Ontology meeting 2019-03-04

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Conference Line

See calendar for details



GOC Meeting Cambridge

  • GOC meeting - Cambridge, UK April 11th - 12th (right after ISB meeting)
    • Make sure you have signed up and let's start thinking about what we want to present.

David and Kimberly to NYC

  • David and Kimberly visited Peter last Thursday and Friday to discuss the Reactome imports and look closely at defining metabolic pathways using has_primary_input.
    • We decided that when a compound is named in a biochemical pathway as an import or an output, then we should categorize that pathway as a metabolism of that chemical. For example 'glucose catabolic process to pyruvate' will be a type of pyruvate metabolism. When a chemical is an intermediate, we will not consider it a type of that chemical's metabolism. For example if we had a term glucose catabolic process to pyruvate via glucose 6-phosphate, we will not categorize this as a glucose 6-phosphate catabolic process. This means that categorization to a metabolic process means the chemical plays some type of significant role in the process. For currency chemicals, we do want these kinds of inferences, so we adjusted the definitions of things like NADP metabolic process accordingly. https://github.com/geneontology/go-ontology/issues/16943
    • We began a branch on Kimberly' machine that incorporates spatial relations into GO cellular components. This turns out to be a rather significant project if we decide to do it by hand. Can we work with a software person to try to automate some of this?
    • We did further work writing rules for importing Reactome models into GO-CAM. I think we should dedicate an entire call in the future to discuss this project.

Discussion topics

  • Getting rid of regulates_o_part_of: The plan going forward
    • Jim has created the file with about 3000 lines. David is continuing to review these. To alleviate logical problems, 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