Ontology meeting 2012-07-25

45-minute meeting

MINUTES: David

ATTENDEES:

FOLLOW-UP ON CELLULAR COMPONENT DISJOINTS

See procedure and to-do list here:

http://wiki.geneontology.org/index.php/Ontology_meeting_2012-07-11#CELLULAR_COMPONENT_DISJOINTS

PROTEIN GLYCOSYLATION

• 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)?
• Q (related): The glycosylation may be with a carbohydrate or with a carbohydrate derivative. In the latter case, where do we place new terms such as O-linked-N-acetylglucosamine (O-GlcNAc) modification? (See e.g. this SF request: https://sourceforge.net/tracker/?func=detail&aid=3537766&group_id=36855&atid=440764)

CHILDREN OF PROTEIN BINDING

(Carried over from last week)

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).

RESPONSE_TO TERMS

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)