LEGO May 16, 2016
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 allow this in AmiGO2?
GAF/GPAD
Still needed before we can import (into MGI):
Essential
- 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)
- Folded annotations for individuals annotated by the regulates relation. (GH Noctua issue #189 - https://github.com/geneontology/noctua/issues/189)
- We can get around this requirement by making the 'extra' annotations to the regulation terms in the interface.
- 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
- Attribution to individual groups. For example 'MGI-Noctua'. (GH Noctua issue #84 - https://github.com/geneontology/noctua/issues/84)
- 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)
- Attribution of curator comments and evidence sentences to the appropriate reference. (https://github.com/geneontology/noctua/issues/280)
Not Yet Tested
- 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?
- Annotations based on orthology that use a GO reference.
Data flow Questions
- 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?