Ontology meeting 2013-05-20

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Minutes: Tanya

Attendees: Judy, Harold, David, Heiko, Becky, Paola, Tanya, Chris, Jane


Judy’s Report from PRO-PO-GO meeting and part of BFO2 meeting


Chris: could introduce standard tag for ‘slated for obsoletion’, could set up RSS feed that use the tag, better: look at number of annotations to terms affected, evaluate this before deciding what to do next – resource: OntoBee (can see what resources are using GO), same functionality might be incorporated into AmiGO 2

Judy: documentation: if you are incorporating GO into your ontology, subscribe to this list, subscribe to the RSS feed


ACTION ITEM: continue to communicate, make files available, encourage subscription to appropriate mailing list, keep documentation up to date

ACTION ITEM: As part of obsoletion procedure, use OntoBee (http://www.ontobee.org/), navigate to ‘Ontologies that use the Class’, to detect usage elsewhere, even outside our mapping files. This is in addition to the check for usage of the term in annotations, checking using AmiGO (and/or QuickGO).

(B) Relations Ontology Effort

ACTION ITEM: For future obsoletion/announcement emails, refer to a two-week, open comment period.


Other business:

(1) New GO Editor interviews 6 interviewed by Skype 4 in the running looking at 6/12 and 6/13 for in person interviews

(2) CHEBI paper – email editor, has been hanging for 2.5 months

(3) Have a separate TG instance for biological attributes. Can request terms for that. ‘Membrane permeability’, any PATO + ENTITY.

(4) Protégé crashing with go-plus.owl loaded– Heiko: Hermit + Chebi = bad, David/Jane: Hermit gives good explanations, ELK is not great, even though it is fast. Heiko and Chris will investigate. Paola wants Jane and Becky to try loading the files.

(a) new subsets (b) New reasoner (from the Oxford group = hybrid of Hermit and ELK, still experimental, maybe too experimental for us for now.

(5) inferring is_a parentage when part_of parentage exists – GOOD or BAD – for future meeting, think about this