Difference between revisions of "Ontology meeting 2018-06-04"

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(Ontology Developers' workshop possibility- Geneva in late August (or maybe September)?)
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== Editors Discussion ==
 
== Editors Discussion ==
  
===Ontology Developers' workshop possibility- Geneva in late August (or maybe September)?===
+
===Ontology Developers' workshop possibility- Geneva in September?===
* Topics
+
* David, Pascale and Kimberly will discuss possible dates and make a doodle poll.
** GH Jamboree
 
** Creating necessary and sufficient logical definitions (We never got around to this in Berkeley)
 
** Updating Documentation
 
** GO-Rhea-Reactome alignment
 
** Dealing with GH conflicts
 
  
 
=== Outstanding Pull Requests ===
 
=== Outstanding Pull Requests ===

Revision as of 05:30, 4 June 2018

Conference Line

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 26 open requests. We are getting better.

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)

(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: