Ontology meeting 2011-12-7

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  • Note that David and Tanya won't be able to attend this week's call, so we've moved some topics to the next call.

Discussion notes - I

Direction of Enzyme Reactions

Amelia will be attending this call.

Many enzyme terms are currently bidirectional. This is a problem when creating Process-Function links. What is the plan for handling these in GO: two separate function terms?

Discussion notes - II

Testing of new TermGenie

Six new regulation terms, added via both the new and old TermGenie, are waiting to go live in the ontology.

They're listed in the gatekeeper review page for TG1 [[1]]. Please make sure you have permissions to access this (ask Heiko if not).



  • Chris
  • Heiko
  • Jane
  • Amelia
  • Rebecca
  • Paola

Bidirectional Enzyme Reactions

Rhea have 4 terms for each reaction (Amelia).

  1. ->
  2. <-
  3. occur in both directions in equilibrium
  4. uncertain direction

For GO, we could pull in all 4 reactions from Rhea, BUT Rhea don't name them, and not all are necessary.

For making process/function links, for most cases we can assume that in the current definitions a+b = c+d, that a+b are input, and c+d are output.

It doesn't make sense to change everything on mass. Do it on a case-by-case basis. Where we want to make process/function links, either create a union term with child reactions in both directions. Or change the '=' to '->' in the current definition.

There are some with comments that the reaction can proceed in either direction. For these, we can create a union and two child terms as we come across them.

Term Genie 1 Testing

TG1 is not taking into account the part_of relationships, when it's choosing an is_a parent for regulates terms, even though regulates is transitive over part_of. Chris and Heiko will look into this.

Continue using TG0 for now, while they investigate.