Ontology meeting 2014-02-13
Attendees: Paola, Heiko, Jane, David OS, David H, Harold, Chris, Judy
Minutes: Paola
Roll-over funding
Any news?
Judy is optimistic, will hopefully know soon.
Follow-up: megafile
Notes and plan of action from last week:
Proposed import dependencies and dataflow post-megafile:
Autogenerated example: http://purl.obolibrary.org/obo/go/extensions/go-plus
Everyone still needs to do some things with GO-plus. Load the file--save--convert to owl etc. Check in the same time next week. If all is good, then we will make the switch after the call. SOP for editing will not change. We will no longer edit logical defs in a separate file.
Useful links:
http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar
http://build.berkeleybop.org/userContent/owltools/owltools
https://code.google.com/p/owltools/wiki/InstallOWLTools
Will switch now! Heiko will stop TG. Chris will e-mail go list.
owl-to-obo issues: should get better soon. Remember to update the extensions directory.
Follow-up: Fixing assert inferences cycle - Bumped to next week
Any Progress?
Notes from last week: 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.
Follow-up: X metabolism/catabolism to Y
Have the templates below been tested?
Notes from last week: Several requests for these types of terms have come through the termgenie free-form recently. Could we generate a new TG template for these with has_input and has_output ChEBI chemicals?
The templates are ready for testing:
- biosynthesis_from
- biosynthesis_via
- catabolism_to
- catabolism_via
Testing is in progress (by Tanya). Then Tanya can announce the new templates please.
Should transport and metabolism be disjoint ?
(DOS)
In discussion of formal definitions of transport, Chris wrote: " I would still like to move towards a single relation for the cargo (which will require more disjointness, e/g/ between metabolism and transport, so that the genus can do the work of the specific relation without confusion)." .... Note that PomBase is using has_input at the moment.
I've looked into this further and think it makes sense for some processes (e.g. 'electron transport') to be both and metabolic processes AND transport. Please can we discuss this.
Note that if some processes can be both, then I think it is safer to have a transport specific relation. This is relatively easy to define logically.
From discussion: We agreed not to add the disjoints and will therefore need a specific transport relation. Choosing has_input as the relation to use here would be purely a matter of convention (has_output could just as easily have been chosen) - so having a more specific relation should be more intuitive for editors and annotators.