Manager Call 2018-04-19
Agenda
NYC Meeting Agenda
- Start working on the agenda in more details
- https://github.com/geneontology/go-ontology/milestone/5
- https://github.com/geneontology/go-annotation/milestone/2
- Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit
- SAB agenda, plans
ACTION POINT Please everyone make slides for your part by Friday April 27 Slides should be added here: https://drive.google.com/drive/u/0/folders/1iOGHjKc9FN_ShrlNEW0CvOmJANzXqep-
Working Groups/Projects
HTP Codes
RCA Evidence Code
- Need to work with several groups to review their annotations:
- Gramene (35815 annotations)
- As an example, 2929 RCA Molecular Function annotations
- Date: 20060831
- Reference: GR_REF:8030
- Manual review of mappings; can we suggest ISM?
- GeneDB
- Some annotations from reviews, but some to papers that describe a systems analysis that is probably more in line with the original intent of RCA
- RCA -> CCA (combined computational analysis)??
- EcoCyc
- AgBase
- AspGD
- PAMGO_MGG
- If we decide to keep RCA, then we'd need to remove the one-year limit; it doesn't make sense.
Documentation
GO Site- Can we explicitly identify which tools/file formats are compatible with which relations/extensions (curator facing)
- SGD wants list of Noctua relations via category- BP to MF, to BP, to CC, MF to BP...
Protein2GO- GO RELS are not in RO. Eliminate some?
- Long term plans? including identifying/removing least common annotation extensions after re-annotation
Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928
Working Group Meetings
- Quarterly?
- Rotate between ontology and annotation (small, focused groups)
- Test virtual meetings, but still focused on the task
Noctua
1.0 Rollout
- Merge Tremayne's fork with Noctua-dev for further testing
- Some outstanding issues on SAE
- Single source file for MODs to consume
Reactome Imports
- David, Kimberly have looked at some imports/translations
- Ben's work looks to be potentially very useful and promising for seeding templates, models
- Will probably require significant manual input, refinement, testing
End User Tools
- What plans do we have for implementing consumption and display of GO-CAM models?
- How does the AGR GO working group fit into this task?
- https://github.com/geneontology/noctua/issues/519
GO Helpdesk
Discuss this ticket: https://github.com/geneontology/go-site/issues/584
This is up for discussion at next Manager meeting. Seems like an outreach task. There is some documentation on GO for curators- 1st step is to contact GO. No guidelines on what GO should do (how to train, submit, who is responsible for maintaining...)
Email forwarded to Suzi A.
Ontology
Announcing changes to the wider user community
- This was brought up by Birgit in the protein complex merge ticket - she was suggesting we make an announcement. However we never made annoucements before (except for obsoletions); should we start? What would be the guidelines? For example when a merge affects more than 100, 1000 annotations ? EXP only ?
- Pascale: changes to definitions of root terms: https://github.com/geneontology/go-ontology/issues/14899; isn't this a big change ? How should we notify people?
- Should we create a label in GH 'Major change', so we can easily pull out the tickets and show them at Ontology and Annotation calls ? (perhaps in annual reports as well)
- Pascale: suggestion: create a new label 'major change' and announce them either on twitter and/or on the website as user stories (or whatever it's called).