Annotation Conf. Call 2018-08-14: Difference between revisions

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*[https://github.com/geneontology/go-annotation/issues/2045 Automatic deletion of ND-evidenced annotations]
*[https://github.com/geneontology/go-annotation/issues/2045 Automatic deletion of ND-evidenced annotations]
*ND annotations to a root node term are intended to signify that the curator looked at all available evidence and the MF, BP, or CC of a gene/gene product is not known
*ND annotations to a root node term are intended to signify that the curator looked at all available evidence and the MF, BP, or CC of a gene/gene product is not known
*When there is experimental or sequence-based evidence for another GO term from the same aspect, then the ND evidence code should be removed
*GOA proposed to remove ND annotations automatically from '''their''' curation database because this was not happening manually
*GOA proposed to remove ND annotations automatically from their curation database because this was not happening manually
**Note that curators can only update or remove annotations from their respective groups in Protein2GO
**Note that curators can only update or remove annotations from their respective groups in Protein2GO
**Annotation from only a select set of evidence codes would result in automatic removal of ND annotations
**Annotation from only a select set of evidence codes would result in automatic removal of ND annotations
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     ECO:0000317 (IGC) and its descendants
     ECO:0000317 (IGC) and its descendants
*Generally agreed that when there is experimental or sequence-based evidence for a more granular annotation, the ND annotation should be removed
**However, 'protein binding' MF annotations are thought of differently by different groups and we need to reach a consensus about how these MF annotations should be considered wrt automatically removing existing ND annotations
*Proposal: as part of QC pipeline, alert groups to genes/gene products that have an ND annotation and also an annotation to a more granular term (any evidence code?)


=== PAINT Annotations ===
=== PAINT Annotations ===

Revision as of 18:09, 13 August 2018

Meeting URL

Montreal Meeting, October Wednesday, 17th - Friday, 19th

GO Conference Calls

Tuesdays

  • 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 Discussion

ND Annotations

  • Automatic deletion of ND-evidenced annotations
  • ND annotations to a root node term are intended to signify that the curator looked at all available evidence and the MF, BP, or CC of a gene/gene product is not known
  • GOA proposed to remove ND annotations automatically from their curation database because this was not happening manually
    • Note that curators can only update or remove annotations from their respective groups in Protein2GO
    • Annotation from only a select set of evidence codes would result in automatic removal of ND annotations
   ECO:0000269 (EXP) and its descendants

   ECO:0006056 (HTP) and its descendants

   ECO:0000250 (ISS) and its descendants

   ECO:0000317 (IGC) and its descendants
  • Generally agreed that when there is experimental or sequence-based evidence for a more granular annotation, the ND annotation should be removed
    • However, 'protein binding' MF annotations are thought of differently by different groups and we need to reach a consensus about how these MF annotations should be considered wrt automatically removing existing ND annotations
  • Proposal: as part of QC pipeline, alert groups to genes/gene products that have an ND annotation and also an annotation to a more granular term (any evidence code?)

PAINT Annotations

Annotation Review

  • 84 open annotation review tickets
  • Reminder, generally, to check go-annotation tracker tickets where your group has been assigned and finish up where you can
  • Questions? Please add questions/comments to the individual tickets
  • We can discuss on future calls, if needed
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