> ## Documentation Index
> Fetch the complete documentation index at: https://docs.rafflesia.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# Lossy & range mappings

> How the ontology relates identities that are the same but imperfect across sources — without pretending the mapping is exact.

[Identity](/ontology/identity) keeps values apart by default, and a
[relationship](/ontology/joins) is what lets two of them join. But
not every biological mapping is a clean one-to-one equality. Some drop rows, some
approximate, and some relate an interval to the positions inside it. The ontology
makes that imperfection **explicit on the relationship itself**, so a query can
see the risk instead of inheriting it silently.

## `is_lossy`

A lossy relationship maps to the same entity but does not preserve every row —
a sequence maps to a structure that only covers part of it, or a mapping that
exists only where an alignment was found. The join is still type-safe; it just
warns that absence of a match is not evidence of absence.

```json theme={"dark"}
{
  "relation": "protein_structure_mappings",
  "cardinality": "many_to_one",
  "local_columns": ["sequence_id"],
  "remote_columns": ["sequence_id"],
  "is_lossy": true
}
```

Under `strict_joins`, lossy edges still join, but the recipe author has declared,
in the ontology, that partial coverage is expected here.

## `is_range_mapping`

A range mapping relates a **position to an interval that contains it**, rather than
matching two equal values. SIFTS observed ranges, genome-interval overlaps, and
flanks all work this way: the join condition is containment, not equality.

```json theme={"dark"}
{
  "relation": "genome_interval_overlaps",
  "cardinality": "many_to_many",
  "local_columns": ["reference_id", "start", "end"],
  "remote_columns": ["reference_id", "position"],
  "is_range_mapping": true
}
```

Marking the relationship as a range mapping is what stops the compiler from
treating `start`/`end` as ordinary equality keys — and what tells the caller the
result is an interval relationship.

## `coordinate_notes`

When a mapping is exact but carries a caveat, the relationship spells it out:

> `structure_residue_number` equals `residue_features.position` exactly — but
> confirm `wildtype_matches` before trusting the mapping.

These notes travel with the ontology, so the warning is visible at query-planning
time rather than discovered in the data.

<Note>
  **Declared, never inferred**

  The ontology never guesses that two identities are the same, and it never
  hides that a mapping is imperfect. `is_lossy`, `is_range_mapping`, and
  `coordinate_notes` are declarations — the deliberate cost that buys a query
  the ability to reason about its own uncertainty.
</Note>

Next: [Relations](/ontology/relations) — the typed sources these
relationships connect.