Ontology meeting 2018-06-04

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Revision as of 06:06, 4 June 2018 by Pascale (talk | contribs) (Editors Discussion)

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GH project link


Editors Discussion

Ontology Developers' workshop possibility- Geneva in late August (or maybe September)?

  • Topics
    • 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

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?


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 150 classes gosubset_prok.yaml (status: obsolete) mf_needs_review.yaml termgenie_unvetted.yaml -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


  • On call: