| name | nmdc-schema-reference |
| description | Use this skill to look up NMDC LinkML slot ranges, value-type wrappers (QuantityValue, ControlledIdentifiedTermValue vs ControlledTermValue) and enum allowed-values via SchemaView before shaping any non-trivial NMDC slot value or diagnosing a validation failure. Other NMDC skills defer here for the canonical value shape. |
NMDC LinkML schema reference
Use this skill when shaping a slot value whose range is not a plain string — nested value-type wrappers, enums with strict allowed values, slots with min/max/range semantics. Curation skills (nmdc-env-triad, nmdc-taxon-resolution) point here for the canonical value-shape rules; source skills point here from their validate step.
Common traps
QuantityValue uses has_numeric_value for scalars but has_minimum_numeric_value / has_maximum_numeric_value for range strings like "0.2 - 0.3 m". Never put a range into has_numeric_value.ControlledIdentifiedTermValue wraps an OntologyClass with id (the CURIE) and name (the official ontology label). If you only have free text and no resolvable CURIE, use ControlledTermValue with has_raw_value instead.- Slot names use snake_case and often have strict enum value ranges (e.g.
study_category, analyte_category, data_category, data_object_type). Pulling an enum value from memory is a common source of validation failures — check the schema.
How to check the schema
Two ways, in order of preference:
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Local package (authoritative for the installed version) — nmdc-schema is a project dependency, so the Python classes are introspectable via linkml_runtime. Use the bundled helper:
uv run python .claude/skills/nmdc-schema-reference/scripts/inspect_slot.py depth Biosample
uv run python .claude/skills/nmdc-schema-reference/scripts/inspect_slot.py --class QuantityValue
It wraps SchemaView(nmdc_schema.get_nmdc_schema_definition()).induced_slot(...); for a class's expected shape, help(nmdc.QuantityValue) in a REPL also works.
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Published docs (useful for browsing and cross-referencing) — https://microbiomedata.github.io/nmdc-schema/. Handy for skimming class hierarchies and allowed enum values, but may be ahead of or behind the installed version — treat the local package as source of truth when they disagree.
