---
language:
- en
license: cc-by-4.0
pretty_name: Ethno-API v2.4.0 — USDA Phytochemical Database Public Sample
task_categories:
- text-retrieval
- feature-extraction
size_categories:
- n<1K
source_datasets:
- extended
tags:
- tabular
- datasets
- parquet
- pandas
- phytochemistry
- ethnobotany
- natural-products
- cheminformatics
- pubchem
- pubmed
- chembl
- patents
- smiles
- rag
- data-engineering
- data-cleaning
configs:
- config_name: default
  default: true
  data_files:
  - split: train
    path: ethno_sample_400.parquet
---

<p align="center">
  <img src="./assets/ethno-api-readme-banner.svg" alt="Ethno-API v2.4.0 — phytochemical data rescue, RAG-ready exports, public dataset metrics, and no medical claims" width="100%">
</p>

# Ethno-API v2.4.0 — Public Sample

> **Hugging Face hosts a 400-row public sample** of Ethno-API v2.4.0: a cleaned and enriched phytochemical data-engineering project derived from the USDA Dr. Duke source data.  
> The full project contains **76,907 records**, **2,313 plant species**, **24,746 unique chemical entities**, and a **16-field public schema** with PubMed, ClinicalTrials.gov, ChEMBL, PatentsView, PubChem CID/SMILES, and partner-assisted CID/IUPAC resolution fields.  
> **No medical claims. No pharmaceutical validation. No safety or efficacy claims. Research and retrieval use only.**

<p align="left">
  <a href="https://doi.org/10.5281/zenodo.19660107"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.19660107.svg" alt="Zenodo DOI"></a>
  <a href="https://huggingface.co/datasets/wirthal1990-tech/USDA-Phytochemical-Database-JSON"><img src="https://img.shields.io/badge/HuggingFace-Dataset-yellow" alt="Hugging Face Dataset"></a>
  <a href="https://creativecommons.org/licenses/by/4.0/"><img src="https://img.shields.io/badge/public%20sample-CC%20BY%204.0-lightgrey.svg" alt="Public sample license: CC BY 4.0"></a>
</p>

---

## What Is Hosted Here

| Item | Value |
|---|---:|
| Hosted file | `ethno_sample_400.parquet` |
| Hosted split | `train` |
| Public sample size | 400 rows |
| Hosted format | Parquet |
| Public sample license | CC BY 4.0 |
| Full project version | v2.4.0 |
| Full project records | 76,907 |
| Full project plant species | 2,313 |
| Full project unique chemical entities | 24,746 |
| Public schema fields | 16 |
| Partner-assisted CID/IUPAC records | 1,197 |
| DOI | `10.5281/zenodo.19660107` |

This Hugging Face repository is a **public sample and documentation surface**, not the full commercial export package.

---

## Load the Public Sample

```python
from datasets import load_dataset

ds = load_dataset(
    "wirthal1990-tech/USDA-Phytochemical-Database-JSON",
    split="train",
)

print(ds)
print(ds.column_names)
print(ds[0])
```

Pandas / Parquet workflow:

```python
import pandas as pd

df = pd.read_parquet("hf://datasets/wirthal1990-tech/USDA-Phytochemical-Database-JSON/ethno_sample_400.parquet")

print(df.shape)
print(df[["chemical", "plant_species", "pubchem_cid", "canonical_smiles"]].head())
```

---

## Dataset Scope

Ethno-API is a machine-readable, enriched version of the USDA Dr. Duke phytochemical and ethnobotanical source data, flattened into a practical JSON/Parquet-oriented structure for:

- data rescue and normalization demonstrations
- retrieval / RAG ingestion experiments
- phytochemical and natural-products data prototypes
- QA-gated identifier workflows
- data-product portfolio proof for client projects

It is **not** a medical product, **not** a clinical validation layer, and **not** evidence that any compound is safe, effective, therapeutically useful, or suitable for use.

---

## Public Schema — v2.4.0, 16 Fields

| Field | Type | Coverage | Notes |
|---|---:|---:|---|
| `chemical` | string | 100% | USDA compound label, normalized for flat-table use |
| `plant_species` | string | 100% | Latin binomial species name |
| `application` | string / null | partial | Source application / activity context where present |
| `dosage` | string / null | partial | Source dosage or concentration text where present; **not usage guidance** |
| `pubmed_mentions_2026` | integer | enrichment layer | PubMed mention-count snapshot |
| `clinical_trials_count_2026` | integer | enrichment layer | ClinicalTrials.gov study-count snapshot; **not clinical validation** |
| `chembl_bioactivity_count` | integer | enrichment layer | ChEMBL bioactivity measurement count |
| `patent_count_since_2020` | integer / float | enrichment layer | PatentsView / patent-density feature |
| `pubchem_cid` | integer / null | approx. 75–82% depending on export/audit view | PubChem CID from enrichment pipeline |
| `canonical_smiles` | string / null | 57,757 records with SMILES | Canonical SMILES retrieved via PubChem |
| `compound_type` | string | 100% | Compound classification used for filtering |
| `patent_count_method` | string | 100% | Method label for patent-count derivation |
| `partner_cid` | integer / null | 1,197 records | Partner-assisted PubChem CID resolution |
| `inchi_key` | string / null | subset | Partner-assisted InChIKey / identifier resolution |
| `iupac_verified` | string / bool / null | subset | Partner-assisted identifier-verification state |
| `partner_match_method` | string / null | subset | Match method used in partner-resolution file |

