Ontology meeting 2017-07-14: Difference between revisions
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**Originally UBERON was designed for use with animals, but UBERON now also includes plants | **Originally UBERON was designed for use with animals, but UBERON now also includes plants | ||
**May ultimately be better to map to CARO (Common Anatomy Reference Ontology) class for anatomical structure | **May ultimately be better to map to CARO (Common Anatomy Reference Ontology) class for anatomical structure | ||
*[https://github.com/geneontology/go-ontology/issues/13725 Import new CHEBI term oxLDL (CHEBI_60151)] | |||
Revision as of 12:45, 14 July 2017
Conference Line
Agenda
DavidH will present a quick workaround for making logical definitions and subclasses using terms with single quotes.
Other discussion: https://github.com/geneontology/go-ontology/projects/1
August Meeting Agenda
- Will be added to the logistics page
Minutes
- On call: Barbara, Chris, David H., David OS, Eric, Jim, Judy, Karen, Kimberly, Paul T., Tanya
Editing Single Quote-Containing Terms
- Can set preferences to show term IDs, not names
- Also a shortcut for setting this preference in view
Review August Ontology Meeting Schedule
- Review OWL
- Review relations
- Review design patterns
- Review imports
- Most are straightforward except for ChEBI, which requires more data management
- Dealing with build failures
- Take screenshots when this happens for documentation
- Tickets
- Divide up backlog of tickets based on expertise, workload
Review github Tickets
- Will try to find tickets that will help bring Barbara up-to-speed
- Edit and release OBO-Edit files
- OBO-Edit provides nice visuals
- Resolution: use the daily release OBO file, instead of the editors OBO file
- Need SOP for avoiding ID clashes when 1 editor has multiple branches awaiting merge
- Protege should remember IDs between Protege session, if that option is selected in preferences in Auto-generated ID section of Setting ID ranges - this preference should be checked
- Do we need checks for potential collisions?
- To fix this, either hand edit the file, or abandon the working branch
- We do want to implement a check that no ID should ever have more than one label, definition, etc.
- Use of uberon classes for generic anatomical structures means taxon restrictions are too strict
- Anatomical structure in UBERON starts with zygote, which excludes PomBase curators from using children that are a descendant of terms that map up to an anatomical structure term
- Originally UBERON was designed for use with animals, but UBERON now also includes plants
- May ultimately be better to map to CARO (Common Anatomy Reference Ontology) class for anatomical structure
- Import new CHEBI term oxLDL (CHEBI_60151)