Ontology meeting 2018-06-04

Conference Line

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

Agenda

GH project link

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

Editors Discussion

Ontology Developers' workshop possibility- Geneva in September?

• David, Pascale and Kimberly will discuss possible dates and make a doodle poll.

Outstanding Pull Requests

There are now 29 open requests. We are getting better.

• chris: 15
• pascale: 5
• dos: 4 (MF refactoring; Pascale will try to close)
• eric: 2
• jim: 1
• karen: 1*
• barbara: 1*

• Need developers to fix

Regenerate Imports File

What is the status of Docker and do we have documentation on its use?

Obsoletion plugin for Protege

Does everyone have Jim's plugin? If not we should all install it and I will update the documentation. What is the status of the merge plugin?

DBxrefs

There was a recent thread about the scope of dbxrefs in the ontology. If we are going to use the dbxrefs to seed an alignment between GO Rhea and Reactome, at least for MF, they should be 1:1.

Did this get covered last week?

GO subsets (slims)

• Pascale
• Create all yaml files https://github.com/geneontology/go-ontology/pull/14277

(pull request failing but we can sort this out another time)

• List of subsets:
• Active:
  • goslim_agr.yaml -> 59 classes - active
  • goslim_pombe.yaml -> 55 classes -active
  • goslim_synapse.yaml -> 344 classes- active
  • goslim_mouse.yaml -> 45 classes - active

• • goslim_aspergillus.yaml -> 85 classes - email xx
  • goslim_candida.yaml -> 89 classes - email xx
  • goslim_goa.yaml -> not used - email Tony and George
  • goslim_metagenomics.yaml -> 116 classes - who to contact ??
  • goslim_pir.yaml -> 462 classes - email Darren
  • goslim_plant.yaml -> 99 classes - email Tanya
  • goslim_virus.yaml -> 29 classes - email Philippe, Patrick and - others ?
  • goslim_yeast.yaml -> 169 classes - email Stacia and Suzi A

• Check at ontology call:
  • goantislim_grouping.yaml -> 49 classes, mostly 'x part'
  • goslim_chembl.yaml -> 310 classes
  • goslim_generic.yaml -> 150 classes
  • gosubset_prok.yaml (status: obsolete)
  • mf_needs_review.yaml
  • termgenie_unvetted.yaml -> all terms are (obviously) obsolete. Is this useful ?
  • virus_checked.yaml -> 244 classes

Minutes

• On call: