Annotation Conf. Call 2017-06-13: Difference between revisions
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=== Noctua and GO-CAM Modeling === | === Noctua and GO-CAM Modeling === | ||
*Noctua/GO-CAM conference call every other Wednesday at 8am PST | *Noctua/GO-CAM conference call every other Wednesday at 8am PST - now on the GO Google calendar | ||
**Next call: Tomorrow, June 14th | **Next call: Tomorrow, June 14th | ||
**Goal: discuss and resolve any barriers to production annotation for consortium members | **Goal: discuss and resolve any barriers to production annotation for consortium members |
Revision as of 09:04, 13 June 2017
Bluejeans URL
https://bluejeans.com/993661940
Agenda
Review Corvallis Meeting Action Items and Discussion Points
Annotation Consistency Exercises
- We would like to continue with some form of annotation consistency exercises.
- Feedback from curators on previous exercises was that we'd perhaps maximized the usefulness of that approach, i.e. each group picks one paper for annotation and discussion.
- Other idea(s):
- Working groups for specific areas of annotation and/or ontology development
- Each group would work on a topic for three months (?) and then produce guidelines, decision trees, Noctua templates for annotation
- Need to establish priority topics, e.g. cell cycle, metabolism, signaling pathways
- Working groups for specific areas of annotation and/or ontology development
Community Interaction
Improve information on citing the GO in analytical publications
Documentation
- Action Item: Transfer annotation documentation from wiki, Google docs to github.
- Action Item: Ask all consortium members to share their curation documentation so we can develop a centralized, consistent source for GO.
Enrichment Analyses
Contact Paul Pavlidis about regular reanalysis of genomic automatic annotations
GO github Projects Page
https://github.com/orgs/geneontology/projects/1
High Throughput Papers
- Action Item: Provide curator documentation.
- Action Item: Update legacy annotations to use new HTP evidence codes.
Infrastructure
Use of YAML files for dataset provenance
Noctua and GO-CAM Modeling
- Noctua/GO-CAM conference call every other Wednesday at 8am PST - now on the GO Google calendar
- Next call: Tomorrow, June 14th
- Goal: discuss and resolve any barriers to production annotation for consortium members
- Action Item: Provide ways for users to recover and digest CAM units. Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.
- Action Item: Make sure that more granular ECO codes map to conventional GO three-letter codes; implement QC check for this.
- Action Item: Working group discussion of evidence on complex Noctua models
- This discussion happened on the Saturday afternoon of the meeting.
- Proposed solution is to uniquely identify instances of activities within models so that those activities can be associated with specific evidence on other edges (relations) within the model.
- Action Item: Establish a working group for when and how to use proteoforms in annotation.
Ontology Development
- BP Refactoring - Cellular Processes vs Multicellular Organism Processes vs Multi-Organism Processes
- Single-Step Processes - What genes/products are annotated to these terms? If removed from the ontology, would there be any information loss?
PAINT
- Discussion of which terms are not used for propagation
- Action Item: Encourage discussion between PAINT curators and other annotators about terms not used for propagation
- Action Item: Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes
- Action Item: Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.
- Action Item: Smooth out the challenge mechanism to make it easier to do make and resolve the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.
- Action Item: Get a list of families where terms have not been propagated (?) - Please check this one for clarity.
- Action Item: (added to github project board) Develop mechanism to trigger review of annotated PAINT families.
Transcription Decision Tree
Action item: Some modifications to decision tree will be made. Follow up?
Working Groups
- BP Refactoring - Cellular Processes vs Multicellular Organism Processes vs Multi-Organism Processes
- Single-Step Processes - What genes/products are annotated to these terms? If removed from the ontology, would there be any information loss?
- Topic-based Annotation Consistency Working Groups
Minutes
- On call: