Ontology meeting 2015-06-04

Attendees:

Minutes:

X dependent process & involved in

We have many X-dependent process terms. My initial reading of the names and definitions of these terms was that the X must be upstream, but typically X (implicitly) is treated as part of the process that depends on it, as shown by the large number of cases of term of the form X involved in X dependent process Y. This may be a good thing, but perhaps could be made clearer with some design patterns.

Prompted by: https://sourceforge.net/p/geneontology/ontology-requests/11713/#a397

Follow-up: New TG templates

Where are we with action items on these? Copying over from last week:

If the export templates are ready, we'll test them, then advertise them along with the ones below:

cellular component binding

cellular component organization

import_across_membrane

import_across_plasma_membrane

import_into_cell

We resolved to change the template for 'cellular component organization' to make 'cellular process' the genus 
(let’s try that, rather than further up the graph, and see what happens). 
Jira ticket: https://www.ebi.ac.uk/panda/jira/browse/GO-327

Once that's done and tested, we can advertise the 5 templates above.

As for the export templates, David OS is still working on them. He'll check that he has all the relevant info in one ticket.

Follow-up: No more merges

Where are we with action items on this? There was a bit of discussion at the managers call too. Copying over from last week:

Ref: https://github.com/owlcs/owlapi/issues/317

Obsolete instead and use the replace tag, as discussed in the recent past.

Chris tracked the Protege request here as it's best done as an extension to Jim's plugin: https://github.com/balhoff/obo-actions/issues/1

Any further action item we need to take to make sure this becomes regular practice in GO?

We need a long-term plan to deal with these changes, alert the databases, make sure the infrastructure is up to speed.
David H will ask Harold about MGI expected behavior.
We need to make a detailed proposal and bring it up as a heads-up on an annotation call.
In the meantime, as a short-term solution, we’ll work on the one outlined in the github link above. Then we need to test AmiGO load before going live. 

(Related) AI for Chris: remember to prepend all existing obsolete term names with ‘obsolete’ 
(see http://wiki.geneontology.org/index.php/Ontology_meeting_2015-04-23#Follow-up:_Prefixing_of_obsolete_to_label_of_all_obsoletes)