Ontology meeting 2011-08-31

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David and Tanya will report on F-P links and Quality control.

Cross-Products: Where are we up to and how we can get moving on the next internal set.

  • Can everyone take a look at SF:3396697 - 'involved in' xps

Discussion notes

  • Check for a consensus from last Editors meeting on how to handle 'regulation of y metabolism by regulation of transcription' terms. The summary of where we are up to is:
    • DH says the regulation is direct if you think of it in this way: If enzyme B is involved in a metabolic pathway, by limiting the amount of kinase B available, you are limiting the activity of kinase B, and therefore the pathway. So, if everyone is in agreement, we can continue to add these terms as we have been.
    • CM: OBO format can't handle nested classes yet, so we'd need to wait for OWL to do this, and will look into whether there is enough information to create logical definitions for TG.

Discussion notes - II

  • Is there any reason we can't expand the xps relationship set a little to allow us to write xps for terms as we add them? I'd like has_participant and its inverse (participes_in??) e.g. just added terms for macropinocytosis and macropinosome. located_in won't work here. [Jane]
  • What's the time-frame for adding new templates to TG? Could just use them in the non-commit mode if it requires extra editing e.g. relies on CHEBI [Jane]

Discussion notes - III

  • Can we add a separate pipeline for non-template terms to TG, mainly for GO power users? See TG tracker

Task List