Annotation Conf. Call 2017-06-13

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Bluejeans URL

https://bluejeans.com/993661940

Agenda

Review Corvallis Meeting Action Items and Discussion Points

AGR

  • AGR gene pages present a GO slim for function Mouse Med28
  • Should there be a single 'generic' GO slim or should there be a 'generic GO slim' as well as organism-specific GO slims?
  • Best practices in GO slim creation?

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, reviewed PAINT families
      • Publicize the outcome of the work - blog, publication
      • Need to establish priority topics, e.g. cell cycle, metabolism, signaling pathways

Annotation Qualifiers

  • We discussed using an expanded list of qualifiers to relate gene/gene products and GO terms
    • This allows for more expressive, and more accurate, annotation
    • This is also necessary for translating Noctua models into GPAD/GAF annotation files
  • Action Item: Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?
  • Action Item: Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.

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

High Throughput Papers

  • Moving forward with new HTP evidence codes?
  • Action Item: Provide curator documentation on how to apply HTP evidence codes.
  • Action Item: Update legacy annotations to use new HTP evidence codes.

Infrastructure

Licensing and GO

  • The GO license should be renewed soon.
  • Action Item: Form a working group to investigate different levels of licensing.

Noctua and GO-CAM Modeling

  • Noctua/GO-CAM conference call every other Wednesday at 8am PST - now on the GO Google calendar
  • Action Item: Provide ways for users to recover and digest CAM units.
    • Rule-based generations of text statements from models
    • Cytoscape view of network described
    • Others?
  • 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, attached to specific gene products, 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

  • Action Item: Form working groups to examine:
    • 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
  • GO Licensing
  • GO Slims
  • High Throughput Papers
  • 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
  • Transcription Decision Tree

New connection info

starting next call, June 27, 2017: https://stanford.zoom.us/j/976175422

Minutes

  • On call: Alice, Emily, George, Giulia, Harold, David, Judy, Karen, Kevin, Kimberly, Li, Pascale, Penelope, Petra, Sabrina, Shur-Jen, Stacia, Stan, Tanya

AGR

  • GO slims - need working group to establish best practices for creation and maintenance of GO slims

Annotation Consistency Exercises

  • Working groups - what curators can participate?
    • Some groups prioritize on a paper-by-paper approach; how can we integrate this?
  • How can we best align curation priorities within groups with these working groups?
  • Term-specific annotation guidelines

Annotation Qualifiers

  • Need a working group here ASAP
  • Look at Noctua models
  • Review legacy annotations
  • Need review of pipeline for annotations from inactive groups

HTP Papers

  • Still some discussion here on exactly what constitutes an HTP paper