Difference between revisions of "Manager 16October2013"

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(Discussion)
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*Judy- Isn't it confusing to say that we don't anything and at the same time saying it is interacting with something? Isn't that knowing something?
 
*Judy- Isn't it confusing to say that we don't anything and at the same time saying it is interacting with something? Isn't that knowing something?
 
*PaulT- The question of is protein binding a 'Function' came up. There are 2 classes of Molecular functions:
 
*PaulT- The question of is protein binding a 'Function' came up. There are 2 classes of Molecular functions:
** biochemical activities (enzymes) that causes something to happen (influences something). These are physical changes which affects something. These are changes in physical Activity. Example: phosphatase regulator
+
** biochemical activities (catalytic activities or binding activities, including protein binding) These cause a physical change in a target: an enzymatic transformation of a chemical entity (small molecule), or a modification of the structure of the protein/complex. Biochemical activities have an effect on a physical property of the target, but not necessarily on a function of a target.  For example, a protein-protein interaction might or might not have an effect on the function of one of the proteins; a kinase might phosphorylate a protein which might or might not influence the activity of the phosphorylated protein.
** actions where the cause is not known (influence is not known). These are changes in just the physical Entity. Example: protein binding
+
** "component functions" (e.g. phosphatase regulator, receptor agonist). These cause a change in the biochemical activity or other function of the target.
 
*Pascale: should we then allow GTP binding etc ?
 
*Pascale: should we then allow GTP binding etc ?
 
*Chris: We should consider this proposal
 
*Chris: We should consider this proposal

Revision as of 10:33, 16 October 2013

  • In Protein2GO we do not allow ND annotations to the root node 'Molecular_Function' to co-exist with protein binding annotations. It has been requested that we allow an ND annotation for molecular function to be added to an entry when the only other function annotations are to protein binding. Curators want to indicate that there is no known activity of the protein, even though interaction partners are known.

We would like a consensus decision on whether this should be allowed.

Discussion

Present: Suzi, Judy(for 10 min), PaulT, Huaiyu, Rama, Pascale, Jane, Kimberley, Rachael, David, Chris

ND annotations with protein binding

  • Kimberley- Making a ND annotation to the root node along with a protein binding annotation allows us to say that we don't know the function but we know the protein binds to something.
  • Judy- Isn't it confusing to say that we don't anything and at the same time saying it is interacting with something? Isn't that knowing something?
  • PaulT- The question of is protein binding a 'Function' came up. There are 2 classes of Molecular functions:
    • biochemical activities (catalytic activities or binding activities, including protein binding) These cause a physical change in a target: an enzymatic transformation of a chemical entity (small molecule), or a modification of the structure of the protein/complex. Biochemical activities have an effect on a physical property of the target, but not necessarily on a function of a target. For example, a protein-protein interaction might or might not have an effect on the function of one of the proteins; a kinase might phosphorylate a protein which might or might not influence the activity of the phosphorylated protein.
    • "component functions" (e.g. phosphatase regulator, receptor agonist). These cause a change in the biochemical activity or other function of the target.
  • Pascale: should we then allow GTP binding etc ?
  • Chris: We should consider this proposal
  • The ontology group will discuss this either during an ontology call or annotation call.

Other activities

  • GeneDB training: Rachael mentioned that GeneDB group is being trained to use protein2GO and they will soon start annotating.
  • MoonProt DB: Rama gave an overview of GO/how to make annotations to the MoonProt group over webex (Mike was present as well). They are going to make some annotations and send it to us. If need be they will visit us for training.