Annotation Conf. Call 2020-01-28: Difference between revisions

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**https://github.com/geneontology/go-annotation/issues/2718
**https://github.com/geneontology/go-annotation/issues/2718
**'activated by' had been used to identify a chemical substance that increases the activity of the gene product.
**'activated by' had been used to identify a chemical substance that increases the activity of the gene product.
**We would like to instead model this with a 'binding activity' that 'directly positively regulates' a second, or main, molecular function enabled by the gene/gene product
**We would like to instead model this as:
**The aim is to capture regulatory molecules, but not things like co-factors.
***GeneProduct 1 'enables' binding (GO:0005488) 'has_input' (some chemical), 'directly_positively_regulates' molecular function
***GeneProduct 1 'enables' molecular function
**The aims are to: 1) model regulatory events in terms of activities enabled by gene products, and 2) capture regulatory molecules, but not necessarily things like co-factors.
**Sample GO-CAM model:  http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296
**Sample GO-CAM model:  http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296



Revision as of 17:42, 27 January 2020

Agenda and Minutes

  • Present:

Annotation Relations

  • Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
  • Relations to discuss this week:
    • 'activated by'
    • https://github.com/geneontology/go-annotation/issues/2718
    • 'activated by' had been used to identify a chemical substance that increases the activity of the gene product.
    • We would like to instead model this as:
      • GeneProduct 1 'enables' binding (GO:0005488) 'has_input' (some chemical), 'directly_positively_regulates' molecular function
      • GeneProduct 1 'enables' molecular function
    • The aims are to: 1) model regulatory events in terms of activities enabled by gene products, and 2) capture regulatory molecules, but not necessarily things like co-factors.
    • Sample GO-CAM model: http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296