Ontology meeting 2018-04-30
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Conference Line
Agenda
GH project link
https://github.com/geneontology/go-ontology/projects/1
Editors Discussion
Discussion of slim maintenance: (Pascale) https://docs.google.com/document/d/1KMASaUdOJSwB1EClRQ69RK77Wqc7AdbWa8EcENidLjM/edit
Minutes
- On call: Barbara, Chris, David H., Eric, Harold, Jim, Judy, Karen, Kimberly, Laurent-Philippe, Pascale, Paul T., Tanya
Outstanding Pull Requests
- There are a lot; please check
- If done, then merge
- Assign a reviewer if waiting for feedback
- Reviewer is not typically merging, but they could if everything is okay
Slim Maintenance
- Pascale looked into who is maintaining what slims
- Information about slims will ultimately go into the subsets.yaml file
- Need to cross-check what is included in the header of the ontology file and what is tracked in the subsets.yaml file
- Should GO archive/obsolete slim subsets that are not maintained?
- What about the prokaryotic subset?
- This pre-dated taxon constraints, but should perhaps be retired.
- We need to reach out and make sure that this is not being used for purposes we haven't thought about.
- AI: Chris/Pascale will add more entries to the subsets.yaml file
- The subsets.yaml file will ultimately drive what is displayed on the website
- What is expected from the person/group who actually maintains the slim?
- Does the person/group need to edit the ontology?
- They at least need to submit tickets to go-ontology, if needed
- They at least need to keep the terms up-to-date
- Does the person/group need to edit the ontology?
- Any GO editor will be allowed to update any slim file
- What are the biological guidelines for maintaining a slim?
- We need to have documentation for this
- In OWL the correct terminology is 'subset'
- Not all subsets are slims; the purposes of a slim vs a subset may be different
- Should we make this distinction clear by using different values for the type field in the subsets.yaml file?
- If so, how?
Precomposed Terms vs Creating GO terms on-the-fly
- SynGO has requested some precomposed terms that are similar to some terms that exist in the ontology
- There is some concern about how this will scale
- Groups could instead precompose as needed
- What would happen to these terms?
- How will they be used for analysis?
- Will those terms get any kind of ID?
- What if other groups wanted to use these terms for analysis?
- What implications does this have for reproducibility?
- Experts often want very specific terms
- Some of these have been added to the ontology, but now some of these are being removed
- What's the best thing to do?
- AI: Barbara will try to get some feedback from users on terms and enrichment expected from GO users at the UCL workshop
Enrichment Results
- David H noticing some changes in enrichment analyses
- Some new enrichment results are showing enrichment to high-level terms that we might not expect to see in enrichment results
- Is this due to changes in annotation or changes in the ontology?
- AI: Refactor the cellular process branch of the ontology.
Signaling Pathways
- When should we create distinct terms for different signaling pathways?
- When there are different downstream effectors?
- Specifically wrt regulation terms for the ERBB4 signaling pathway, we will request that the curator annotate to the less specific parent terms
- AI: Pascale will get feedback on the different ERBB signaling pathway terms and if they are really needed in GO
Assertion that appear and disappear
- AI: Harold has been put on the case; Val should supply more information about ontology versions
- It's not clear from the ontology file what is going on
- The same terms seem to be disappearing
SAB
- David will present the ontology slides
- Will not go into great detail on the specific ontology actions, more about priorities and procedures