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obophenotype / bio-attribute-ontology

source files for OBA (Ontology of Biological Attributes)
https://obophenotype.github.io/bio-attribute-ontology
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PR:000000001 and protein (CHEBI:36080) has cyclic dependency #313

Closed gabbysantos closed 1 month ago

gabbysantos commented 4 months ago

Hi there, PR:000000001 and protein (CHEBI:36080) has cyclic dependency suggest removing the subclass relation.

Thanks Gabby

matentzn commented 4 months ago

Thank you for the report @gabbysantos - deeply appreciated.

There are 10 such cycles in OBA it seems:

  1. GO:0000313 GO:0005840
  2. GO:0099568 GO:0005737
  3. CHEBI:18111 SO:0000252
  4. CHEBI:36080 PR:000000001
  5. GO:0005938 GO:0099738
  6. CHEBI:33699 SO:0000234
  7. GO:0090068 GO:0045787
  8. GO:0010564 GO:0051726
  9. GO:0045786 GO:0010948
  10. GO:0005829 GO:0099522

These are all victims of an OBA preprocessing step which I am fixing:

  1. GO:0099568 GO:0005737
  2. GO:0005938 GO:0099738
  3. GO:0000313 GO:0005840
  4. GO:0005938 GO:0099738
  5. GO:0010564 GO:0051726
  6. GO:0045786 GO:0010948
  7. GO:0005829 GO:0099522

These are asserted:

  1. CHEBI:18111 SO:0000252
  2. CHEBI:33699 SO:0000234
  3. CHEBI:36080 PR:000000001

I will implement the following solution unless anyone screams:

  1. for the asserted cases, I will remove the three SO terms and PRO terms after reasoning. The correct solution would be https://github.com/ontodev/robot/issues/1060 but I do not have time to deal with that right now
  2. For the other cases I need to check something with the GO team.