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

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=== Outstanding Pull Requests ===
 
=== Outstanding Pull Requests ===
 
There are now 29 open requests. We are getting better.
 
There are now 29 open requests. We are getting better.
chris: 15
+
* chris: 15
pascale: 5
+
* pascale: 5
dos: 4 (MF refactoring; Pascale will try to close)
+
* dos: 4 (MF refactoring; Pascale will try to close)
eric: 2
+
* eric: 2
jim: 1
+
* jim: 1
karen: 1*
+
* karen: 1*
barbara: 1*
+
* barbara: 1*
  
 
* Need developers to fix
 
* Need developers to fix
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* Check at ontology call:  
 
* Check at ontology call:  
goantislim_grouping.yaml -> 49 classes, mostly 'x part'
+
** goantislim_grouping.yaml -> 49 classes, mostly 'x part'
goslim_chembl.yaml -> 310 classes
+
** goslim_chembl.yaml -> 310 classes
goslim_generic.yaml -> 150 classes
+
** goslim_generic.yaml -> 150 classes
gosubset_prok.yaml (status: obsolete)
+
** gosubset_prok.yaml (status: obsolete)
mf_needs_review.yaml
+
** mf_needs_review.yaml
termgenie_unvetted.yaml -> all terms are (obviously) obsolete. Is this useful ?  
+
** termgenie_unvetted.yaml -> all terms are (obviously) obsolete. Is this useful ?  
virus_checked.yaml -> 244 classes
+
** virus_checked.yaml -> 244 classes
  
 
= Minutes =
 
= Minutes =

Revision as of 07:53, 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 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)

(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: