Annotation Conf. Call 2018-06-12

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Meeting URL

GO Annotation Meetings

  • Still will be Tuesdays at 8am PDT
  • Proposed meeting schedule:
    • 1st Tuesday: Alliance Gene Function
    • 2nd Tuesday: GO Consortium
    • 3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
    • 4th Tuesday: GO-CAM Working Group
    • 5th Tuesday: ad hoc, as needed
  • One Zoom URL for all - https://stanford.zoom.us/j/976175422

Annotation Reviews

Signaling Projects

Canonical Wnt Signaling

  • Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway'
    • Outstanding reviews: BHF-UCL, MGI, PARL, UniProt, Zfin
  • Review annotations wrt GO:0060070 'canonical Wnt signaling pathway'
    • Outstanding reviews: ARUK-UCL, BHF-UCL, DFLAT, MGI, ParkinsonsUK-UCL, UniProt, WB, Zfin
    • Annotation questions:
      • Wnt ligands can be part of canonical, non-canonical pathways and, as well, as part of one type of Wnt signaling pathway, can regulate another type of Wnt signaling pathway
        • Therefore, it's difficult to say definitively which Wnts are part of which types of Wnt signaling pathways; the experiments and context should be the guiding information
      • Downstream targets, e.g. Myc and cyclin D, should not be annotated to canonical Wnt signaling
        • Information about downstream targets could be captured, for example, as transcriptional targets in AEs, or better yet, in GO-CAM models that can more expressively show how they fit into a specific canonical Wnt signaling pathway
      • Upstream components
        • Gene products involved in secretion could be annotated to 'Wnt protein secretion' for now; GO-CAM models will also help to capture this information better

Annotation File Pipelines

Minutes

On call: George, Giulia, Harold, Kimberly, Li, Michele, Midori, Penelope, Rob, Ruth, Sabrina, Sandy, Stacia, Suzi A., Suzi L., Tanya, Val

GO Annotation Meetings

  • Will switch to new schedule above, effective immediately.
  • Will use https://stanford.zoom.us/j/976175422 for all calls
  • email will be sent to go-consortium list to alert everyone to the new schedule

Annotation Reviews

Signaling Projects

Canonical Wnt Signaling

  • Please continue to review canonical Wnt signaling annotations in the spreadsheets and mark the action you've taken
  • Only annotations that potentially need review were included in the spreadsheets
  • If there are any questions about whether or not a gene product, particularly a Wnt ligand, is part of or regulating Wnt signaling, feel free to post information about that in the relevant github ticket for discussion

Annotation File Pipelines

  • Groups can now post a Source URL in their datasets.yaml file to have annotation files, and gpi files, retrieved by GO Central as part of the new release pipeline
  • Monthly releases of GO data will be versioned and archived for end-users; will correspond to data that is displayed in AmiGO for that month
  • Daily snapshot releases are also available for consortium groups to consume the latest ontology files, or get timely feedback on annotation QA/QC
    • Note that we are still discussing what files groups should display on their respective websites, but leaning towards the versioned, monthly releases
  • Groups should start checking the reports files on snapshot.geneontology.org
    • There are multiple reports, but we are hoping to consolidate these into fewer files with one main report in HTML
    • Things that need to be addressed in reports:
      • URLs for annotation rules don't resolve to an accessible webpage - gives an Access denied page on geneontology.org (Harold will put in a ticket for this)
  • Note that information on annotation rules can be found on geneontology/go-site/metadata: https://github.com/geneontology/go-site/tree/master/metadata/rules
  • Issues that need to be reported wrt the annotation file pipelines should be added to the tracker at: https://github.com/geneontology/pipeline/issues
  • We need to confirm whether the various gp2 . files are still needed