Annotation Conf. Call, January 28, 2014: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 6: Line 6:
** At the last call we agreed that annotations to this and its children terms be limited to gene products that directly regulate (e.g. bind to) an enzyme. But what are the sorts of experiments that one would see to show direct binding and regulation?
** At the last call we agreed that annotations to this and its children terms be limited to gene products that directly regulate (e.g. bind to) an enzyme. But what are the sorts of experiments that one would see to show direct binding and regulation?


** oes the binding and regulation need to be demonstrated in the same
** oes the binding and regulation need to be demonstrated in the same experiment? Is this even possible?
experiment? Is this even possible?


** If the answer to #1 is no, is it sufficient to use an IDA evidence code
** If the answer to #1 is no, is it sufficient to use an IDA evidence code if the binding is demonstrated in, and annotated from, another experiment,
if the binding is demonstrated in, and annotated from, another experiment,
either within the same paper or in another paper?
either within the same paper or in another paper?


** If regulation is demonstrated by an in vitro assay, but binding is not
** If regulation is demonstrated by an in vitro assay, but binding is not demonstrated, what should the annotation be?
demonstrated, what should the annotation be?


** If binding is demonstrated in another organism, is it okay to infer
** If binding is demonstrated in another organism, is it okay to infer binding based on sequence similarity and make annotation for regulator activity and an ISS annotation for binding?
binding based on sequence similarity and make annotation for regulator
** Should the term's parentage be changed in the ontology to be a child of enzyme binding (the definition has already been changed to include the binding component)
activity and an ISS annotation for binding?
** Should the term's parentage be changed in the ontology to be a child
of enzyme binding (the definition has already been changed to include the binding component)


** How do we focus our efforts on re-annotation if we change how this term should be used?
** How do we focus our efforts on re-annotation if we change how this term should be used?

Revision as of 13:51, 27 January 2014

Agenda

  • Enzyme regulator activity (GO:0030234)
    • At the last call we agreed that annotations to this and its children terms be limited to gene products that directly regulate (e.g. bind to) an enzyme. But what are the sorts of experiments that one would see to show direct binding and regulation?
    • oes the binding and regulation need to be demonstrated in the same experiment? Is this even possible?
    • If the answer to #1 is no, is it sufficient to use an IDA evidence code if the binding is demonstrated in, and annotated from, another experiment,

either within the same paper or in another paper?

    • If regulation is demonstrated by an in vitro assay, but binding is not demonstrated, what should the annotation be?
    • If binding is demonstrated in another organism, is it okay to infer binding based on sequence similarity and make annotation for regulator activity and an ISS annotation for binding?
    • Should the term's parentage be changed in the ontology to be a child of enzyme binding (the definition has already been changed to include the binding component)
    • How do we focus our efforts on re-annotation if we change how this term should be used?
  • Future Annotation calls
    • we would like to have an open discussion on what are the sorts of issues the Annotation call should focus on.