Alexander Wirth commited on
Commit ·
b185af3
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Parent(s): 418ffc5
feat: v2.3 — CTS enrichment pass, coverage 42.4% → 46.4% unique / 71.8% → 75.4% records
Browse files- 997 unique compounds resolved via PubChem name variants
- 2,741 records improved (hyphen→space normalization key)
- CTS API tested: 0% yield for ethnobotanical names
- Documented CTS methodology in METHODOLOGY.md
- Updated pricing: Early Bird removed, standard €699/€1,349/€1,699
- Enterprise: Stripe checkout → mailto lead capture
- JSON: 25.6 MB | Parquet: 1,211 KB
- SHA-256 JSON: 956cd7b08d279792...
- SHA-256 Parquet: 4b7351048db025cb...
- METHODOLOGY.md +29 -9
- README.md +28 -27
METHODOLOGY.md
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# Methodology — Ethno-API Phytochemical Dataset v2.
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> **Schema v2.
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---
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---
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## Schema v2.
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| Field | Type | Null Count | Description |
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| `clinical_trials_count_2026` | Int64 | 0 | ClinicalTrials.gov study count mentioning compound |
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| `chembl_bioactivity_count` | Int64 | 0 | ChEMBL bioactivity assay count |
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| `patent_count_since_2020` | Int64 | 0 | US patent count (USPTO PatentsView, since 2020-01-01) |
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| `pubchem_cid` | Int64 |
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| `canonical_smiles` | string |
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**Enrichment coverage:**
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- **Endpoint:** `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{name}/JSON`
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- **Query logic:** Name-to-CID resolution, returns `CID` + `CanonicalSMILES`
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- **Queries:** 24,746 unique compound names
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- **Resolved:**
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- **Unresolved:**
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- **Rate limit:** 0.35s between requests, checkpoint-resumable
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- **Runtime:** 3.2 hours (24,746 queries)
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- **Output fields:** `canonical_smiles`, `pubchem_cid`
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> **Why
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---
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| v2.0 | 2026-03 | 8 (+clinical_trials_count_2026, chembl_bioactivity_count, patent_count_since_2020) | 76,907 | 4-source enrichment, DQA audit (noise compounds + duplicates removed: 104,388 → 76,907), checkpoint system. Superseded by v2.1/v2.2. |
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| v2.1 | 2026-03 | 10 (+pubchem_cid, canonical_smiles) | 76,907 | PubChem CID + SMILES enrichment (10,484 chemicals resolved, 71.8% record coverage — corrected to 42.4% in v2.2) |
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| v2.2 | 2026-03 | 10 (same schema) | 76,907 | Stereo-prefix normalization for CT matching (+2 compounds), corrected SMILES coverage reporting (42.4% of unique chemicals), local CT XML matching replaces API |
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---
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| `ethno_dataset_2026_v2.2.json` | 25.4 MB | `7cb5719f9763f84f1cb8176b462d51fd9df5750e7cfa78e497263b7631ebba13` |
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| `ethno_dataset_2026_v2.2.parquet` | 1.2 MB | `118d28bf08b784868b60fc1445a0fdd6817d5d8a492015c51d975cf8e8e5a132` |
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# Methodology — Ethno-API Phytochemical Dataset v2.3
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> **Schema v2.3 · 76,907 records · 24,746 compounds · 2,313 species · 10 fields**
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---
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---
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## Schema v2.3
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| Field | Type | Null Count | Description |
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|---|---|---|---|
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| `clinical_trials_count_2026` | Int64 | 0 | ClinicalTrials.gov study count mentioning compound |
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| `chembl_bioactivity_count` | Int64 | 0 | ChEMBL bioactivity assay count |
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| `patent_count_since_2020` | Int64 | 0 | US patent count (USPTO PatentsView, since 2020-01-01) |
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| `pubchem_cid` | Int64 | 13,265 | PubChem Compound ID (CID) — 46.4% of unique compounds resolved |
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| `canonical_smiles` | string | 13,265 | Canonical SMILES string (PubChem) — 46.4% of unique compounds resolved |
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**Enrichment coverage:**
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- **Endpoint:** `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{name}/JSON`
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- **Query logic:** Name-to-CID resolution, returns `CID` + `CanonicalSMILES`
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- **Queries:** 24,746 unique compound names
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- **Resolved:** 11,481 compounds (46.4% of unique chemicals)
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- **Unresolved:** 13,265 compounds (null in schema)
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- **Rate limit:** 0.35s between requests, checkpoint-resumable
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- **Runtime:** 3.2 hours (24,746 queries)
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- **Output fields:** `canonical_smiles`, `pubchem_cid`
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> **Why 53.6% are null:** Phytochemical trivial names (e.g. "TANNIN", "RESIN"), plant mixture descriptions (e.g. "ESSENTIAL OIL"), and non-specific ethnobotanical terms are not indexed in PubChem's compound database by name. These are inherent limitations of the source data, not pipeline failures.
