A worked example, end to end

This page follows one chunk all the way through the pipeline, using real values from a foods build, so every concept on the other pages has something concrete to point at.

Our chunk:

tb_0421 (textbook) — “One cup of milk provides about 300 mg of calcium, and the lactose it contains aids calcium absorption. Fortified milk is also a source of vitamin D.”

1. Annotation — mentions → FoodOn ids

GLiNER finds the mention spans; the dense linker resolves each to a FoodOn id by embedding it (BioLORD) and taking its nearest ontology term (cosine ≥ nel_min_sim):

mention	→ FoodOn id	label
milk	FOODON:03310029	cow milk
calcium	CHEBI:… (nutrient)	calcium
lactose	…	lactose

The chunk is also embedded once with BGE-base (768-d) for retrieval and Layer B Pass 1. See Annotation.

2. Layer A — which shelves it lands on

The linked id cow milk is walked up the real FoodOn is-a chain. Each class on the way gains lifted support from this chunk, and the chunk attaches to the surviving shelves on that path:

        flowchart TD
    A[cow milk] --> B[mammalian milk product<br/>FOODON:03315150]
    B --> C[milk or milk based food product<br/>FOODON:00001257]
    C --> D[dairy food product]
    D --> E[vertebrate food product]
    E --> F[animal food product]
    F --> G[Foods]
    

So tb_0421 attaches to mammalian milk product (and its ancestors) — it is one of that shelf’s 649 chunks. That shelf’s support tells the story: direct 1, lifted 648 — almost nobody writes the literal phrase “mammalian milk product”, but the corpus is full of its descendants (cow milk, goat milk, …). Contrast a genuine topic like fruit produce (633 direct, 0 lifted), which the corpus names outright. See Layer A and support_direct vs support_lifted in the glossary.

3. Layer B — which theme it joins

Within the mammalian milk product shelf, Layer B’s two passes cluster the chunks. Our chunk — calcium, lactose, absorption — lands in the relatedness theme below (it shares the entities cow milk, calcium, lactose with its theme-mates). Real themes on this shelf, by origin:

discovery_pass	theme label	chunks	top keywords
relatedness	milk calcium lactose	167	milk, calcium, lactose, vitamin, fat
relatedness	milk protein foods	103	milk, protein, foods, eggs
global_similarity	calcium vitamin milk	123	calcium, vitamin, milk, protein
global_similarity	breast milk breast infant	98	breast milk, breast, infant, formula

tb_0421 joins “milk calcium lactose”. (This build produced no merged themes — a real, instructive outcome: it means the embedding and entity passes didn’t overlap enough to cross the merge threshold, which is a tuning signal, not a bug.) See Layer B.

4. Layer C — the card that cites it

build_layer_c writes a cited card for the shelf/theme. Every sentence must be grounded in member chunks — including ours:

Calcium in dairy milk — evidence quality: high Milk is a major dietary calcium source, ~300 mg per cup [tb_0421], and its lactose content supports calcium absorption [tb_0421, ab_088]. Fortified milk additionally supplies vitamin D [tb_0421]. cited_chunk_ids: [tb_0421, ab_088, gd_0203]

See Layer C.

5. Retrieval — answering a query

Now a user asks “Is dairy a good source of calcium?”:

1. Hybrid search (Elasticsearch): BM25 + kNN over the query, fused by RRF, filtered to shelf_ids ∋ mammalian milk product. tb_0421 ranks high.

2. Theme expansion (Neo4j → ES): follow tb_0421’s theme_ids to the milk calcium lactose theme and pull its sibling chunks — adding complementary evidence (absorption studies, fortification) that worded things differently.

3. Present: the chunks, plus the shelf’s Layer C card, with full provenance chunk → shelf → theme → source doc.

That provenance trail is the whole point: the answer can cite exactly where every claim came from. See Architecture for the two-store machinery underneath.

Note

Steps 1–3 use the values shown above verbatim from a real foods build; the chunk text and the card are representative (Layer C wasn’t built in this snapshot), but the shelf, its support numbers, the is-a chain, and the themes are exactly as the graph contains them.