Implement automatic term namespace insertion

[balhoff]

Fixes #13359.

[github-actions]

Here's a diff of how these changes impact the classified ontology:

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2025-03-12/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-master.owl/reasoned.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2025-03-12/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

Removed

• default-namespace "gene_ontology"

default-namespace http://www.geneontology.org/formats/oboInOwl#default-namespace

Removed

• AnnotationProperty: default-namespace

negatively regulates characteristic http://purl.obolibrary.org/obo/RO_0019002

Removed

• negatively regulates characteristic has_obo_namespace "gene_ontology"

positively regulates characteristic http://purl.obolibrary.org/obo/RO_0019001

Removed

• positively regulates characteristic has_obo_namespace "gene_ontology"

regulates characteristic http://purl.obolibrary.org/obo/RO_0019000

Removed

• regulates characteristic has_obo_namespace "gene_ontology"