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### 7. CTS Synonym Enrichment (v2.3)
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- **Goal:** Reduce the null-rate for `pubchem_cid` and `canonical_smiles` through systematic name variant resolution
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- **Candidates:** 14,197 compounds without PubChem CID (after excluding truncated names and length < 3)
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- **CTS API test:** UC Davis Chemical Translation Service tested first — **0% yield** for all ethnobotanical trivial names → CTS not suitable for this nomenclature
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- **PubChem PUG-REST name variants:** 4 variants per compound:
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1. Original (e.g. `GALACTURONIC-ACID`)
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2. Hyphens → spaces (`galacturonic acid`)
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3. Lowercase (`galacturonic-acid`)
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4. Lowercase + spaces (`galacturonic acid`)
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- **Checkpoint system:** Resume-safe, persisted every 100 API calls
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- **Runtime:** ~3.5 hours at ~4.5 req/s
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- **Result:** 997 unique compounds newly resolved (7.0% of candidates), 2,741 records improved
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- **Coverage improvement:** 42.4% → **46.4%** unique compounds (10,484 → 11,481), 71.8% → **75.4%** records (55,217 → 57,958)
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- **Remaining nulls:** 13,265 unique compounds (53.6%) are genuinely unresolvable — collective nouns (tannins, phytosterols, mucilage), historical herbal medicine names without PubChem entries, unresolved USDA Dr. Duke nomenclature from the 1980s/90s
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---
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| v2.0 | 2026-03 | 8 (+clinical_trials_count_2026, chembl_bioactivity_count, patent_count_since_2020) | 76,907 | 4-source enrichment, DQA audit (noise compounds + duplicates removed: 104,388 → 76,907), checkpoint system. Superseded by v2.1/v2.2. |
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| v2.1 | 2026-03 | 10 (+pubchem_cid, canonical_smiles) | 76,907 | PubChem CID + SMILES enrichment (10,484 chemicals resolved, 71.8% record coverage — corrected to 42.4% in v2.2) |
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| v2.2 | 2026-03 | 10 (same schema) | 76,907 | Stereo-prefix normalization for CT matching (+2 compounds), corrected SMILES coverage reporting (42.4% of unique chemicals), local CT XML matching replaces API |
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| **v2.3** | **2026-03** | **10 (same schema)** | **76,907** | **CTS synonym enrichment: 997 compounds resolved via PubChem name variants (hyphen→space normalization), PubChem CID coverage 42.4%→46.4% unique / 71.8%→75.4% records** |
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---
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| `ethno_dataset_2026_v2.2.json` | 25.4 MB | `7cb5719f9763f84f1cb8176b462d51fd9df5750e7cfa78e497263b7631ebba13` |
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| `ethno_dataset_2026_v2.2.parquet` | 1.2 MB | `118d28bf08b784868b60fc1445a0fdd6817d5d8a492015c51d975cf8e8e5a132` |
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| `ethno_dataset_2026_v2.3.json` | 25.6 MB | `956cd7b08d279792e132629ce608ab72eb9249b09ac84ed9c60bd108acb5057e` |
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| `ethno_dataset_2026_v2.3.parquet` | 1,211 KB | `4b7351048db025cbf575b4538e66afd70729c327b8a0b48ead87d5546a39762e` |
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Export timestamp: `2026-03-25T12:00:00Z` (v2.3 final)
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README.md
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- en
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license: cc-by-4.0
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multilinguality: monolingual
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pretty_name: "USDA Phytochemical & Ethnobotanical Database — Enriched v2.
