Ontology meeting 2018-04-23

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Conference Line

Agenda

GH project link

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

Editors Discussion

GOC meeting and SAB are coming up in three weeks. I think we are in good shape with respect to reports etc.


Minutes

  • On call: Barbara, Chris, David H., Eric, Harold, Jim, Karen, Kimberly, Laurent-Philippe, Pascale, Tanya

Drug terms in GO

  • Feedback we’ve gotten from a few contacts in Pharma is that GO is not the main source of functional information wrt gene products and GO

Trypanosome tickets

  • reservosome
    • Are these organelles lysosomes, endosomes, or do they have characteristics of both?
    • Should this be a new term in the ontology or a synonym of an existing term?
      • How about adding narrow synonyms annotated with a taxon ID?
    • How will users find the right annotations to this term, even in a GO-CAM model, if it is one of many synonyms?
    • We need more biological expertise here.

Requesting new terms

  • TAIR has a new curator; the nice guidelines that were written previously do not show up at the top of the GitHub page for Issues
  • Can we put the Contributing doc linked from a banner at the top of the page?
  • It used to be part of GitHub that a contributing doc would automatically show up at the top of the issues(?) page

Vacuolar acidification

  • This term is believed to be a process, not just a phenotype.

Protein binding child terms

  • Will we continue to create the more specific child terms or we will just use protein binding and eventually mine the With/From field for more specific annotations?
  • We need to make a good argument for using simpler terms along with a way to query more specific annotations.
  • For now, we will continue to create the more specific terms but think about the best way to make the query.
  • Use cases!! Do the more specific terms ever show up in enrichment analysis or are they more often used for queries or GO term display on gene pages? These two uses seem to be at odds for ontology development.

Robot and OWL tools

  • To allow people to run anything in MAKEFILE with docker
  • Need to figure out a time to train editors on this