Ontology meeting 2017-07-07
From GO Wiki
This week we will have Pascale go over the work she is doing on targeting.
Other discussion: https://github.com/geneontology/go-ontology/projects/1
- On call: Barbara, Chris, David H, David OS, Harold, Jim, Karen, Kimberly, Pascale
Protein Targeting vs Localization
- Pascale presented slides on the work on these terms
- Targeting refers to using a molecular signal to effect transport to a specific location
- Currently, targeting is a child of transport
- But is this in agreement with the original meaning of these terms?
- Some annotations to targeting have been made to the protein that is being targeted (i.e. the object of the transport)
- Precise meaning and correct use of targeting, importing, localizing terms seem to be unclear to curators
- Github ticket: merged protein targeting to nucleus and protein localization to nucleus
- Localization seems the broadest term that would include establishment (targeting, transport, import) and maintenance (anchoring)?
- Need to review term definitions for this discussion
- Localization defines the endpoint that experimenters look at
- As a high-level term, localization can be used to annotate when the mechanism is not known, but there is an (phenotypic) effect
- But we need to be clear, then, on what processes the establishment and maintenance terms refer to
- Review design patterns for these terms
- What is the meaning of 'directed movement'? How many terms does that really apply to? If there is only one mechanism, then is transport sufficient and establishment not needed?
- For targeting terms, we should look at the referenced papers to see if they elucidate the mechanism. From there, decide if the terms should be merged into transport terms?
- Add annotation comments to illustrate what types of activities/gene products should be annotated to the specific process terms
- Localization vs location - which makes most sense? Localization is probably the majority usage in the literature, so will stick with that.
Failed Travis Checks
- How to re-run
- Follow link to Travis
- Click on Restart build
- Note that whether or not this will fix the problem depends on why the build failed
- edit and release OBO files don't open in OBO-Edit
- Is this just the result of a simple header issue? Can it be fixed reasonably quickly?
- Do we want to continue doing any work in OBO-Edit?
- AI: David OS will investigate further and then we'll decide what OBO-Edit can/should be used for
- If you're going to obsolete a term, you need to make sure you've checked where else the term is used
- Logical definitions
- External ontologies?
- AI: Update documentation to reflect that checking how the term is used should be the first step.
- Always need to send out an email giving two-weeks notice for term obsoletion.
- We will review in August how to edit the md documentation files in github.
- Proposal - anyone can update the docs, but one person will be tasked with reviewing the pull requests and approving.
Adding Terms to the Imports
- See: https://github.com/geneontology/go-ontology/blob/master/docs/AddTermToImport.md
- Will review this pipeline in August
Suggestions for Review
- Not working? Can't suggest reviewers?
Cell Type-Specific Terms
- Added the last one?
- Need a plan for dealing with new terms going forward?
Issues with Merges
- Travis build is failing, because the merged term ID appears to still exist in the ontology
- Need to double-check the order of the merge
- The losing term had an alt_id of its own
- Note: don't search Protege with term ids; use an underscore or the IRI fragment
- Will review this merge together on next Friday's call
August Meeting Agenda
- Will be added to the logistics page