Ontology meeting 2011-10-12

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Discussion notes - I


  • A plea for a re-cap on what information is needed to make a cross-product, in reference to the involved_in terms.

See http://sourceforge.net/tracker/?func=detail&aid=3396697&group_id=36855&atid=440764

Discussion notes - II

(revisiting our favourite topic from previous meetings): regulation of Y process by regulation of transcription from RNA polymerase II promoter'

  • Since we haven't been able to find a good solution for the XPs for these, could we have a template in TG to add these in with two is_a relations, and XPs to match the existing terms. Then we can fix them en-masse later, when we can capture primary regulation, secondary regulation, tertiary regulation etc ? It's a fudge, but would mean the annotators get an ID for their terms.

See positive regulation of gluconeogenesis by negative regulation of transcription from RNA polymerase II promoter ; GO:0035949, for an existing example.

Discussion notes - III

Coming back to an earlier discussion: How are the 'regulation of' terms related, when the two parent processes are connected by a part_of relationship?

Clarification required for: https://sourceforge.net/tracker/?func=detail&aid=3317785&group_id=36855&atid=440764

When requesting a term 'regulation of pigment cell development', TG does not create a relationship between 'regulation of pigment cell development' and 'regulation of pigment cell differentiation'. Surely it should?

Or, the reasoner should be able to do it. Chris, is this the case?

Discussion notes - IV

  • Can we add 'HAS_PART' relationships between function and process terms? E.g. for 'x process via y function' terms or biochemical pathways?
  • Stems from this SF item: [1]