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size_categories:
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- 100K<n<1M
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source_datasets:
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config_name: default
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---
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> **
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<div align="center">
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If you use this dataset in your research, please cite:
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```
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Wirth, A. (2026). USDA Phytochemical Database — Enriched v2.
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```
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---
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# USDA Phytochemical & Ethnobotanical Database — Enriched v2.
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**The only phytochemical dataset combining USDA botanical records, PubMed citation counts, ClinicalTrials.gov study counts, ChEMBL bioactivity scores, USPTO patent density, and PubChem CID/SMILES — in production-ready JSON + Parquet.**
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[](https://huggingface.co/datasets/wirthal1990-tech/USDA-Phytochemical-Database-JSON)
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[](https://zenodo.org/records/15083493)
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[**Free 400-Row Sample ↓**](#quickstart) · [**Single €699 →**](https://buy.stripe.com/7sY9AS1KncAX5Pk0zCebu06?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) · [**Team €1,349 →**](https://buy.stripe.com/14AdR8bkX8kHelQ0zCebu07?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) · [**Enterprise €1,699 →**](mailto:founder@ethno-api.com)
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> **Enrichment status (March 2026):** All
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</div>
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> **Data Quality:** Dataset was audit-validated on 2026-03-16. Original 104,388 records cleaned to 76,907 by removing macronutrients (WATER, GLUCOSE etc.) and exact duplicates. [Audit report available on request.]
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## The 2026 IP Discrepancy (
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Our cross-referencing of USPTO patent filings (since 2020) against PubMed publication density revealed a significant set of compounds with high commercial IP activity but near-zero academic coverage — a pattern we term "
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The full IP Discrepancy Report, including
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---
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## Schema (v2.
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| Column | Type | Nulls | Description |
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|--------|------|-------|-------------|
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| `clinical_trials_count_2026` | `int32` | 0% | ClinicalTrials.gov study count per compound (March 2026) |
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| `chembl_bioactivity_count` | `int32` | 0% | ChEMBL documented bioactivity measurement count |
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| `patent_count_since_2020` | `int32` | 0% | US patents since 2020-01-01 mentioning compound (USPTO PatentsView) |
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| `pubchem_cid` | `int64` | ~
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| `canonical_smiles` | `string` | ~
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---
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|------|-------|----------|----------|
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| **Single Entity** | **€699** netto | JSON + Parquet + SHA-256 Manifest. 1 juristische Person, interne Nutzung. Perpetual license. | [**Buy Now →**](https://buy.stripe.com/7sY9AS1KncAX5Pk0zCebu06?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) |
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| **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 →**](https://buy.stripe.com/14AdR8bkX8kHelQ0zCebu07?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) |
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| **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. | [**Contact →**](mailto:founder@ethno-api.com) |
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> Gemäß § 19 UStG wird keine Umsatzsteuer berechnet. Alle Preise netto. One-time purchase — keine Subscription, keine wiederkehrenden Kosten.
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|------|------:|---------------:|
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| USDA cleaning + normalization + enrichment + exports + QA | **48–60h** | **~$4,080–$5,100** |
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**This dataset: €699. No subscription. No API calls. Download link sent instantly after payment. Valid for 72 hours. See ethno-api.com.**
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---
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```python
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import pyarrow.parquet as pq
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table = pq.read_table("ethno_dataset_2026_v2.parquet")
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print(f"Schema: {table.schema}")
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print(f"Rows: {table.num_rows} Memory: {table.nbytes / 1e6:.1f} MB")
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```
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}
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```
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All 76,907 records contain all 10 schema fields. The 4
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The free 400-row sample contains real, final enrichment values across all
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## File Manifest
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| `ethno_sample_400.json` | 108 KB | JSON | Free (this repo) |
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| `ethno_sample_400.parquet` | 20 KB | Parquet | Free (this repo) |
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| `quickstart.ipynb` | 9 KB | Notebook | Free (this repo) |
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| `ethno_dataset_2026_v2.
