MGI GPAD file is missing 'MGI:' in column 2

[ukemi]

Recently column 2 in the GPAD output has been changed so that identifiers no longer contain the 'MGI:'. Instead, they just have the numerical portion of the identifier.

https://build.berkeleybop.org/job/export-lego-to-gpad-sparql/lastSuccessfulBuild/artifact/legacy/mgi.gpad

[kltm]

@cmungall @balhoff Has there been any upstream change to explain this?

[balhoff]

There has been change in the JSON-LD context files (geneontology/go-site#617). I will need to dig further to see if that is the culprit.

[ukemi]

@loricorbani

[balhoff]

I think this is an issue with the GO JSON-LD context, which is included in Minerva and also available at https://github.com/prefixcommons/biocontext/blob/master/registry/go_context.jsonld

The entry for MGI is:

"MGI": "http://identifiers.org/mgi/MGI:"

The identifiers in the models look like http://identifiers.org/mgi/MGI:1919103. So when this is shortened it becomes MGI:1919103, which is split to go into the GPAD columns.

@cmungall shouldn't this be: "MGI": "http://identifiers.org/mgi/"

[balhoff]

This behavior isn't appearing in Noctua right now, but it may have been a while since Minerva was updated there.

[ukemi]

In Noctua I see the identifiers being of the correct prefix--identifier format. Looking at:
http://noctua.berkeleybop.org/editor/graph/gomodel:5b318d0900000110

The enabled by individual for Cdc42 is represented as '[MGI:MGI:106211] Cdc42 mouse' this should parse correctly into MGI in column 1 and MGI:106211 in column 2.

[pgaudet]

So this is resolved ?

[cmungall]

curl -L -s https://build.berkeleybop.org/job/export-lego-to-gpad-sparql/lastSuccessfulBuild/artifact/legacy/mgi.gpad | grep MGI

no, not resolved

[balhoff]

This should be resolved now.