Ontology meeting 2012-11-08

From GO Wiki
Jump to navigation Jump to search

MINUTES: Tanya

ATTENDEES:


FOLLOW-UP: ChEBI paper

References up to date. Restructuring done by Tanya, passed back to David. Make sure your Dropbox folder has version 13 in it.

FOLLOW-UP: import/export template

David and Tanya to report. Added xps from Chris' file to go_xp_chebi.obo. Heiko to begin working on template when opportunity arises.

CHEBI roles in crossproduct file

We currently have xps to CHEBI terms that are roles in the xp file. Do we keep them or not? If we keep them, should we allow TermGenie to create terms using such CHEBI terms? For example, SF request [1].

  [Term]
  id: GO:0042493 ! response to drug
  intersection_of: GO:0050896 ! response to stimulus
  intersection_of: has_input CHEBI:23888 ! drug


Related 'response to' question: Lots of requests for these types of terms where x = chemical. The chemical itself may not occur naturally. What do we think about the synthetic chemicals? Our annotation guideline: 'A gene product should be annotated with terms reflecting its normal activity and location.' Is something like 'response to GW 7647' something normal? Add these regardless of origin? It may be a pain to go back and pull out all of the synthetic chemicals (thinking of drugs now and that slew of terms requested by Diane). Thoughts?

  [Term]
  id: GO:1901593
  name: response to GW 7647
  namespace: biological_process
  def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, 
  secretion, enzyme production, gene expression, etc.) as a result of a GW 7647 stimulus." [GOC:TermGenie]
  is_a: GO:0010033 {is_inferred="true"} ! response to organic substance
  intersection_of: GO:0050896 ! response to stimulus
  intersection_of: has_input CHEBI:70778
  relationship: has_input CHEBI:70778 {is_inferred="true"}

GO chemical terms where chemical is_a mixture

Stemming from placement of 'phlobaphene metabolic process'. See email thread among some of us editors.


TermGenie template for 'cellular response to'

This type of term is frequently requested via SF. I think we've discussed its addition previously, but don't remember if we reached a resolution - can't find anything on wiki or email threads. Would it be possible to implement a sort of 'decision tree' for the non-ChEBI parents? Or shall we leave this for the non-template-able term requests procedure?

E.g. see this SF request: https://sourceforge.net/tracker/?func=detail&aid=3580560&group_id=36855&atid=440764 [Paola]


Transport and localization logical definitions

Follow up from last week, Jane to report.


Endosomal transport

Follow up from last week, Tanya to report.

SF corner

disulphide bond enzymes

Is it okay to merge a process into a function? See [2]

Enzymes that can use more than one substrate

Are they separate molecular functions? See SF3571860 and GO:0016619.

Change xps for amino acid GO terms?

So that they use CHEBI:33704 alpha-amino acid instead of ChEBI:33709 amino acid (see [3]). This corresponds better to what biologists think of as amino acids. If we do this, it might be best to just delete all current children of aa terms and re-infer.