Ontology meeting 2012-07-04

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FOLLOW-UP: EC numbers in GO

For background, see: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-05-02#DISCUSSION_ITEM_II:_EC_numbers_in_GO and http://wiki.geneontology.org/index.php/Ontology_meeting_2012-06-06#FOLLOW-UP:_EC_numbers_in_GO

We should ask Rafael to point us the RHEA file in advance. Then, with the help of Chris, we should set up an automated filtering process so that we can retain only the master reactions, and start to figure out how to automate adding the pertaining EC numbers in GO. Once this process has started, we can then have another meeting with the RHEA people to define details and procedures.


These questions stem from Emily and Marijns work to provide more information for protein binding terms (see Annotation call for June 26th).

When you refer to the protein binding terms (E.g. phosphatase binding/EGFR binding), do you mean:

  1. Binding to a GP of that name
  2. Binding to a GP that is capable of having that function
  3. Binding to a complex that is capable of having that function.
  • Example 1: The definition of 'epidermal growth factor-activated receptor activity ; GO:0005006' is that the receptor must bind to the ligand EGF and transduce this signal. Does 'epidermal growth factor receptor binding ; GO:0005154' refer to binding to a GP with this activity, or does it mean binding to an EGFR gene product (which binds TGF, FGF, EGF etc: see Q01279).
  • Example 2: Phosphatases often exist in the cell as a regulatory subunit complexed to a catalytic subunit. Does 'protein phosphatase binding ; GO:0019903' mean binding to the complex (i.e. either the regulatory OR the catalytic subunit) or binding to a protein that has phosphatase activity (e.g. the catalytic subunit)?

At the moment, we have a mismash:

protein phosphatase binding ; GO:0019903
--[isa]protein phosphatase 1 binding
--[isa]protein phosphatase 2A binding
protein binding ; 
--[isa]protein kinase A binding ; 
----[isa]protein kinase A catalytic subunit binding ; GO:0034236
----[isa]protein kinase A regulatory subunit binding ; GO:0034237
--[isa]protein kinase binding ; GO:0019901
----[isa]protein kinase A catalytic subunit binding ; GO:0034236
----[isa]protein kinase C binding ; GO:0005080
kinase binding ; GO:0019900
--[isa]phosphatidylinositol 3-kinase binding ; GO:0043548 (lots of annotations to this refer to binding to the regulatory subunit of PI3K).