Ontology meeting 2017-11-13

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Conference Line

Agenda

  • Logical definition vs. asserted terms

(Pascale): I have been removing SubClasses when they are redundant with the logical definition. But in some releases of the ontology they are not added back. Would it be safer to always assert both? See for example: GO:0015603 - I would have removed the SubClasses.

Yes -> TO DOCUMENT

GH project link

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


Discussion

  • On call: Barbara, Chris, Eric, Harold, Karen, Kimberly, Pascale, Tanya

Travis Checks

  • Can sometimes take a long time (e.g. 30-60 minutes)
  • This is not correlated with the number and types of changes
  • Travis checks take place in the cloud, so depending on usage/demand it could take a while
  • Editors can return to pull requests at a later time to confirm merge
  • May need to refresh browser to see final results
  • Can always check on the details of the Travis checks to see times, details
  • Chris checked Barbara's pull request and it looked like checks were taking on the order of 8-10 minutes
  • Perhaps this could be made faster
  • ACTION:Need to review workflow for starting work on a new branch when previous pull requests have not yet been merged
  • ACTION:Eric will try running Travis locally to see if there are any bottlenecks that can be addressed

Logical definition vs. asserted terms

(Pascale): I have been removing SubClasses when they are redundant with the logical definition. But in some releases of the ontology they are not added back. Would it be safer to always assert both? See for example: GO:0015603 - I would have removed the SubClasses.

Yes -> TO DOCUMENT

Transporter Logical Defs

 Option 1: 'transmembrane transporter activity'
 and ('transports or maintains localization of' some 'pyrimidine nucleotide-sugar')
  • OR
 Option 2: 'transporter activity'
 and ('transports or maintains localization of' some 'pyrimidine nucleotide-sugar')
 and ('results in transport across' some membrane)
  • Should use the less granular MF parent in the design pattern
  • Therefore, option 2 is the preferred pattern

Sexual Reproduction

  • ACTION:Karen will update the definition; Kimberly and Tanya will check

Term Request Documentation

  • Will make some changes and add a screenshot

Ontology Issues

Imports