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Everything else in the ontology rests on one idea: a column is not just a name and a type, it carries a declared kind, and — where it matters — an identifier namespace or a coordinate system. Two values are only the same identity when those declarations agree. This is what lets a join be certified instead of guessed. The whole catalog lives in one declarative file, ontology.v1.json, which versions the entity types, namespaces, coordinate systems, and relations together. Its SHA-256 digest is folded into every query identity, so a query cannot silently acquire different semantic validation.

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Column kinds

Every physical column declares a value_kind: The kind is what stops two columns that both hold small integers from being joined just because the numbers line up — a coordinate is never treated as a measurement, and two coordinates in different systems never match.

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Identifier namespaces

A namespace records which authority mints an identifier. The ontology declares seven, so the same protein addressed two ways is never compared as a raw string: There is deliberately no canonical sequence-identifier namespace. Sequence ids reach the lake as whatever the source FASTA header or importer supplied, and nothing resolves them to a common authority, so source_sequence_records.sequence_id is declared source_record — a source-assigned id, not a Rafflesia-minted one. The content address of a sequence is sequence_sha256. This is why the sequence-search relations declare no identifier namespace on their query and subject ids: those values are raw aligner output, and claiming otherwise would license a join that silently returns wrong rows.

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Coordinate systems

A coordinate system records what a position is measured against. These are the single most common way a biology query goes silently wrong, because they all look like plain 1-based integers: A structure_residue_number and a protein_sequence_position can point at the same residue, but they are different coordinate systems. Equating them directly is the classic silently-wrong join — the ontology treats them as distinct until a mapping relates them.
Entities behind the columnsColumns are grounded in seventeen declared entity types — protein, structure, residue, sequence, variant, ligand, pocket, interface, taxon, and more — so a relation always knows which kind of thing each identifier and coordinate belongs to.

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The rule in one sentence

Two values refer to the same thing only when their kind, namespace, and coordinate system agree — or when the ontology declares a relationship that maps one to the other. Everything else stays distinct.
Next: Lossy & range mappings — how the ontology relates identities that are the same but imperfect across sources.