Ontology meeting 2017-07-14
From GO Wiki
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
- 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
- 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)
- Chris will investigate further
- ntr: process for D-erythroascorbic acid, biosynthesis
- Placement of this new term - under vitamin? under co-factor?
- The vitamin and co-factor portion of GO doesn't completely align with ChEBI roles
- Should GO have things like drug, hormone, toxin, vitamin?
- Should we obsolete 'vitamin' terms?
- Will discuss and try to document what happens in August
- Obsolete virus receptor activity ?
- Paul T. proposed grouping term of 'highjacked molecular function' for terms like 'virus receptor activity'
- Should the term be obsoleted? Can terms like this be isolated in a separate branch of the MF?