Ontology meeting 2012-07-25

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45-minute meeting


ATTENDEES:Paola, Heiko, Harold, David, Judy, Tanya


We don't know if Chris has done something. He comes back at the beginning of August.


See procedure and to-do list here:


Who is working on this? Paola will meet with Jane tomorrow and the EBI editors will work on this.


  • protein glycosylation ; GO:0006486 is_a: cellular carbohydrate metabolic process ; GO:0044262
  • Q: Do we want to restrict our definition of 'carbohydrate metabolism' to EXCLUDE cases where the carbohydrate is the MODIFIER (NOT the target that is being modified)?

Don't give the parent dual is_a parentage, but when we talk about the specific terms, we can make them is_a carbohydrate or carbohydrate-derivative metabolic processes. We will expand on the definition of protein glycosylation to reflect this.

ACTION ITEM (Paola): Paola will change the definition of the term when she does the SF item. DONE.


(Carried over from last week) Carry over again.

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).


We had initially left these aside, but we have more and more requests coming through SF, so we need to work out a strategy for adding these in via TG.

E.g.: https://sourceforge.net/tracker/?func=detail&aid=3544656&group_id=36855&atid=440764, https://sourceforge.net/tracker/?func=detail&aid=3540146&group_id=36855&atid=440764

(There are some xps in an old file called biological_process_xp_stimulus.obo in the scratch directory)

Chris wanted to merge the xp-files into the main ontology file before doing this. We should work out the genus and relationships that we want to use in the logical definitions. We should also use protege to check to see if the existing terms are placed properly. (David & Tanya)

Chebi x-products

There are still some GOCHE x-produxts in the file. Tanya will check to see the status of these. In the chemical importer in protege, you should see the remaining goche IDs and some orphan chebi IDs. These should be checked too.