On Mar 26, 2009, at 8:33 AM, Michel_Dumontier wrote:

The Gene Ontology says a Protein (GO:0003675) is a Thing (the entity
was removed, but then later added so the identifier wouldn't be reused)

More accurately: very early versions of the GO had a term named "protein", but this was obsoleted because it was out of scope for the GO. The term was obsoleted, but a historic record is maintained. GO does not intend to say "protein is_a thing", what you are seeing is probably an artefact of the translation of obsoletion metadata to OWL.

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