Ontology meeting 2011-09-28

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Discussion notes

Discussion notes - I

(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 - II


  • A plea for a re-cap on what information is needed to make a cross-product.

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?

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]

Discussion notes - V

  • ChEBI stuff
    • diff file
      • ACTION: David and Tanya will look through the diff file and generate a user-friendly file of suggested errors/missing links in ChEBI
    • new compounds to add
      • ACTION: Chris to generate a block of stanzas for the new terms to paste directly into goche, and an additional set of intermediate is_a terms to go through manually

Task List