Core Entities
- Crop — plant asset being analyzed.
- Parameter — growth/handling variable (light, EC, pH, stress, harvest timing).
- Nutrient — measured compound or antinutrient outcome.
- Claim — extracted directional statement tied to a source span.
Glass Biome · AI-native research infrastructure
Cultivation protocols from agricultural research, validated at the lab.
91 cultivars across 13 verticals. AI scans agricultural research papers, extracts cultivar × parameter × nutrient × outcome findings, and validates them at the USDA-ARS lab on campus. Each cycle adds to the database.
S.01 The Engine
Research Coverage
Live view of the evidence base: papers ingested, claims extracted, and connections discovered. Scans run against Europe PMC, Semantic Scholar, and OpenAlex with Unpaywall full-text enrichment.
Scan
Extract
Link
Model
Protocol
Scan Frontier
Ontology
Depth Signals
- Full Text — body text ingested (best depth).
- Abstract Only — title + abstract only.
- Title Only — title-level metadata only.
Direction + Confidence
- Direction — positive / negative / nonlinear / undetermined.
- Confidence — heuristic extraction confidence, not statistical significance.
- Undetermined — entities found but no explicit increase/decrease signal.
Scan Lanes
- Claim Yield — scanned lane produced claims.
- Scanned, No Claim — scanned but no valid triple extracted.
- Not Scanned — queued in plan, not run yet.
S.03 Pipeline Health
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Pipeline health at a glance: papers ingested, claims extracted, links discovered, and extraction yield rates.
Pipeline Overview
A.01 Where the Evidence Sits
Distribution of evidence across crops, parameters, and nutrients. Identifies where the strongest signals are and where coverage gaps remain.
Claims by Crop
Claims by Parameter
Claims by Nutrient
Crop × Nutrient Evidence Map
Cell intensity = claim count for each crop-nutrient pair. Hover for details.
Coverage Gap Matrix
Red cells = zero evidence for this crop-nutrient pair across the full ontology.
First-Order Aggregates
Aggregated crop × parameter × nutrient relationships. Each row summarizes all claims for a triple into a dominant direction and mean confidence — the basis for dose-response models and protocol recommendations.
| Crop | Parameter | Nutrient | Claims | Direction | Confidence |
|---|
A.02 Extraction Quality
Extraction quality metrics. Direction indicates whether a parameter increases, decreases, or has nonlinear effects on a nutrient. Confidence reflects extraction certainty, not statistical significance.
Direction Distribution
Direction Signal Detail
Confidence Bands
Papers by Year
Reference Ingestion Depth
Nutrient Gap Status
A.04 Nutrient Synergies & Parameter Interactions
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Nutrient pairs and triads that respond to the same growing parameters within a crop — potential shared metabolic pathways. Higher scores indicate stronger co-occurrence across multiple independent studies.
Network Overview
A.05 Gaps the Engine is Filling
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Nutrients ranked by research priority: human deficiency prevalence weighted against available evidence depth. High-priority gaps are where growing protocols could have the most impact on public health outcomes.
Priority Overview
A.07 Complex Links
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Pre-LLM structural links: dose-response fits, hidden nutrient synergies, and third-order triads. These are computed from co-occurrence and ontology rules — causal validation requires Opus extraction.
Dose-Response Models –
| Crop | Parameter | Nutrient | Model | Strength | Direction | N | Mean Effect % |
|---|
Hidden Synergies –
| Crop | Nutrient Pair | Relationship | Bioavail. Score | Deficiency Adj. | Claims | Note |
|---|
Third-Order Triads –
| Crop | Nutrient Triplet | Anchor | Triad Score | Hypothesis |
|---|
A.08 Mechanistic Predictions
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First-principles pathway predictions: the inference engine maps (crop × parameter × nutrient) triples through KEGG pathways and signal mappings to predict nutrient directions without relying on empirical claims. Unconfirmed predictions are novel hypotheses warranting experimental validation.
| Crop | Parameter | Nutrient | Predicted Direction | Confidence | Category | Pathways |
|---|