Add DOSDP pattern for disease progression traits and seed initial progression terms

[Copilot]

This introduces a compositional OBA pattern for disease/phenotype progression so GWAS-style “disease + progression measurement” annotations can be represented as single trait terms. It establishes a reusable template and seeds initial terms to support immediate curation.

• New disease progression pattern

  • Added src/patterns/dosdp-patterns/disease_progression.yaml.
  • Models progression as temporal distribution quality (PATO:0002323) inhering in a disease/phenotype filler.
  • Generates labels as "[disease/phenotype] progression" and synonym "progression of [disease/phenotype]".
  • Includes definition xref annotation (AUTO:patterns/patterns/disease_progression).

• New pattern data table + seeded terms

  • Added src/patterns/data/default/disease_progression.tsv.
  • Seeded:
    • OBA:2100006 — disease progression (MONDO:0000001)
    • OBA:2100007 — Alzheimer disease progression (MONDO:0004975)

• Generated ontology updates

  • Regenerated src/patterns/definitions.owl to include new class declarations and equivalence axioms from the new pattern/data.

Example generated axiom shape:

EquivalentClasses(
  <http://purl.obolibrary.org/obo/OBA_2100007>
  ObjectIntersectionOf(
    <http://purl.obolibrary.org/obo/OBA_0000001>
    <http://purl.obolibrary.org/obo/PATO_0002323>
    ObjectSomeValuesFrom(
      <http://purl.obolibrary.org/obo/RO_0000052>
      <http://purl.obolibrary.org/obo/MONDO_0004975>
    )
  )
)

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[aleixpuigb]

Please see inline comments.
I am not very used to disease patterns, so maybe it would be good to consult the equivalence axiom with a person who is more knowledgeable with disease.
Not all patterns have extra fiels such as synonyms or ORCID, but I think they should be included. However, this is only a suggestion.

[aleixpuigb]

missing underscore symbol

Suggested change

	pattern_name: disease progression
	pattern_name: disease_progression

[aleixpuigb]

As the pattern name is deisease progression, why not disease only?

[aleixpuigb]

RO:0000052 is 'characteristic_of', although in some ontologies is relabelled as 'inheres_in'