feat: add microbiology domain scaffolding (closes #314)

[Zeesky-code]

Pull Request

Description

Adds the microbiology NER domain scaffolding across the label taxonomy,
zero-shot label map, model registry, and policy profiles. This allows
organism/antibiotic/susceptibility extraction for infectious-disease and
antimicrobial-stewardship use cases, distinct from the existing generic
Species family.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Code refactoring
• Performance improvement
• Test addition/improvement

Changes Made

• openmed/zero_shot/data/label_maps/defaults.json: added microbiology
  domain with labels Microorganism, Antibiotic, Susceptibility, Specimen
  source, Culture result
• openmed/core/labels.py: added canonical labels MICROORGANISM,
  ANTIBIOTIC, SUSCEPTIBILITY as CLINICAL_CONCEPT with system hints
  (SNOMED/LOINC/RxNorm) and alias entries (organism, pathogen,
  antimicrobial, etc.)
• openmed/core/model_registry.py: added Microbiology entry to
  _CATEGORY_ENTITY_TYPES; added dedicated routing keywords (culture,
  gram stain, mrsa, resistant, susceptib…) to get_model_suggestions
  distinct from the Species pattern
• openmed/core/policies/*.json: added keep/mask actions for the three
  new labels across all six policy profiles to satisfy the
  CANONICAL_LABELS coverage invariant enforced at load time

Testing

• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• I have tested this change with different models/inputs

uv run pytest tests/ --ignore=tests/integration -q → 1600 passed, 12 skipped

New TestMicrobiologyDomain class in tests/unit/ner/test_label_map_consistency.py
covers all acceptance criteria from the issue:

• available_domains() includes microbiology
• get_default_labels('microbiology') returns a non-empty label set
• normalize_label('susceptibility') == 'SUSCEPTIBILITY'
• normalize_label('antibiotic') == 'ANTIBIOTIC'
• normalize_label('microorganism') == 'MICROORGANISM'
• normalize_label('organism') == 'MICROORGANISM' (alias)
• get_model_suggestions('Blood culture grew MRSA, resistant to oxacillin') runs without error

Documentation

• I have updated the documentation accordingly
• I have added docstrings to new functions/classes
• I have updated the CHANGELOG.md

Code Quality

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• My changes generate no new warnings

Dependencies

• I have not added any new dependencies

Checklist

• I have read the contributing guidelines
• My commits have clear, descriptive messages
• I have squashed/organized my commits appropriately

Related Issues

Closes #314
Related to #289 (zero-shot domain label maps for biomedical NER families)

[maziyarpanahi]

Thank you @Zeesky-code. I reviewed this against #314 and the related #289 context, then added a maintainer merge-resolution commit: Merge remote-tracking branch 'origin/master' into feat-microbiology-domain.

What changed:

• resolved the branch against current master, preserving the newer Cardiology domain work while adding Microbiology;
• kept the policy profile changes minimal by adding only MICROORGANISM, ANTIBIOTIC, and SUSCEPTIBILITY actions, removing the older full-file JSON formatting churn;
• tightened the regression coverage so microbiology text routes through _match_categories() before generic Species, while get_model_suggestions() still returns only live registered model categories until a dedicated Microbiology model exists;
• kept the microbiology zero-shot labels in the current letters-only display-label style: SpecimenSource and CultureResult.

Verification:

• /Users/maziyar/Developer/openmed/.venv/bin/python -m pytest tests/unit/core/test_labels_policy_spine.py tests/unit/core/test_policy_profiles.py tests/unit/ner/test_label_map_consistency.py tests/unit/ner/test_labels.py -q -> 78 passed
• /Users/maziyar/Developer/openmed/.venv/bin/ruff check openmed/core/labels.py openmed/core/model_registry.py tests/unit/core/test_labels_policy_spine.py tests/unit/ner/test_label_map_consistency.py -> passed
• /Users/maziyar/Developer/openmed/.venv/bin/ruff format --check openmed/core/labels.py openmed/core/model_registry.py tests/unit/core/test_labels_policy_spine.py tests/unit/ner/test_label_map_consistency.py -> passed

I copied #314 labels onto the PR. The branch is mergeable with no conflicts. GitHub has not reported hosted checks for this fork head, so the validation above is local.

[Zeesky-code]

Thank you for the review and the merge-resolution commit. I'll take note of the display-label style (CamelCase, no spaces) and the JSON formatting conventions for future contributions.