5 Oct 2021 PAINT Conference Call
Anushya, Dustin, Peifen, Huaiyu
PAINT software update (Anushya)
Continue the current implementation of IBA propagation in the PAINT tool. To ensure that all possible conflict leaf annotations are reviewed before propagation, the following improvement is suggested. When an IBD is propagated, and if there are conflict leaf experimental annotations, they are listed in a dialog box. Curator can check if IBA should be propagated to any of them.
The current software implementation flags annotations with conflicting qualifiers via background color of cell in Matrix. For conflicting 'NOT' qualifiers, the background is colored in pink. For other conflicting qualifiers, the background is colored in yellow. For example, PTHR43791 - PTN000185192 IBD to term MF GO:0015225 Leaf node has NOT IGI annotation on PomBase:SPAC1B3.15c (PTN000185197) - IBA is still propagated, but, cell background is pink.
- Taxon constraint check is still in the PAINT tool. It doesn't automatically insert TCVs. Instead it displayes a warning to the curator. Currently, the warning is only to the node that a GO term is intended to be propagated to.
- Anushya is worried that the curators may have difficulties the identify the descendant nodes to insert TCV annotations. One suggestion is to add the possible TVC nodes in the warning as well.
- The perl script that generates the IBA files relies on the TCV annotations to remove taxon constrain violation. With all TCVs turned off in the PAINT tool, the GAFs generated by perl and PAINT tool are basically the same. TC is only enforced by the GO pipeline. GO report has numbers of annotations removed from PAINT IBAs due to TC (http://current.geneontology.org/reports/gorule-report.html).
Monthly IBA release update
Preparation for GO consortium meeting
- Huaiyu will prepare some overview slides.
- Anushya will prepare a slide about the PAINT updates.
- Dustin will prepare a slide about any monthly updates.
- Will ask Marc about PAINT tickets.