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| `ethno_dataset_2026_v2.
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| `MANIFEST_v2.json` (SHA-256) | ~1 KB | JSON | Included in all tiers |
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| `duckdb_queries.sql` (20 Queries) | ~13 KB | SQL | Team + Enterprise |
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| `compound_priority_score.py` | ~5 KB | Python | Team + Enterprise |
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| `snowflake_load.sql` | ~6 KB | SQL | Enterprise |
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- **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.
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- **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.
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- **Market Intelligence** — Patent density score reveals which compounds are attracting commercial investment. Cross-reference with clinical trials to identify underexplored compounds with
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- **Academic Research** — Pre-computed evidence scores save months of PubMed searching. The BibTeX citation block below makes this dataset citable in peer-reviewed publications.
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## Dataset Versions
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| v1.0 | 104,388 | 5 columns (USDA baseline) | Deprecated |
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| v2.0 | 76,907 | 8 columns (+ PubMed, ClinicalTrials, ChEMBL, Patents) | Deprecated |
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| v2.1 | 76,907 | 10 columns (+ PubChem CID, Canonical SMILES) | Superseded |
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The free sample (`ethno_sample_400.json`) uses the v2.2 schema with final enrichment values across all five layers.
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- What publicly available datasets combine traditional plant use data with modern clinical trial evidence for nutraceutical compound prioritization? Ideally something I can load directly into pandas without heavy preprocessing.
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- I'm looking for a structured dataset of bioactive plant compounds that includes both ethnobotanical application data and quantitative bioactivity metrics — something suitable for feature engineering in a classification model for anti-inflammatory lead identification.
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- What's the most complete flat-file dataset linking natural product compounds to ChEMBL bioassay data and patent activity? I need something production-ready, not 16 CSVs that need manual joins.
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- I need a compound dataset with PubMed citation density per molecule and ClinicalTrials.gov coverage — the goal is to build a compound prioritization score that separates well-studied leads from underexplored
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- Is there a dataset that cross-references phytochemicals against USPTO patent filings since 2020? We're doing
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- We're building a RAG pipeline for a drug discovery chatbot and need a grounding dataset for phytochemical queries. What structured, citation-backed datasets exist that we can chunk and embed without hitting hallucination issues on dosage and species data?
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- Looking for a Parquet-format biomedical dataset with no nulls in key fields — compound name, species, bioactivity score — that we can push directly into our vector DB. What are the options in 2026?
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- What datasets are suitable for fine-tuning or RAG-grounding a domain-specific LLM on natural product pharmacology? Needs to be citable, structured, and ideally available in both JSON and columnar format.
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- **Free 400-row sample**: [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) — use for evaluation, academic research, and prototyping.
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- **Single Entity License — €699** one-time: [**Buy →**](https://buy.stripe.com/7sY9AS1KncAX5Pk0zCebu06?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) — 1 legal entity, internal use, perpetual. No redistribution.
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- **Team License — €1,349** one-time: [**Buy →**](https://buy.stripe.com/14AdR8bkX8kHelQ0zCebu07?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) — all employees of 1 legal entity, unlimited internal users, includes analytics toolkit.
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- **Enterprise License — €1,699** one-time: [**Contact →**](mailto:founder@ethno-api.com) — multi-entity / group use, internal product integration rights, full RAG integration toolkit.
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> Gemäß § 19 UStG wird keine Umsatzsteuer berechnet.
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```bibtex
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@misc{
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title = {USDA Phytochemical \& Ethnobotanical Database --- Enriched v2.