**Partner-resolution file:** `exports/iupac_cid_resolutions.json` — 1,197 partner-assisted CID/IUPAC resolution records.

---

## Enrichment Layers

| Layer | Function | Limitation |
|---|---|---|
| PubMed | Mention-count snapshot | Search-density proxy only |
| ClinicalTrials.gov | Study-count snapshot | Not clinical validation |
| ChEMBL | Bioactivity-count feature | Count metadata, not safety or efficacy proof |
| PatentsView | Patent-density feature | Innovation / IP-density proxy |
| PubChem | CID and canonical SMILES enrichment | Coverage depends on successful identifier matching |
| Partner-assisted resolution | CID/IUPAC identifier resolution subset | Identifier-level contribution only |

---

## QA Pipeline

1. Normalize USDA source records into a flat analytical schema.
2. Add external enrichment layers from PubMed, ClinicalTrials.gov, ChEMBL, PatentsView, and PubChem.
3. Retrieve PubChem CID and canonical SMILES where available.
4. Add compound classification and patent-count method fields.
5. Add partner-assisted CID/IUPAC resolution subset.
6. Run reverse-SMILES QA as a downstream identifier-consistency gate.
7. Export JSON and Parquet samples for analysis and retrieval experiments.

### Reverse-SMILES QA Audit — v2.4.0

| Verdict | Count | Interpretation |
|---|---:|---|
| `validated` | 11,981 | Strict round-trip pass |
| `plausible` | 8,370 | Pass with caveats |
| `review_required` | 37,361 | Visible but not auto-trusted |
| `invalidated` | 45 | Failed validation; excluded from default retrieval-ready export |
| `insufficient_data` | 19,150 | No SMILES available |
| **Total** | **76,907** | Full v2.4.0 input set |

**Default retrieval-ready rule:** exclude `invalidated` and `insufficient_data`. Keep `review_required` visible, but do not auto-trust it.

**Export-eligible records by the stated QA rule:** 57,712  
`validated + plausible + review_required = 11,981 + 8,370 + 37,361`

Known v2.4.0 QA fixes include thiol-false-alcohol detection, non-carboxylic-acid classifier correction, and strictest-verdict-wins CID tainting logic.

---

## Intended Use

| Use case | Fit |
|---|---|
| Retrieval experiments | Build test corpora for vector search and RAG pipelines |
| Data cleaning demos | Show normalization, enrichment, and QA-gating workflows |
| Natural-products data prototypes | Explore structured phytochemical source data |
| Portfolio proof | Demonstrate data rescue → enrichment → QA → export architecture |
| Review workflows | Inspect identifier-resolution and QA-gate logic on a bounded public sample |

---

## Limitations — Read Before Use

- **Public sample only.** This Hub dataset contains a 400-row public sample, not the full 76,907-record export.
- **No pharmaceutical validation.** This dataset does not confirm biological activity, safety, efficacy, dosage relevance, or clinical utility.
- **No medical claims.** Nothing in this repository constitutes medical advice, treatment guidance, product guidance, or usage recommendation.
- **Source dependency.** Baseline relationships reflect USDA/source-database records and may contain historical terminology, sparse annotations, or context limitations.
- **Coverage gaps.** Not all records have PubChem CID, SMILES, InChIKey, dosage/source-concentration text, or activity context.
- **Partner validation is scoped.** The 1,197 partner-assisted records are identifier-resolution work, not full pharmacological validation.
- **QA verdicts are not clinical verdicts.** Reverse-SMILES QA checks identifier consistency, not biological truth.
- **Snapshot.** v2.4.0 reflects a point-in-time enrichment snapshot. External databases can change.

---

## Distribution

| Channel | URL |
|---|---|
| Website | https://ethno-api.com |
| GitHub | https://github.com/wirthal1990-tech/USDA-Phytochemical-Database-JSON |
| Hugging Face | https://huggingface.co/datasets/wirthal1990-tech/USDA-Phytochemical-Database-JSON |
| Kaggle | https://www.kaggle.com/datasets/alexanderwirth/usda-phytochemical-database-json |
| Zenodo DOI | https://doi.org/10.5281/zenodo.19660107 |

---

## Citation

```bibtex
@misc{ethno_api_v24_2026,
  title     = {USDA Phytochemical & Ethnobotanical Database -- Enriched v2.4.0},
  author    = {Wirth, Alexander},
  year      = {2026},
  publisher = {Ethno-API},
  url       = {https://ethno-api.com},
  doi       = {10.5281/zenodo.19660107},
  note      = {76,907 records, 24,746 unique chemical entities, 2,313 plant species}
}
```

---

## Credits

| Role | Contributor |
|---|---|
| Data pipeline and project architecture | Alexander Wirth |
| Scientific review / partner-resolution contribution | Dominic Fagan (BSc Chemistry) |

---

## License

Public sample files in this repository: **CC BY 4.0** unless otherwise stated.  
Full commercial dataset: separate Ethno-API license terms.  
Code snippets / methodology scripts: MIT only where explicitly marked.