LEGO May 16, 2016

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Bluejeans

https://bluejeans.com/969313231

Agenda

Software Updates

Form Interface for Curation

  • Revisit this? How high a priority is this for wider adoption of the tool?

RO View for Curators

  • Being able to browse the RO might be helpful for curators doing LEGO curation
  • Are there any plans to add this functionality to AmiGO2?

GAF/GPAD

Still needed before we can import (into MGI):

Essential

  1. Stable purl from which to retrieve files. We will use GAF for now, but we have a ticket in to be able to use GPAD. (GH Noctua issue #200 - https://github.com/geneontology/noctua/issues/200)
  2. Folded annotations for individuals annotated by the regulates relation. (GH Noctua issue #189 - https://github.com/geneontology/noctua/issues/189)
    1. We can get around this requirement by making the 'extra' annotations to the regulation terms in the interface.
  3. For full adoption to all curation (at least at MGI), we will need the ability to annotate to proteoforms/isoforms and have this information processed correctly in the GAF or GPAD files. In the GAF file, this information is in column 17, but the object in the enabled_by field populates column 2. This issue needs to be solved.

Desirable

  1. Attribution to individual groups. For example 'MGI-Noctua'. (GH Noctua issue #84 - https://github.com/geneontology/noctua/issues/84)
  2. An automated QC check on annotations made in Noctua. For example, tagging annotations that don't have evidence. (https://github.com/geneontology/noctua/issues/255)
  3. Attribution of curator comments and evidence sentences to the appropriate reference. (https://github.com/geneontology/noctua/issues/280)

Not Yet Tested

  1. For full adoption to all curation (at least at MGI), we will need the ability to annotate to proteoforms/isoforms and have this information processed correctly in the GAF or GPAD files. In the GAF file, this information is in column 17, but the object in the enabled_by field populates column 2. This issue needs to be solved. In the GPAD format, this issue is solved in column #2, but how will Noctua 'know' that the isoform ID entered into the enabled by field is associated with a mouse gene? Is Noctua aware of the GPI file?
  2. Annotations based on orthology that use a GO reference.

Data flow Questions

  1. Once we have imported annotations into MGI from Noctua, those annotations will be incorporated into our output files, GPAD and GAF. Is there a strategy for them not being duplicated when they are picked up by the GOC?