Ontology meeting 2012-07-11

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45-minute meeting




Chris to have something by the time he goes on holiday next week


  • Cam-Eds to take care of the google spreadsheet from now-on (it doesn't make sense for David and Tanya to comment then hand back to us) and look at all of them with CHEBI on Thursdays. We have another meeting with ChEBI tomorrow to go through them bit-by-bit.
  • acid/base ID consistency issues may be reason for some of questions (e.g mandelate). We need to look at the IDs in the XP file.
  • We will need to add 'carbohydrate derivative metabolism' terms into GO (via TG1) to match the ChEBI hierarchy. Then regenerate the file, as this fix will probably remove lots of the issues

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

DONE: We've asked Rafael to point us to the RHEA file(s), see below.

TO DO: With help from 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.

  • Progress: to investigate using OPPL as a generic tool that can help us with the data processing here. Added to list of ontology processing tasks

Rafael pointed us to a BioPAX file including Rhea IDs and EC numbers: ftp://ftp.ebi.ac.uk/pub/databases/rhea/biopax/rhea-biopax.owl.gz

For the next release - scheduled very soon - Rhea intends to export also flat files, one of them with just the mapping Rhea ID to EC number.

  • The major issue here is getting new enzymes from Rhea into GO.
  • For directionality, we'll take the NEUTRAL direction term as standard (as that fits with the current GO terms).
  • AI: Chris and co to write scripts for OPPL that will pull reactions out of Rhea and into GO (August: initial feasability study). There will need to be a manual step pulling in names from KEGG because Rhea dont name their reactions.
  • For peoples SF items, tell them that we're putting an automatic pipeline in place and to please wait for that.


  • There's 2 types of ubiquitin ligases:
    • Where substrate binding and ubiquitin transfer are done by the same protein.
    • Where substrate binding is done by one subunit, and ubiquitin transfer is done by the second subunit.
  • Dianna suggests the following new terms:
- small conjugating protein ligase activity (GO:0019787)
-- (is_a) ubiquitin-protein ligase activity (GO:0004842)
--- (has_part) ubiquitin-protein ligase ubiquitin transfer to substrate (GO:new1)
--- (has_part) ubiquitin-protein ligase substrate binding (GO:new2)
- protein binding (GO:0005515)
--(is_a) ubiquitin-protein ligase substrate binding (GO:new2)
  • Q: How best to do this, without creating a set of 'substrate binding' terms?
  • Q: Are we agreed that 'ubiquitin ligase activity ; GO:0004842' (catalysis of ....) encompassese both substrate binding and ubiquitin transfer?

*Agreed that in GO, we should't get down to the level of enzyme mechanics. Annotate to 'contributes_to'.


  • Is everyone ok with the Cam-Editors adding in some more disjoints in cellular component? E.g. between 'nucleus' and 'cytoplasm'?
    • Also consider merging some axioms from x-disjoint.owl across into the main ontology
      • (however, owl is required for stringer part-disjointness where we don't name "X part" terms)
      • (I believe we may have decided to keep the disjoints in a separate ontology also because they look awful in OE?)

Procedure for adding in disjoints:

  1. In Protege, open: extensions/x-disjoint.owl
  1. Click on 'cytoplasm'
  1. In Expression editor type: 'nuclear part'
  1. Run Reasoner (Hermit).
  1. Save x-disjoint.owl file.
  1. In terminal, type: svn diff x-disjoint.owl (NB: the diff will be huge because it reorders stuff).
  1. Commit x-disjoint.owl back to the repository
  1. Watch Jenkins to check the build is all ok.
  • Need to add in disjoints between:
    • nucleus and cytoplasmic part
    • nuclear part and cytoplasmic part
    • cytoplasm and nucleus


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).

come back to!


DONE Paola/Jane/Becky to send David and Tanya a summary of what we do for our week on the SF rota... won't take long to describe.