Include paint_other.gaf in GO release GAF load

[dustine32]

It recently came up that not all GO-pipeline-vetted IBAs are passed on to the GO release GAFs available at http://current.geneontology.org/annotations/index.html. In fact only IBAs to organisms tied to a GO release product (e.g. mgi.gaf, wb.gaf) are included in the GO release. In particular, this is preventing the IBAs in paint_other.gaf from being cycled back in to the PANTHER GO complete enrichment data set.

For the GOlr/AmiGO load, paint_other.gaf is loaded in addition to the GO release GAFs. Thus, you can find some IBAs in AmiGO that you can't find in the PAINT tool or contribute to enrichment results.

This should be an easy fix for us to align the datasets. We just download the GO release's version of paint_other.gaf (http://current.geneontology.org/products/annotations/paint_other.gaf.gz) and include in the GAFs input to the fullGoMappingPthrHierarchy job. Just a couple lines in Makefile are needed for this.

Also possibly related to geneontology/go-site#1375 but still need to look for those specific Reactome annotations to confirm.

Tagging @kltm @huaiyumi @pgaudet

[kltm]

@dustine32 A great description! To add a bit more details, the paint_other file is technically in the release (third paragraph), but it is not merged into a "main product GAF" (i.e. something that appears in the down products pages) like the others: For an example, see: https://github.com/geneontology/go-site/blob/master/metadata/datasets/paint.yaml#L19

The GAFs that get loaded into an AmiGO release are found here: https://github.com/geneontology/pipeline/blob/release/Jenkinsfile#L107
It may be beneficial to spin that out into metadata that can be more easily shared (but has not to date due to the history that got it there in the first place).

[dustine32]

The download of paint_other.gaf from the GO release was added in commit ef42299.

[kltm]

To clarify further action, we would need to append paint_other.gaf to an output product.