Ontology meeting 2012-11-15

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Follow-up on action items from last week (http://wiki.geneontology.org/index.php?title=Ontology_meeting_2012-11-08)

Tanya sent Dropbox invite to authors. Deadline for comments: Friday 16th. People have started commenting.

David will go through figures; flow charts.? Chris using OmniGraffle or Jane to give to Chris; Jane to write
cover letter and submit?

FOLLOW-UP: import/export template

All done from last week? (http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-08#FOLLOW-UP:_import.2Fexport_template)


Just working on the non-entailed transport and localization links. For these ones:

EXISTS, NOT-ENTAILED SubClassOf(GO:0032974 'amino acid export from vacuole' GO:0034487 'vacuolar amino acid transmembrane transport')
EXISTS, NOT-ENTAILED SubClassOf(GO:0032975 'amino acid import into vacuole' GO:0034487 'vacuolar amino acid transmembrane transport')

I ended up adding new genus terms, but looking at the xps they're still not right:

id: GO:0032974 ! amino acid transmembrane export from vacuole
intersection_of: GO:0044746 ! amino acid transmembrane export
intersection_of: results_in_transport_or_localization_to GO:0005773 ! vacuole
id: GO:0032975 ! amino acid transmembrane import into vacuole
intersection_of: GO:0044745 ! amino acid transmembrane import
intersection_of: results_in_transport_or_localization_to GO:0005773 ! vacuole

export is obviously from, and not to the vacuole. The import one might be okay logically, but it still doesn't across that it's into rather than to the vacuole.

Using the imports/exports relations doesn't solve the problem because it's the location that we need to capture.

Chris suggested the use of has_target to get around this?

FOLLOW-UP: instantiating inferred/removing redundant links

Heiko has provided script. Editors have looked at the results. Tanya has added the implied links and removed the redundant links. She's also added the instructions to this Curator Guide page on the Wiki:



FOLLOW-UP: TermGenie template for 'cellular response to'

All done from last week? (http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-08#TermGenie_template_for_.27cellular_response_to.27)

  • File created, reviewed. Cross-products added to go_xp_chebi.obo.
Currently no SF items to test on. Paola suggests advertising the new templates

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:

  id: GO:0016197  ! endosomal transport
  intersection_of: GO:0006810 ! transport
  intersection_of: results_in_transport_to_from_or_mediated_by GO:0005768 ! endosome
  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 template

Can we extend this to include MFs involved_in BPs?

Jenkins check?

 Not catching term with definitions but not def references?  Used to be fatal error in OE but isn't anymore.
 Check obo script (perl) catches, but  not yet a feature in in Oort.Feature needs to be requested.

Capturing explicit cell lineage in GO

Stemming from this paper:


But also see:


Paper states GO does not caputre cell types and their development
But  GO DOES capture their development and differentiation
Differentiation terms  have cell linage info embedded; 
Example: There exists a cell C, that can arise from either cell A or cell B
 Then Cell C development: process where cell becomes a C, there exists two paths:
  a. cell A to C
  b: cell B to C
Previously hard if only is_a and part_of. But we could do now. 
if there are choices, we could do unions (a or b) but is not satisfying. . 
better to do two.
 Note: if  say cell a from cell b, CL must define these as two different cells.
So when does one cell change into another? 
Could use col 16 to define both cells. 
Action item: to be continued;improve doc on what GO can and cannot do.

Annotations to part terms

Stemming from thread on go-discuss

It was decided to discourage annotation to these terms. These will be added to the high level annotation subset
 (terms not to be used for annotation)