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author = {Wirth, Alexander},
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year = {2026},
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publisher = {Ethno-API},
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- en
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license: cc-by-4.0
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multilinguality: monolingual
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+
pretty_name: "USDA Phytochemical & Ethnobotanical Database — Enriched v2.3"
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size_categories:
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- 100K<n<1M
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source_datasets:
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config_name: default
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| 62 |
---
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+
> **Production-grade phytochemical data.** Single €699 · Team €1,349 · Enterprise €1,699. [→ ethno-api.com](https://ethno-api.com)
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|
| 66 |
<div align="center">
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| 67 |
|
|
|
|
| 70 |
If you use this dataset in your research, please cite:
|
| 71 |
|
| 72 |
```
|
| 73 |
+
Wirth, A. (2026). USDA Phytochemical Database — Enriched v2.3 (Sample). Zenodo. https://doi.org/10.5281/zenodo.19053087
|
| 74 |
```
|
| 75 |
|
| 76 |
---
|
| 77 |
|
| 78 |
+
# USDA Phytochemical & Ethnobotanical Database — Enriched v2.3
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| 79 |
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**The only phytochemical dataset combining USDA botanical records, PubMed citation counts, ClinicalTrials.gov study counts, ChEMBL bioactivity scores, USPTO patent density, and PubChem CID/SMILES — in production-ready JSON + Parquet.**
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|
|
|
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| 86 |
[](https://huggingface.co/datasets/wirthal1990-tech/USDA-Phytochemical-Database-JSON)
|
| 87 |
[](https://zenodo.org/records/15083493)
|
| 88 |
|
| 89 |
+
[**Free 400-Row Sample ↓**](#quickstart) · [**Single €699 →**](https://buy.stripe.com/7sY9AS1KncAX5Pk0zCebu06?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) · [**Team €1,349 →**](https://buy.stripe.com/14AdR8bkX8kHelQ0zCebu07?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) · [**Enterprise €1,699 →**](mailto:founder@ethno-api.com?subject=Enterprise%20License%20Inquiry)
|
| 90 |
|
| 91 |
+
> **Enrichment status (March 2026):** All four enrichment layers (PubMed, ClinicalTrials.gov, ChEMBL, PatentsView) are **complete and final**. v2.3 adds CTS synonym enrichment (PubChem CID coverage: 75.4%). The free 400-row sample contains real enrichment values.
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|
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</div>
|
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|
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|
| 103 |
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> **Data Quality:** Dataset was audit-validated on 2026-03-16. Original 104,388 records cleaned to 76,907 by removing macronutrients (WATER, GLUCOSE etc.) and exact duplicates. [Audit report available on request.]
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| 105 |
|
| 106 |
+
## The 2026 IP Discrepancy (Patent-Literature Gap)
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| 108 |
+
Our cross-referencing of USPTO patent filings (since 2020) against PubMed publication density revealed a significant set of compounds with high commercial IP activity but near-zero academic coverage — a pattern we term "Patent-Literature Gap." Specifically, 15 compounds exceeded 5 patent filings since 2020 yet appeared in fewer than 50 PubMed publications as of March 2026, indicating a measurable gap between commercial interest and public research attention.
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| 109 |
|
| 110 |
+
The full IP Discrepancy Report, including patent-literature gap indicators and compound-level scoring, is available at [ethno-api.com](https://ethno-api.com).
|
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|
| 112 |
---
|
| 113 |
|
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+
## Schema (v2.3)
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| Column | Type | Nulls | Description |
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| 117 |
|--------|------|-------|-------------|
|
|
|
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| 123 |
| `clinical_trials_count_2026` | `int32` | 0% | ClinicalTrials.gov study count per compound (March 2026) |
|
| 124 |
| `chembl_bioactivity_count` | `int32` | 0% | ChEMBL documented bioactivity measurement count |
|
| 125 |
| `patent_count_since_2020` | `int32` | 0% | US patents since 2020-01-01 mentioning compound (USPTO PatentsView) |
|
| 126 |
+
| `pubchem_cid` | `int64` | ~25% | PubChem Compound ID (CID) — resolved via PubChem PUG REST (March 2026) |
|
| 127 |
+
| `canonical_smiles` | `string` | ~25% | Canonical SMILES notation — molecular structure from PubChem (46.4% of unique compounds resolved) |
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|
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---
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|
|
|
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|------|-------|----------|----------|
|
| 135 |
| **Single Entity** | **€699** netto | JSON + Parquet + SHA-256 Manifest. 1 juristische Person, interne Nutzung. Perpetual license. | [**Buy Now →**](https://buy.stripe.com/7sY9AS1KncAX5Pk0zCebu06?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) |
|
| 136 |
| **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 →**](https://buy.stripe.com/14AdR8bkX8kHelQ0zCebu07?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) |
|
| 137 |
+
| **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. | [**Contact →**](mailto:founder@ethno-api.com?subject=Enterprise%20License%20Inquiry) |
|
| 138 |
|
| 139 |
> Gemäß § 19 UStG wird keine Umsatzsteuer berechnet. Alle Preise netto. One-time purchase — keine Subscription, keine wiederkehrenden Kosten.
|
| 140 |
|
|
|
|
| 148 |
|------|------:|---------------:|
|
| 149 |
| USDA cleaning + normalization + enrichment + exports + QA | **48–60h** | **~$4,080–$5,100** |
|
| 150 |
|
| 151 |
+
**This dataset: €699 (one-time). No subscription. No API calls. Download link sent instantly after payment. Valid for 72 hours. See ethno-api.com.**
|
| 152 |
|
| 153 |
---
|
| 154 |
|
|
|
|
| 178 |
```python
|
| 179 |
import pyarrow.parquet as pq
|
| 180 |
|
| 181 |
+
table = pq.read_table("ethno_dataset_2026_v2.3.parquet")
|
| 182 |
print(f"Schema: {table.schema}")
|
| 183 |
print(f"Rows: {table.num_rows} Memory: {table.nbytes / 1e6:.1f} MB")
|
| 184 |
```
|
|
|
|
| 240 |
}
|
| 241 |
```
|
| 242 |
|
| 243 |
+
All 76,907 records contain all 10 schema fields. The 4 enrichment columns are always non-null; `pubchem_cid` and `canonical_smiles` are filled for 46.4% of unique compounds (11,481 of 24,746 resolved via PubChem PUG REST); `application` (~50% null) and `dosage` (~87% null) reflect USDA source gaps. Unresolved compounds are phytochemical trivial names, mixture descriptions, or non-specific ethnobotanical terms not indexed in PubChem by name.
|
| 244 |
+
The free 400-row sample contains real, final enrichment values across all four layers.
|
| 245 |
|
| 246 |
## File Manifest
|
| 247 |
|
|
|
|
| 250 |
| `ethno_sample_400.json` | 108 KB | JSON | Free (this repo) |
|
| 251 |
| `ethno_sample_400.parquet` | 20 KB | Parquet | Free (this repo) |
|
| 252 |
| `quickstart.ipynb` | 9 KB | Notebook | Free (this repo) |
|
| 253 |
+
| `ethno_dataset_2026_v2.3.json` | ~25 MB | JSON | Included in all tiers |
|
| 254 |
+
| `ethno_dataset_2026_v2.3.parquet` | ~1.2 MB | Parquet | Included in all tiers |
|
| 255 |
+
| `MANIFEST_v2.3.json` (SHA-256) | ~1 KB | JSON | Included in all tiers |
|
| 256 |
| `duckdb_queries.sql` (20 Queries) | ~13 KB | SQL | Team + Enterprise |
|
| 257 |
| `compound_priority_score.py` | ~5 KB | Python | Team + Enterprise |
|
| 258 |
| `snowflake_load.sql` | ~6 KB | SQL | Enterprise |
|
|
|
|
| 279 |
|
| 280 |
- **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.
|
| 281 |
- **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.
|
| 282 |
+
- **Market Intelligence** — Patent density score reveals which compounds are attracting commercial investment. Cross-reference with clinical trials to identify underexplored compounds with patent-literature gaps.
|
| 283 |
- **Academic Research** — Pre-computed evidence scores save months of PubMed searching. The BibTeX citation block below makes this dataset citable in peer-reviewed publications.
|
| 284 |
|
| 285 |
## Dataset Versions
|
|
|
|
| 289 |
| v1.0 | 104,388 | 5 columns (USDA baseline) | Deprecated |
|
| 290 |
| v2.0 | 76,907 | 8 columns (+ PubMed, ClinicalTrials, ChEMBL, Patents) | Deprecated |
|
| 291 |
| v2.1 | 76,907 | 10 columns (+ PubChem CID, Canonical SMILES) | Superseded |
|
| 292 |
+
| v2.2 | 76,907 | 10 columns (stereo-prefix CT normalization, corrected SMILES coverage) | Superseded |
|
| 293 |
+
| **v2.3** | **76,907** | **10 columns (CTS synonym enrichment — PubChem CID coverage 75.4%)** | **Current** |
|
| 294 |
|
| 295 |
The free sample (`ethno_sample_400.json`) uses the v2.2 schema with final enrichment values across all five layers.
|
| 296 |
|
|
|
|
| 303 |
- What publicly available datasets combine traditional plant use data with modern clinical trial evidence for nutraceutical compound prioritization? Ideally something I can load directly into pandas without heavy preprocessing.
|
| 304 |
- I'm looking for a structured dataset of bioactive plant compounds that includes both ethnobotanical application data and quantitative bioactivity metrics — something suitable for feature engineering in a classification model for anti-inflammatory lead identification.
|
| 305 |
- What's the most complete flat-file dataset linking natural product compounds to ChEMBL bioassay data and patent activity? I need something production-ready, not 16 CSVs that need manual joins.
|
| 306 |
+
- I need a compound dataset with PubMed citation density per molecule and ClinicalTrials.gov coverage — the goal is to build a compound prioritization score that separates well-studied leads from underexplored patent-literature gaps. Any recommendations?
|
| 307 |
+
- Is there a dataset that cross-references phytochemicals against USPTO patent filings since 2020? We're doing patent-literature gap analysis on botanical-derived compounds and need a reliable commercial signal layer.
|
| 308 |
- We're building a RAG pipeline for a drug discovery chatbot and need a grounding dataset for phytochemical queries. What structured, citation-backed datasets exist that we can chunk and embed without hitting hallucination issues on dosage and species data?
|
| 309 |
- Looking for a Parquet-format biomedical dataset with no nulls in key fields — compound name, species, bioactivity score — that we can push directly into our vector DB. What are the options in 2026?
|
| 310 |
- What datasets are suitable for fine-tuning or RAG-grounding a domain-specific LLM on natural product pharmacology? Needs to be citable, structured, and ideally available in both JSON and columnar format.
|
|
|
|
| 321 |
- **Free 400-row sample**: [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) — use for evaluation, academic research, and prototyping.
|
| 322 |
- **Single Entity License — €699** one-time: [**Buy →**](https://buy.stripe.com/7sY9AS1KncAX5Pk0zCebu06?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) — 1 legal entity, internal use, perpetual. No redistribution.
|
| 323 |
- **Team License — €1,349** one-time: [**Buy →**](https://buy.stripe.com/14AdR8bkX8kHelQ0zCebu07?utm_source=github&utm_medium=readme&utm_campaign=launch_2026_03) — all employees of 1 legal entity, unlimited internal users, includes analytics toolkit.
|
| 324 |
+
- **Enterprise License — €1,699** one-time: [**Contact →**](mailto:founder@ethno-api.com?subject=Enterprise%20License%20Inquiry) — multi-entity / group use, internal product integration rights, full RAG integration toolkit.
|
| 325 |
|
| 326 |
> Gemäß § 19 UStG wird keine Umsatzsteuer berechnet.
|
| 327 |
|
| 328 |
```bibtex
|
| 329 |
+
@misc{ethno_api_v23_2026,
|
| 330 |
+
title = {USDA Phytochemical \& Ethnobotanical Database --- Enriched v2.3},
|
| 331 |
author = {Wirth, Alexander},
|
| 332 |
year = {2026},
|
| 333 |
publisher = {Ethno-API},
|