Ontology meeting 2011-11-02

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Discussion notes

Discussion Notes I: cross-products timeline

Discussion Notes II: RESID Terms in GO

  • A while ago, MA added in a set of RESID (protein modification) terms for John Garavelli (search on RESID DBXref to find them). These are not well used for annotation and are often long and confusing. They're currently processes but many probably represent enzyme activities. Should we continue to add them in? (John G pointed out that there's a set of RESID modifications that are lacking GO terms).
  • For many, the only evidence is the end modification (with a possible starting substrate).
  • Some are spontaneous modifications (self-modification). Presumably these shouldn't be included in GO?


Discussion Notes III: gamete generation

Chris sent round emails to GO editors asking about the definition and placement of 'gamete generation' terms. Is this the same as 'gamete formation'? or 'gamete formation AND the subsequent maintenance processes?.

Is gamete generation restricted to multicellular organisms?


Discussion Notes IV: Follow up on OWL Protege Tutorial

  • Check dates work for all (Mon 30th and Tues 31st January 2012).

Discussion Notes V: canonical cell cycle

The cell cycle terms need some work - we've asked Val whether she can help and recommend experts and we're also contacting the cell cycle ontology people. I'm wondering whether we might need to create a set of canonical cell cycle terms, because one of the problems when Amelia tried to do this last time was that there is always some organism that has an exception so many of the obvious relationships e.g. cytokinesis part_of cell cycle couldn't be made. What do we think of this? Has this strategy worked for other ontologies?


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