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

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: