wirthal1990-tech/USDA-Phytochemical-Database-JSON

USDA Phytochemical & Ethnobotanical Database — Enriched v2.0

The only phytochemical dataset combining USDA botanical records, PubMed citation counts, ClinicalTrials.gov study counts, ChEMBL bioactivity scores, and USPTO patent density — in production-ready JSON + Parquet.

Free 400-Row Sample ↓ · Single Entity €699 → · Team €1.349 → · Enterprise €1.699 →

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Records	Compounds	Species	Enrichment Layers
104,388	24,771	2,315	4

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Schema (v2.0)

Column	Type	Nulls	Description
chemical	string	0%	Standardised compound name (USDA Duke’s nomenclature)
plant_species	string	0%	Binomial Latin species name
application	string	~40%	Traditional medicinal application (e.g. “Antiinflammatory”)
dosage	string	~55%	Reported dosage, concentration, or IC50 value
pubmed_mentions_2026	int32	0%	Total PubMed publications mentioning this compound (March 2026 snapshot)
clinical_trials_count_2026	int32	0%	ClinicalTrials.gov study count per compound (March 2026)
chembl_bioactivity_count	int32	0%	ChEMBL documented bioactivity measurement count
patent_count_since_2020	int32	0%	US patents since 2020-01-01 mentioning compound (USPTO PatentsView)

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Pricing & Licensing

Tier	Price	Includes	Purchase
Single Entity	€699 netto	JSON + Parquet + SHA-256 Manifest. 1 juristische Person, interne Nutzung. Perpetual license.	Buy Now →
Team	€1.349 netto	Alles aus Single + duckdb_queries.sql (20 Queries, 5 Kategorien) + compound_priority_score.py + 4 Pre-computed Views (Top-500 nach PubMed, Trials, Patent-Dichte, Anti-Inflammatory Panel). Unbegrenzte interne Nutzer einer juristischen Person.	Buy Now →
Enterprise	€1.699 netto	Alles aus Team + snowflake_load.sql + chromadb_ingest.py + pinecone_ingest.py + embedding_guide.md (ClinicalBERT, RAG-Pipelines) + Compound Opportunity Matrix + Clinical Pipeline Gaps CSV + Pre-chunked RAG JSONL. Multi-Entity / Konzernnutzung, interne Produktintegration erlaubt.	Buy Now →

Gemäß § 19 UStG wird keine Umsatzsteuer berechnet. Alle Preise netto. One-time purchase — keine Subscription, keine wiederkehrenden Kosten.

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Why Not Build This Yourself?

Normalising and cross-referencing 24,771 phytochemicals against four authoritative databases is not a weekend project:

Task	Hours	Cost @ $85/hr
USDA data cleaning + deduplication	12h	$1,020
ClinicalTrials.gov async enricher	8h	$680
ChEMBL REST + PubChem fallback pipeline	10h	$850
PatentsView API integration	8h	$680
Parquet export + SHA-256 manifest	4h	$340
QA, assertions, null-count validation	6h	$510
Total	48–60h	~$4,080–$5,100

This dataset: €699 one-time. No subscription. No API calls. Instant download.

Why This Dataset Exists

Large language models hallucinate botanical taxonomy. A biotech team’s RAG pipeline confidently outputting “Quercetin found in 450 species at 2.3 mg/g” sounds plausible — but the real number of species in our data is 215, and dosage varies by three orders of magnitude depending on the plant part.

The raw USDA Dr. Duke’s database is spread across 16 relational tables. Joining them correctly requires understanding non-obvious foreign keys, handling >40% null values in application fields, and normalising species names against accepted binomial nomenclature. Most teams give up after a week.

Quickstart

Python — Load 400-row sample

import pandas as pd

url = "https://raw.githubusercontent.com/wirthal1990-tech/USDA-Phytochemical-Database-JSON/main/ethno_sample_400.json"
df = pd.read_json(url)
print(f"{df.shape[0]} records, {df['chemical'].nunique()} unique compounds")
df.head()

PyArrow — Parquet (full dataset, after purchase)

import pyarrow.parquet as pq

table = pq.read_table("ethno_dataset_2026_v2.parquet")
print(f"Schema: {table.schema}")
print(f"Rows: {table.num_rows}  Memory: {table.nbytes / 1e6:.1f} MB")

DuckDB (analytical queries — sample included)

import duckdb

result = duckdb.sql("""
    SELECT
        chemical,
        MAX(pubmed_mentions_2026)       AS pubmed_score,
        MAX(clinical_trials_count_2026) AS trial_count,
        MAX(chembl_bioactivity_count)   AS bioassays,
        COUNT(DISTINCT plant_species)   AS species_count
    FROM read_json_auto('ethno_sample_400.json')
    GROUP BY chemical
    ORDER BY trial_count DESC
    LIMIT 20
""")
result.show()

HuggingFace Datasets

from datasets import load_dataset

ds = load_dataset(
    "wirthal1990-tech/USDA-Phytochemical-Database-JSON",
    split="sample",
    trust_remote_code=False
)
df = ds.to_pandas()
print(f"Records: {len(df)} | Columns: {list(df.columns)}")
df.head()

Note: The split="sample" loads ethno_sample_400.json (400 rows, 8 columns). The full 104,388-row dataset is available at ethno-api.com.

