Projects stand up meeting 2021-11-03
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Attendees
- Present:
- Regrets:
- Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris
Announcements
Discussion points
Alliance all hands
next meeting is early December; is there anything GO wants to present?
- Chris: suggestion pathway widget
- Kimberly; maybe present future plans?
- Chris will add this to an Alliance Pathways call
- Suggestions for Alliance All Hands Topics
Switching default to isa-part-of closure in amigo
- do we proceed?
2021 progress reports
What is needed and when?
- Need to ask Paul whether this is due for the last cycle of the grant
- Pascale : will create a new doc for this
Japonicus db
- Now in Metadata as a MOD, loaded by Val and Midori
- We have no formal process for integrating new MODs; how do we decide to 'accept' a new MOD?
- Picked up by the pipeline process; we now have a new source in the public release
- New MODs also have entries in the stats
- What are other implications?
Discussion
- METADATA should also have tickets, not just PRs
- Internal SOP:
- people would propose species, and the GOC agrees (or not) to include the species our data set
- if this has not been done, maybe we revert the merge? until things have been decided
- also need to document all changes that need to be made, for eg in the geneontology.org stats
- update metadata
- update stats code: http://geneontology.org/docs/contributing-to-go/
- update stats dropdown
- add to amigo metadata
- Action Item improve external SOP
- Action Item add GH ticket template with check list
Priorities & objectives for remainder of 2021
API redesign
Chris, Seth, were to define objectives for the project Right now - only fixes; only Sierra for now
Noctua
- Technical
- Wrap up outstanding curator request tickets in current project
- Resources needed: Tremayne (full time for xx time); Kimberly, Seth, Jim
- Will focus on fixing issues that create bad data and closing issues that are almost done
- Implement annotation and model copy
- Shallow model copy: Resources needed: Dustin + Kimberly
- Annotation copy: Tremayne has a prototype
- Clean up bad or incorrect data highest priority
- Ontology terms
- Relations
- Evidence codes
- Noctua visual editor:
- Resources needed: Tremayne 1 month (November 2021 ??) + Paul T
- Wrap up outstanding curator request tickets in current project
- Documentation/Guidelines
- Annotation extension usage
- Process-specific guidelines
- Signaling pathways
- Metabolism
- Gene expression
- Improve error reports when running the ShEx (that appear when running the reasoner)
- Resources needed: David, Kimberly, Jim, Seth
MOD imports
- Import annotation sets from Protein2GO (SGD and WB)
- Resources: Dustin, Kimberly
- Resolve outstanding GPAD output issues
- Resources: Jim, Kimberly
- Put WB fully into production?
- Create roadmap for annotation data exchange amongst all relevant resources
- Meeting last Wed with GOA, FlyBase, wormbase, SGD to discuss dataflow, will meet again today
- 5 main things to address:
- Alex is importing Noctua GPAD in P2GO, but this doesn't seem to be working, he is investigating
- Patrick and Sylvain from SP are making GO-CAM, but these are 'development', so not exported
- How do GO annotations get into Alliance? Probably this just needs documentation
- ---> This gets in by the GO Monthly release
- Inferred annotations generated by reasoning: people dont know what gets generated and output; inferences generated not always useful. Needs to look into this more closely, as part of the large GPAD output discussion
- Redundant annotations
- 5 main things to address:
- Meeting last Wed with GOA, FlyBase, wormbase, SGD to discuss dataflow, will meet again today
New Taxon constraints
- Some terms need logical definitions
- usage of occurs_in for inferences would add a number of constraints
- AI set up a jamboree to complete taxon constraints?
Ontology
- Pascale contacted by Gerard Manning to classify protein kinases
- GO helpdesk contacted by TEMTIA, (https://temtia.org/) annotating epithelial and mesenchymal cellular phenotypes (email 21 October 2021)
- Chris and Mike also interested to join
- Opportunities to work with experts to improve the ontology and annotations
- Boomer + Reports by Anne: errors in GO-RHEA mappings
- ChEBI Roles: AI set up a jamboree to finish?
- Other projects
- transcription:
- epigenetic processes, miRNA, and related
- biological processes
- multiorganism processes:
- remove MF in BP (modulation of host x activity)
- fix high level terms to make browsing more logical
- Obsolete single step processes
- Implement design patterns
- transcription:
- Immunology/immune system processes + cytokine production terms
ECO-GO alignment
GOC meeting follow up
- Summary metrics workshop: https://docs.google.com/document/d/15tBWdDNQuw9IdfDKk0pxpuDjfrnW3vT-xKnwO8_c1D0/edit#
- API redesign would facilitate this
- AI set up a meeting to discuss which of these metrics we'd like to use
- Summary subsets workshop
- DONE Implementation documentation workshop suggestions - will discuss at the next annotation call
Project updates
Clean up Google drive, calendar, and GH to remove part project members
https://github.com/orgs/geneontology/people
Asynchrony issues in the release pipeline
https://github.com/geneontology/go-site/issues/1742