lot of problems associated with general regulation terms. To alleviate logical problems that exist now, Jim has devised a way to make the inferences in the ontology and then strip the property chain from the relations upon release.

  • Ensure slim documentation is generated from yaml in new GO site: what do we want to show?


Other business

On Call