Ontology meeting 2017-11-27

Conference Line

• Zoom: https://stanford.zoom.us/j/828418143

Agenda

GH project link

https://github.com/geneontology/go-ontology/projects/1

Editors Guidelines

• Closing old tickets
• When? How?
• It seems an SOP would be helpful here.

Minutes

• On call: Barbara, Chris, Eric, Harold, Jim, Judy, Kimberly, Pascale, Paul, Tanya

Synaptic vesicle endocytosis

• Barbara will modify definition of existing term to be inclusive of more mechanisms
• Then create more specific mechanism-based child terms

Editors guidelines

• What to do with old tickets?
• For some it makes sense to keep, especially if the ticket is wrt an issue that is currently under discussion
• Specific tickets that require feedback but don't get it could be closed - use 'waiting for feedback' label for these
  • How long should we wait for feedback?
  • Six weeks - first reminder
  • Next six weeks - change or close
  • All contributors to the ticket should be listed as assignees
  • Can automation help with sending reminders?
    • Look for the label 'waiting for feedback' and given a certain amount of time would prompt a reminder update to the ticket
    • 21 open tickets with 'waiting for feedback' label
  • https://help.github.com/articles/understanding-the-search-syntax/
  • https://github.com/geneontology/go-ontology/issues?q=is%3Aopen+is%3Aissue+label%3A%22waiting+for+feedback%22+sort%3Aupdated-asc
• Use a label to distinguish these tickets - 'won't fix'
• When editors have time, they should try to review old tickets
• Perhaps a jamboree in the future to address old tickets would be helpful

Adding annotation rules

• See https://github.com/geneontology/go-site/tree/master/metadata/rules
• First check existing rule summary to avoid duplication of rules
• Then update the list by adding a new rule
• Generate a pull request and assign to Eric so he can create the rule

Reasoning over roles in Protege

• https://github.com/geneontology/go-ontology/issues/14626
• Does this happen?
• For example, 'cocaine binding' should infer to be a type of 'drug binding'
• Something wrong with the import chain? Is there a relationship missing in the ChEBI import?
• Drugs are not listed as leaf nodes in Protege

Checking for obsolete terms in external ontologies

• We need to make sure external ontologies are kept in sync
• https://github.com/geneontology/go-ontology/issues/14605