Ontology meeting 2017-04-14: Difference between revisions
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**Trying to standardize pipelines for ontology release | **Trying to standardize pipelines for ontology release | ||
**To fix in GO, Chris changed the import pipeline to filter GO from other, external ontologies | **To fix in GO, Chris changed the import pipeline to filter GO from other, external ontologies | ||
**Tanya - is there a way to see the taxon constraints outside of Protege? | |||
***Chris - there is an open AmiGO ticket for this | |||
Revision as of 12:36, 14 April 2017
- Bluejeans: https://bluejeans.com/164681006
Agenda
Documentation
- Format for documentation on github: Kimberly and David have been working on the SOP Google document.
- Need to test this on a new user and transition to github md format
GOC Meeting, Corvallis, Oregon
- GOC Meeting Agenda - Ontology-Related Issues
- http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda
- What to discuss in Corvallis?
- Is there time for more ontology editors training in Corvallis or should we try to schedule another workshop over the summer?
Term Genie-type Requests
- We are getting tickets for adding terms that previously would have come in through TermGenie.
- What is the long-term plan for replacing TermGenie?
Ontology Tickets
Editors Rota
- David H away 4/14 - 4/23
- Kimberly away 4/17 - 4/22
- Pascale away 4/14 - ?
Minutes
- On call: Chris, Harold, Karen, Kimberly, Moni, Pascale, Tanya
- github email notifications don't always seem to correspond to the person who actually commented
- not sure what's going on
Documentation
- Please check Google document and give feedback
- Organization
- Protege
- github
- Ontology editing
- readthedocs - use this
Files for download
- What files are people loading locally? If older, go-basic.obo, is that still being fully supported?
- go-basic.obo is behind; Chris will look into this
- Check this URL: geneontology.org/page/download-ontology
GOC Meeting - Corvallis, Oregon
- Ontology issues
- Single-step biological processes - can/should be deleted or removed?
- Modified protein binding proposal
- Proposal was emailed from Pascale
- Please look over and we can talk about in ~two weeks (or sooner)?
- Ontology editing
- Karen, Harold will not be in attendance, so probably not the best time for a full blown workshop
- Equivalence axioms - editors would like more guidelines on how to construct these
- This is why the design patterns are so critical
- Github ticket is open to remove the design patterns repo into the ontology repo
- Workshop this summer? Bar Harbor?
TermGenie
- Long-term plans for TermGenie
- Design patterns will drive TermGenie in the future
- Will use a table-like editor; work on this is progressing
- Would be good for editors to familiarize themselves with the design patterns to be ready for the new system
Ontology Tickets
- Import pipeline
- GO imports other ontologies to be able to make linkages between them or make use of things like NCBITaxon
- However, some ontologies, like RO, contain subsets of other ontologies, like GO, and they can go stale in one or the other
- Trying to standardize pipelines for ontology release
- To fix in GO, Chris changed the import pipeline to filter GO from other, external ontologies
- Tanya - is there a way to see the taxon constraints outside of Protege?
- Chris - there is an open AmiGO ticket for this