Ontology meeting 2012-11-29

MINUTES: Paola

ATTENDEES:

ChEBI paper?

All done?

TG templates for 'cellular response to chemical', 'import' and 'export'

Have they been tested? If so, advertise on GO mailing list.

Documenting decisions

We need to develop a SOP for doing this, otherwise we won't do it. Let's take the example of the metal cations from last week and figure out how we should do it. We should get into the habit of when we have come to a decision like this, making a ticket for someone to make the doc.

Other examples?

Adding has_parts for antiporters

Arose from this SF ticket: [1]

Essentially Ruth wants to infer both calcium export and sodium import from calcium:sodium antiporter activity. I've suggested we could use has_part, but this is probably something we'd want to do globally. Do we want to do this? What would be the implications? Could we extend to other transporter types? We have transporter part_of transport elsewhere...this is kind of the inverse of what's being suggested.

FOLLOW-UP: Endosomal transport

All done from last week? (http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-08#Endosomal_transport)

Plan was: create vesicle-mediated endosomal transport as of endosomal transport, put all current kids under this (parent can be removed from vesicle-mediated parentage), send email to dbs to either move or leave in place, still correct

Did this: removed vesicle-mediated transport (VMT) as parent of endosomal transport, revisited all kids, copied those that referred to transport using vesicles to VMT. No new term created. Annotators can annotate to 'endosomal transport' or more specific kids, as they see fit.

Chris created xp for endosomal transport with new relationship:

  [Term]
  id: GO:0016197  ! endosomal transport
  intersection_of: GO:0006810 ! transport
  intersection_of: results_in_transport_to_from_or_mediated_by GO:0005768 ! endosome

  [Typedef]
  id: results_in_transport_to_from_or_mediated_by
  name: results_in_transport_to_from_or_mediated_by
  comment: This relation is so far only used for one class, 'endosomal transport' (GO:0016197), which groups 
  together disparate roles the participants can play - it is defined as 'The directed movement of substances into, 
  out of *or mediated by* an endosome...'
  is_a: has_participant

Discussion deferred until Tanya can join.

involved_in TG template

Can we extend this to include MFs involved_in BPs?

TG restrictions (in view of 'global' TG tool)

David and Paola suggest to prevent submitters from creating regulation terms if the target term is a descendant of 'regulation of biological quality'.

E.g. 'regulation of maintenance of presynaptic active zone structure' is wrong because 'maintenance of presynaptic active zone structure' is a grandchild of 'regulation of biological quality'.

FOLLOW-UP: Capturing explicit cell lineage in GO

See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-15#Capturing_explicit_cell_lineage_in_GO