Repair obsolete terms in imports

[allenbaron]

The count of owl:deprecated properties/classes from imports in doid-merged.owl, release v2022-06-07 is:

import	deprecated
RO	1
GENO	2
HP	147

These should be reviewed and removed or repaired as necessary.

The deprecated RO & GENO property/classes are:

• http://purl.obolibrary.org/obo/RO_0002218 (obsolete has active participant)
• http://purl.obolibrary.org/obo/GENO_0000142 (obsolete dominant inheritance)
• http://purl.obolibrary.org/obo/GENO_0000150 (obsolete autosomal recessive inheritance)

The deprecated HP classes are listed in the following file: HP_deprecated_v2022-06-07.txt

[allenbaron]

It appears that none of these property/classes are used in any triples in the doid-merged.owl file. They probably just need to be excluded the next time we update these imports.

[allenbaron]

The deprecated HP terms are all defined in the src/ontology/ext.owl file and do not exist in the src/ontology/import/hp_import.owl file.

[lschriml]

@allenbaron - Can we close this ticket ?

[allenbaron]

Not yet. None of these deprecated terms have been addressed.

[lschriml]

Can you add an estimate of when this will be addressed or time-frame for this resolution ?

[allenbaron]

HP:0011007 has been merged into 'Onset' (HP:0003674) and the class has been completely removed from hp.owl, instead of deprecated, so it can be removed ext.owl.

All of the remaining HP terms are in the hp.owl file and none of those are deprecated.

[allenbaron]

The remaining HP deprecation statements have been removed. Closed by b691c5b