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pombase / pombase-chado

PomBase code for accessing Chado
MIT License
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Cope with loading Canto annotation with alt_id and extension #597

Closed kimrutherford closed 7 months ago

kimrutherford commented 8 years ago

The Canto JSON loader is failing in the case with an alt_id is used in an annotation and that annotation has an extension. The bug is that the is_a relationship between the base term (eg. "decreased intergenic meiotic recombination") and the term+extension (eg. "decreased intergenic meiotic recombination [has_expressivity] medium") doesn't get stored.

These terms without the is_a cause the GAF exporter to fail (see #595).

ValWood commented 2 years ago

Is this still current (I don't fully understand the issue)

kimrutherford commented 2 years ago

As far as I know the bug is still there.

ValWood commented 1 year ago

Is this still current? Are e losing these annotations (I don't really understand so maybe we should discuss)

kimrutherford commented 1 year ago

Is this still current? Are e losing these annotations

Sorry, I didn't make a good note of what goes wrong in this case. #595 isn't very helpful.

I'll check and make sure we at least get a loud log message if this problem is noticed by the loading code.

kimrutherford commented 7 months ago

I can't reproduce this now so I'm going to close the issue until it happens again.