Investigate problem with upper level equivalences

[matentzn]

This has no bearing on the release, but during qc I noticed that there are some strange equivalences that need to be investigated:

2019-08-16 07:42:48,375 ERROR org.obolibrary.robot.ReasonOperation - Only equivalent classes that have been asserted are allowed. Inferred equivalencies are forbidden.
2019-08-16 07:42:48,376 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/CL_0000003> == <http://purl.obolibrary.org/obo/CL_0000000>
2019-08-16 07:42:48,377 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/CL_0000000> == <http://purl.obolibrary.org/obo/CARO_0000013>
2019-08-16 07:42:48,377 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: <http://purl.obolibrary.org/obo/CL_0000003> == <http://purl.obolibrary.org/obo/GO_0005623>

In particular I dont like the two CL equivalences..

[Clare72]

GO_0005623 'cell'
CARO_0000013 'cell'
CL_0000000 'cell'
CL_0000003 'native cell'

asserted equivalence:
GO:cell == CL:cell (no longer present due to obsoletion of GO:cell)
CARO:cell == CL:native cell (in CARO import)
GO:cell == CARO:cell (in CARO import)

[Clare72]

I think with the "GO:cell == CL:cell" assertion gone, we now only have the third inference - "CL:native cell == GO:cell"

[matentzn]

I made this Tickeet : obophenotype/caro#23

But I doubt it will ever be done without @dosumis deciding we should just do it ourselves.

[dosumis]

I think with the "GO:cell == CL:cell" assertion gone, we now only have the third inference - "CL:native cell == GO:cell"

How is that possible if GO:cell is now obsolete? Is this just an out of date import in CARO?

[matentzn]

Yes. CARO has not been updated in years!