Binding Terms Conference Call Information: Difference between revisions

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The way we capture catalytic binding may change the decision on whether or not we should capture catalytic binding.  However, this is a bit of a chicken and an egg situation as deciding that catalytic binding should not be captured at all will mean that discussions about how to capture catalytic binding would be irrelevant.
The way we capture catalytic binding may change the decision on whether or not we should capture catalytic binding.  However, this is a bit of a chicken and an egg situation as deciding that catalytic binding should not be captured at all will mean that discussions about how to capture catalytic binding would be irrelevant.


For more information/comments about options to capture catalytic binding please see [http://wiki.geneontology.org/index.php/Binding_terms_working_group working group wiki] and [http://wiki.geneontology.org/index.php/User:JimHu/Binding_termsJim's cross-product approach].
For more information/comments about options to capture catalytic binding please see [http://wiki.geneontology.org/index.php/Binding_terms_working_group working group wiki] and [http://wiki.geneontology.org/index.php/User:JimHu/Binding_terms Jim's cross-product approach].

Revision as of 05:56, 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, this is a bit of a chicken and an egg situation as deciding that catalytic binding should not be captured at all will mean that discussions about how to capture catalytic binding would be irrelevant.

For more information/comments about options to capture catalytic binding please see working group wiki and Jim's cross-product approach.