Ontology meeting 2014-02-20

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Attendees:

Minutes: David OS

SF push

There are 280 open tickets in SF. We should try to spend some quality time with them and lessen the number before the GOC meeting, e.g. by devoting a couple of days to SF alone.

(Today Paola 1) closed a dozen tickets that Dianna Fisk had left open, 2) emailed Harold and Chris a list of tickets assigned to them, 3) emailed David H a few old transcription-related tickets assigned to Karen, and 4) next week she'll look into pending tickets assigned to Becky.)

All agreed that we should spend at least 2 days on SF items ONLY before the Texas meeting.

Next steps in the post-megafile world

[Chris] https://www.ebi.ac.uk/panda/jira/browse/GO-222

I'd like to push on with subtasks 5 and 6 since this should simplify the file dependencies

Tentatively agreed that disjoints should and taxon constraints should go into main file,  with the exception of GCI disjoints - pending testing in OE
TODO - David to test OE with editors GO file + disjoints, with a global filter in place to remove them from view.
 Note that reasoning with taxon constraints won't work without expansion.
 TODO - Chris to add make option for GCI expansion (EL version) of taxon constraint assertions.

Follow-up: Fixing assert inferences cycle

Any Progress?

Notes from two weeks ago: Still on hold for now. Still a bug in the report. Open a JIRA item to report this (David OS). For the moment we are nor not asserting any inferences. Should we turn them on? Remove the redundancy stripping and then turn them back on.

DONE: DOS to move details from google doc to JIRA ticket.

Follow-up: TG template for organelle parts (lumen, membrane)

See Jira ticket: https://www.ebi.ac.uk/panda/jira/browse/GO-185

We agreed this would have to wait for the megafile (sorry, "editors' file"). Shall we schedule work/completion now, or do we want to set a lower priority for this task while we iron out details?

Agreed - no TG template.  But there should be a standard design pattern for this.  
See slides attached to ticket for new proposed relation.  
DOS to add this relation to RO and sketch design pattern.

Follow-up: TG template for 'catabolism to'

Let's review the inferred parents.

 [Term] id: GO:1902706 name: hexose catabolic process to acetate 
 namespace: biological_process 
 def: "The chemical reactions and pathways resulting in the breakdown of hexose to acetate." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744] 
 synonym: "acidogenesis" BROAD [GOC:tt] 
 synonym: "hexose breakdown to acetate" EXACT [GOC:TermGenie]  
 synonym: "hexose catabolism to acetate" EXACT [GOC:TermGenie] 
 synonym: "hexose degradation to acetate" EXACT [GOC:TermGenie] 
 is_a: GO:0006083 {is_inferred="true"} ! acetate metabolic process 
 is_a: GO:0019320 {is_inferred="true"} ! hexose catabolic process 
 intersection_of: GO:0009056 ! catabolic process 
 intersection_of: has_input CHEBI:18133 ! hexose   
 intersection_of: has_output CHEBI:30089 ! acetate 
 relationship: has_input CHEBI:18133 {is_inferred="true"} ! hexose 
 relationship: has_output CHEBI:30089 {is_inferred="true"} ! acetate 
 created_by: tb creation_date: 2014-02-19T18:43:23Z  
 Modified relations for term GO:0019658 with label: glucose catabolic process to lactate and acetate	
 id: GO:0019658 
 is_a: GO:0019659 {is_inferred="true"} ! glucose catabolic process to lactate 
 is_a: GO:0019662 ! non-glycolytic fermentation 
 is_a: GO:1902706 {is_inferred="true"} ! hexose catabolic process to acetate 
 intersection_of: GO:0009056 ! catabolic process 
 intersection_of: has_input CHEBI:17234 ! glucose 
 intersection_of: has_output CHEBI:24996 ! lactate 
 intersection_of: has_output CHEBI:30089 ! acetate 
 relationship: has_input CHEBI:17234 {is_inferred="true"} ! glucose 
 relationship: has_output CHEBI:24996 {is_inferred="true"} ! lactate 
 relationship: has_output CHEBI:30089 {is_inferred="true"} ! acetate
 Discussion of whether catabolic process and biosynthetic process should be disjoint (they currently are declared to be). 
 Harold: You don't want every ATP -> ADP reaction being classed as ADP biosynthesis.
 Jane: But there are definitely some (many?) cases that are considered biosynthesis and that are catabolic - we argued about this extensively re request for 'Hydrogen biosynthesis'
 General agreement - shouldn't be disjoint, requires judgment?
 Note that we don't automatically get classification as X biosynthesis based on has_output' - also needs biosynthesis genus.