Ontology meeting 2012-11-15
FOLLOW-UP: ChEBI paper
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:
[Term] 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
[Term] 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?
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'
- 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:
[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.
Can we extend this to include MFs involved_in BPs?
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)