HERD integration: species ontology terms

[bendichter]

Closes #1771.

What

Adds neuroconv.tools.ontology and wires it into make_nwbfile_from_metadata so that a subject's species is both recommended in a standardized form and annotated with a machine-readable NCBITaxon reference in the written file.

Two behaviors:

1. Suggestion (non-blocking). validate_species warns with a concrete recommendation when Subject.species is a recognized common name (e.g. "mouse") or a likely typo (e.g. "Homo sapien"), pointing at the canonical Latin binomial and its NCBITaxon id (Mus musculus / NCBITaxon:10090). Valid-but-uncommon binomials pass silently.
2. HERD annotation. add_species_external_resource attaches an external-resource reference mapping a recognized Subject.species binomial to its NCBITaxon entity, stored in-file under /general/external_resources via HDMF's HERD. This is the HERD integration the issue asked for — downstream tools (e.g. DANDI) can resolve the term without guessing.

The species table is a small curated, offline, dependency-free lookup of common neuroscience species (no network, no ontology client).

Notes

• In-file HERD storage requires pynwb ≥ 4.0.0, already the minimum pin (Update pynwb minimum to 4.0 #1769).
• The HERD is constructed with pynwb's type map, which is required for the Subject.species attribute spec to resolve; without it add_ref raises. The write is idempotent and extends a pre-existing external_resources HERD in place rather than replacing it.

Testing

• tests/test_minimal/test_tools/test_ontology_species.py — table integrity, common-name/typo suggestions, get_species_term resolution, warning behavior.
• tests/test_minimal/test_tools/test_ontology_external_resources.py — no-op cases, annotation, idempotency, extend-in-place, and a full write→read round trip confirming the reference persists in the NWB file.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.51%. Comparing base (8457f90) to head (017f1fd).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1772      +/-   ##
==========================================
+ Coverage   82.40%   82.51%   +0.10%     
==========================================
  Files         176      179       +3     
  Lines       13992    14080      +88     
==========================================
+ Hits        11530    11618      +88     
  Misses       2462     2462              

Flag	Coverage Δ
unittests	82.51% <100.00%> (+0.10%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
...nv/tools/nwb_helpers/_metadata_and_file_helpers.py	92.04% <100.00%> (+0.23%)	⬆️
src/neuroconv/tools/ontology/__init__.py	100.00% <100.00%> (ø)
...rc/neuroconv/tools/ontology/_external_resources.py	100.00% <100.00%> (ø)
src/neuroconv/tools/ontology/_species.py	100.00% <100.00%> (ø)

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