Ontology meeting 2014-10-23

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Plan A (if Chris can attend): Relationships

Follows up to GOC meeting discussion with Ruth on Annotation extension relationships. The action item was:

"Ontology group will dedicate a meeting to looking through the list of all relations used in annotation extensions. They will document those that are used in the ontology and will indicate whether the remainder should be dropped or kept and therefore documented. They will also note any new relations that need to be added e.g. adjacent_to.

Ontology group will make sure all the relationships are modeled correctly in LEGO."

Also see email thread 'Annotation extension relations'.

Chris writes: "The first task will be to migrate the editors version of the annotators extensions to RO to OWL so we can better manage these."

Plan B (if Chris can't attend): items below

Monthly review of Jira tickets

TermGenie and removal of all relationships

A couple of weeks ago, a TG commit resulted in the loss of ALL relationships from the obo file. This appears to be a one time glitch. We need to keep an eye on this, in case it reoccurs. We were made aware of this by Tony when the UniProt load of the GO failed.

A related issue: in the long run, we may want to consider moving away from term merges (as they may cause confusion in other ontologies) and just stick to 'obsolete + replaced by = merge; obsolete + consider = really obsolete'.

What's in the cell and what's out

Transcription factor activity

We had a request from the GOC meeting to add a union term for DNA-binding sequence-specific etc TF and protein-binding sequence-specific etc TF. What do we call this term? Should 'transcription factor activity' be reserved for DNA-binding only?

Other action items for the whole team from GOC meeting?

Minutes here: https://docs.google.com/document/d/1NonH97s8xEpDdx6DfonKPKI_RdHbbG-yft85UZtUmF0/edit#

Follow-up: cell migration

Action items from last call here: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-10-09#TG_template_for_.27cell_migration.27

For the ontology bit, I made a SF ticket and assigned it to myself with priority 7. TG fix also to-do at the time of writing (but we were all traveling!).