Organoid Protocol Atlas
A license-safe public slice of the organoid protocol corpus, turned into structured, queryable protocol records: source cells, matrix, base media, and signaling cocktail rows with DOI-linked evidence snippets. The full local pipeline tracks the larger verified corpus; this hosted build exposes the public CC subset without redistributing full methods text.
Browse protocols ->
One public recipe card per paper: cells, matrix, media, signaling cocktail with concentrations and evidence snippets. Faceted by organoid type, source cell, license.
Morphogen grammar ->
The signature view: every canonical signaling factor by every public organoid system, as a heatmap. See which morphogens recur and which are lineage-specific; figure-confirmed cells are marked when available.
Consensus recipes ->
The canonical recipe per organoid system: each factor's usage frequency across that type's public protocols, core cocktail vs variable additions, with modal doses. Computed, not asserted.
Ask the Atlas ->
Natural-language questions retrieve grounded rows from the public knowledge graph. If a local model is attached, it synthesizes answers; otherwise the evidence rows are shown.
Track one reagent ->
See how a single factor, such as CHIR99021, EGF, or R-spondin, is used and dosed across every public protocol that includes it.
Explore & search ->
A fast, bespoke search over every extracted reagent — filter by organoid type, kind, role, and grounding; each result links to its evidence and source DOI.
Grounding coverage ->
How much of each public protocol's cocktail is evidence-grounded. The honest quality signal that drives where to improve next.
Gold candidates ->
Public rows can be filtered for benchmark candidates, while human-verified gold evaluation remains a gated local workflow.
TRAPI / Biolink KG ->
The committed KGX graph is live-queryable via TRAPI 1.5: POST /trapi/query with a single-hop Biolink message, or GET /trapi/meta_knowledge_graph for the schema. Every node carries an SRI-resolved CURIE.
Analytics dashboard ->
Corpus-level metrics in one page: grounding coverage, quality tier distribution, MIOR completeness, top organoid systems, and assay clusters — all from committed, reproducible pipeline artifacts.