Sample Record

Below is a real record from the dataset — QUERCETIN, one of the most-studied plant compounds:

{
  "chemical": "QUERCETIN",
  "plant_species": "Abelmoschus esculentus",
  "application": "5-Lipoxygenase-Inhibitor",
  "dosage": "IC50 (uM)=4",
  "pubmed_mentions_2026": 31310,
  "clinical_trials_count_2026": 847,
  "chembl_bioactivity_count": 4231,
  "patent_count_since_2020": 312
}

All 8 fields are populated for all 104,388 records in the full dataset. The free 400-row sample contains real values for pubmed_mentions_2026; the three enrichment fields (clinical_trials_count_2026, chembl_bioactivity_count, patent_count_since_2020) contain representative placeholder values pending completion of the full enrichment run.

File Manifest

File	Size	Format	Access
ethno_sample_400.json	108 KB	JSON	Free (this repo)
ethno_sample_400.parquet	20 KB	Parquet	Free (this repo)
quickstart.ipynb	9 KB	Notebook	Free (this repo)
ethno_dataset_2026_v2.json	~18 MB	JSON	Included in all tiers
ethno_dataset_2026_v2.parquet	~900 KB	Parquet	Included in all tiers
MANIFEST_v2.json (SHA-256)	~1 KB	JSON	Included in all tiers
duckdb_queries.sql (20 Queries)	~13 KB	SQL	Team + Enterprise
compound_priority_score.py	~5 KB	Python	Team + Enterprise
snowflake_load.sql	~6 KB	SQL	Enterprise
chromadb_ingest.py	~6 KB	Python	Enterprise
pinecone_ingest.py	~6 KB	Python	Enterprise
embedding_guide.md	~7 KB	Markdown	Enterprise

Data Sources & Methodology

Source	Access	Date	Method
USDA Dr. Duke’s Phytochemical and Ethnobotanical Databases	Public domain	2026	Full 16-table PostgreSQL import, normalized
NCBI PubMed	E-utilities API	March 2026	esearch per compound, total publication count
ClinicalTrials.gov	v2 API	March 2026	Study count per compound name
ChEMBL	REST API (v34)	March 2026	Bioactivity measurement count via molecule search
USPTO PatentsView	REST API v1	March 2026	US patents since 2020-01-01 mentioning compound

All enrichment scripts are deterministic, checkpoint-resumable, and respect API rate limits. Source code available upon request for enterprise customers.

Use Cases

• RAG Pipelines — Ground LLM responses with verified phytochemical data. Each record has a PubMed evidence score — use it to weight retrieval results and filter hallucinations.
• Drug Discovery — Prioritise natural product leads by combining PubMed citations, clinical trial presence, ChEMBL bioactivity depth, and patent landscape. One query replaces weeks of manual lit review.
• Market Intelligence — Patent density score reveals which compounds are attracting commercial investment. Cross-reference with clinical trials to identify underexplored compounds with IP whitespace.
• Academic Research — Pre-computed evidence scores save months of PubMed searching. The BibTeX citation block below makes this dataset citable in peer-reviewed publications.

Dataset Versions

Version	Records	Schema	Status
v1.0	104,388	5 columns (USDA baseline)	Deprecated
v2.0	104,388	8 columns (+ PubMed, ClinicalTrials, ChEMBL, Patents)	Current

The free sample (ethno_sample_400.json) uses the v2.0 schema. Enrichment fields contain representative values pending completion of the full enrichment pipeline.

License & Commercial Access

• Free 400-row sample: CC BY-NC 4.0 — use for evaluation, academic research, and prototyping.
• Single Entity License — €699 one-time: Buy → — 1 legal entity, internal use, perpetual. No redistribution.
• Team License — €1.349 one-time: Buy → — all employees of 1 legal entity, unlimited internal users, includes analytics toolkit.
• Enterprise License — €1.699 one-time: Buy → — multi-entity / group use, internal product integration rights, full RAG integration toolkit.

Gemäß § 19 UStG wird keine Umsatzsteuer berechnet.

Citation

@misc{ethno_api_v2_2026,
  title     = {USDA Phytochemical \& Ethnobotanical Database --- Enriched v2.0},
  author    = {Wirth, Alexander},
  year      = {2026},
  publisher = {Ethno-API},
  url       = {https://ethno-api.com},
  note      = {104,388 records, 24,771 unique chemicals, 2,315 plant species, 8-column schema with PubMed, ClinicalTrials, ChEMBL, and PatentsView enrichment}
}

Contact

• Website: ethno-api.com
• Email: founder@ethno-api.com
• GitHub: @wirthal1990-tech

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_{Built by Alexander Wirth · PostgreSQL 15 · Python 3.12 · Hetzner CCX33}