Binding Terms Conference Call Information: Difference between revisions

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ACTION ITEMS:
ACTION ITEMS:
Peter (lead), Ruth, Debbie, Jim form a workgroup to examine the issues raised in the discussion. Should GO capture catalytic binding? Mike, Ben, Emily, David also joined this discussion
Peter (lead), Ruth, Debbie, Jim form a working group to examine the issues raised in the discussion. Should GO capture catalytic binding? Mike, Ben, Emily, David also joined this working group.


== [http://www.surveymonkey.com/s.aspx?sm=A0B2eXQRXLzUcvYGFmGL1w_3d_3d Binding terms survey] ==
== [http://www.surveymonkey.com/s.aspx?sm=A0B2eXQRXLzUcvYGFmGL1w_3d_3d Binding terms survey] ==

Revision as of 05:50, 4 June 2009

What problems are we trying to solve?

This issue was originally brought up in the GOC meeting in Oregon [binding minutes]

This meeting identified that

  1. The documentation is confusing on the proper use of binding
  2. There were conflicting views about whether or not GO should include catalytic substrate annotations such as 'ATP binding' and the problem of including both substrate and product from a catalytic reaction.
  3. Most people agreed that GO should capture non-transformative binding, eg. binding of X resulting in an allosteric change to the thing doing the binding.
  4. Perhaps cross product annotations should be used to describe majority of binding annotations (see Annotation_Cross_Products#binding_example)
  5. There was a concern about how limiting 'binding' annotations to non-catalytic interactions may affect queries for genes involved in 'ATP binding', for example, researchers might reasonably expect to get back kinases by such a query.
  6. It was unclear whether there should be a transfer of 'binding' term annotations via ISS/ISO

ACTION ITEMS: Peter (lead), Ruth, Debbie, Jim form a working group to examine the issues raised in the discussion. Should GO capture catalytic binding? Mike, Ben, Emily, David also joined this working group.

Binding terms survey

This survey was written to address this first key issue: Should GO capture catalytic binding? The way we capture catalytic binding may change the decision on whether or not we should capture catalytic binding. However, if it is decided that catalytic binding should not be captured at all, then the method would be irrelevant.

  • Proliferation of "x binding terms" in the MF ontology.
  • The binding terms are currently a mess - proliferation will only make it worse
  • The ability to annotate to x binding without needing a new term request (NTR)