Ontology meeting 2012-08-01

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30-minute meeting




(Carried over to next week)


(From last week: Tanya, please report on this) 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.


  1. Only one GOCHE id (cyanophycin) left in go_xp_chebi.obo now. SF item [1] for ChEBI has been opened.
  2. 20-some CHEBI 'orphans' when viewed in Protege. Appear to be cases of secondary ids used in the go_xp_chebi.obo file and/or preliminary ChEBI entries. Are the preliminary entries not in the ChEBI file that we access?


  2-polyprenylphenol [2]
  id: GO:0032193  ! ubiquinone biosynthetic process via 2-polyprenylphenol
  intersection_of: GO:0009058 ! biosynthetic process
  intersection_of: has_output CHEBI:16389 ! ubiquinones
  intersection_of: has_intermediate CHEBI:1269 ! 2-Polyprenylphenol
  thienylcyclohexylpiperidine [3]
  id: GO:0016596 ! thienylcyclohexylpiperidine binding
  intersection_of: GO:0005488 ! binding
  intersection_of: has_input CHEBI:126971

'% complex' terms and their relationship to 'integral to x'

Current relationship is part_of but should be is_a. Agree?

integral to membrane definition = Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane.

  --integral to membrane
  ----[p] cytochrome o ubiquinol oxidase complex
  ----[p] ion channel complex


(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 ; GO:0051018
----[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).

Also see this SF item:




  • To look into how we should be using and naming the 'protein complex binding' terms.
  • Come up with a Comment to make it clearer when we should be using 'protein complex binding' and when we should be using 'protein binding'. Suggested in call was that the 'complex binding' terms would require IDA as an evidence code as you don't know which subunit of the complex is being bound. If you know which subunit is being bound, annotate to the 'protein binding' term with IPI and a protein ID in the with column.
  • Based on these guidelines, when an enzyme exists as a complex of regulatory and catalytic subunit (e.g. protein kinase A) consider changing the existing generic term to 'enzyme COMPLEX binding'. E.g. 'protein kinase A binding ; GO:0051018' would become 'protein kinase A COMPLEX binding ; GO:0051018'.
  • Will need to consider binding to a homodimeric protein complex: e.g. dimerization of some receptors creates a binding site for a ligand (the binding site doesn't exist on either of the monomeric subunits).


  • Flatten out the enzyme binding node, and make 'protein kinase A binding ; GO:0051018 a sibling of the catalytic and regulatory subunit binding terms. Since this will impact on searching, need to add comments to terms to point out the more specific terms to consider.
  • Will need to look at the PI3K binding term, and look into making a 'PI3K regulatory subunit binding' term to transfer many of the existing annotations to.
phosphatidylinositol 3-kinase regulatory subunit binding ; GO:0036312
phosphatidylinositol 3-kinase catalytic subunit binding ; GO:0036313


(Carried over to next week)

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 please report on this)