Ontology meeting 2016-06-16

Attendees:

Regrets: Tanya

Minutes:

ETINEs update

Report on work done during the past week.

https://github.com/geneontology/go-ontology/issues/12315

- [x]  Using information in [etines.tsv](https://github.com/geneontology/go-ontology/blob/master/refactoring_inference_pipeline/etines.tsv), strip 'inferred-from=true tag where status = 1 and manual =1.  This needs to be scripted.

ETINE processing: Old file used! (DOS: my fault!) Need to either roll back or project the list of S=1 and M=1 etines onto the current ontology.

Changes to inference pipeline:

- [x] Move (tagged) inferred classifications to an imported file https://github.com/ontodev/robot/issues/66 https://github.com/ontodev/robot/pull/81
- [x] Ensure  classifications are tagged https://github.com/ontodev/robot/issues/67 https://github.com/ontodev/robot/pull/81
- [x] switch off assertion in TG (or TBD: change TG architecture) @hdietze 
   -  (Better to generate the assertions, but push the imported file?)
   -  Treat relaxation to relationship differently to actual inference?  Should these actually be in the editor's file?  They don't come in via other routes anymore?
- [ ] sign off from all editors that they have updated their OE config
   - [ ] @dosumis 
   - [ ] @mcourtot 
   - [ ] @paolaroncaglia 
   - [ ] @tberardini 
   - [ ] @ukemi 
- [x] modify jenkins job  build.berkeleybop.org/view/GO/job/build-go-assert-inferences
    - Runs with every commit, and regenerates go_inferences.obo
- [x] ensure redundant axioms are only removed from release files, never editors: https://github.com/ontodev/robot/issues/16
    - Note - It should be possible to devise a safe redundancy stripping mechanism for the editors file once we can easily separate instantiated inferences.
- [ ] Add more documentation about how editing practises will change  = OE setup @dosumis

To discuss

1. How often inference happens

• Should inference happen automatically at every commit, or do we want to retain the reporting step?
• Current new setting is automatic at every commit. There is an ~ 30' lag from commit to the change, so eds won't see this until they update again.

2. How do editors track changes: Diffs on inference file???

Xrefs to Reactome

Looks like this wasn't fully addressed yet. See email thread here:

https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007619.html

https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007620.html

https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007621.html