Spec 007: the answer cascade

[adamjohnwright]

Analysis branch first, then embeddings → Reactome Search API → Tavily.

                    ┌─ analysis question? ──> MCP analysis agent
question ──> detect ┤
                    └─ otherwise ──> embeddings ──> Search API ──> Tavily
                                       (no match)     (0 entries)

Half of it already exists

The completeness_grader already decides whether an answer was good enough and already gates the Tavily call. So the skeleton — retrieve, judge, fall back — is real. What you are asking for is one step inserted in the middle and one branch at the top.

step	today
classify	intent_classifier
embeddings	the RAG chain
"good enough?"	completeness_grader
Tavily	tavily_wrapper
Search API	nothing
analysis routing	nothing

The order is easy; the signal is not

Search API — free and unambiguous. Measured: PALB2 → 39 entries, Impaired BRCA2 binding to PALB2 → 89, zzzznotathing → 0. The result count is the signal. No model call, no threshold to tune. Cheapest step in the cascade.

Embeddings — the genuinely hard one. This spec is careful not to pretend otherwise: similarity search has no empty result. It always returns its k nearest documents, so "does not find a match" describes an intent, not a mechanism. That is D1, and it is the only non-obvious decision here.

Analysis — a classifier, and there is one. intent_classifier should gain the destination rather than acquire a sibling, which is #142's mistake: a second classification call in a pipeline where cutting calls from 21 to one was the point of spec 001.

Cost

Both new steps are cheap — the Search API well under a second, and analysis measured at 0.2s through reactome-mcp (eight genes, 108 pathways).

Recorded as unverified: nobody knows how often a question would actually fall through to the Search API. That number decides whether this cascade is worth building or whether the bundle is simply stale — and the Release 98 rebuild may change it a lot. Worth measuring before building.

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