Alexander Wirth Claude Sonnet 4.6 commited on
Commit ·
639dd41
1
Parent(s): cab5cc6
feat: v2.1 FINAL — 10-field sample (incl. pubchem_cid + canonical_smiles), updated quickstart.ipynb + MANIFEST
Browse files- ethno_sample_400.json: regenerated with all 10 fields (stratified: 280 with SMILES, 120 without, seed=42)
- quickstart.ipynb: updated pricing to full prices (€699/€1,349/€1,699), v2.1 filenames, 5 enrichment layers
- MANIFEST_v2.json: v2.1 SHA-256 hashes, schema_version 2.1, 71.8% PubChem fill rate
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- MANIFEST_v2.json +27 -45
- ethno_sample_400.json +0 -0
- quickstart.ipynb +5 -5
MANIFEST_v2.json
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{
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"schema_version": "2.
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"export_timestamp": "2026-03-
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"record_count": 76907,
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"unique_chemicals": 24746,
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"unique_species": 2313,
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"fields": [
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"chemical",
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"plant_species",
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"pubmed_mentions_2026",
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"clinical_trials_count_2026",
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"chembl_bioactivity_count",
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"patent_count_since_2020"
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],
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"sha256_json": "cf517675c263eefb96c18a74a0238d0e142067eda2175259fde10db66a081bc3",
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"sha256_parquet": "cd152dd830f769a8e86c2661f0650f20bd936452835d6ee4cad60549068c7b40",
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"json_size_bytes": 17125604,
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"parquet_size_bytes": 819511,
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"null_counts": {
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"chemical": 0,
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"plant_species": 0,
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"application": 38149,
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"dosage": 67132,
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"
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"
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"chembl_bioactivity_count": 0,
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"patent_count_since_2020": 0
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},
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"enrichment_statistics": {
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"
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"mean": 8645.7,
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"non_zero_count": 60266,
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"non_zero_pct": 78.36
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},
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"clinical_trials_count_2026": {
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"min": 0,
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"max": 4094,
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"mean": 11.69,
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"non_zero_count": 18575,
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"non_zero_pct": 24.15
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},
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"chembl_bioactivity_count": {
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"min": 0,
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"max": 7679,
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"mean": 85.26,
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"non_zero_count": 24560,
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"non_zero_pct": 31.93
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},
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"patent_count_since_2020": {
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"min": 0,
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"max": 866143,
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"mean": 165.47,
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"non_zero_count": 28577,
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"non_zero_pct": 37.16
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}
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},
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"
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{
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"schema_version": "2.1",
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"export_timestamp": "2026-03-20T00:00:00Z",
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"record_count": 76907,
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"unique_chemicals": 24746,
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"unique_species": 2313,
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"sha256_json": "ae86ba33d76273dc52330ca5d75234d93f8a6d3a8db106186d39470a3c1a0db0",
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"sha256_parquet": "5b1050529c3e2f372f4910b5647724b6449064c3aa3ae9ece103176293919b87",
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"file_sizes": {
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"json_mb": 24.5,
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"parquet_kb": 1194.7
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},
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"fields": [
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"chemical",
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"plant_species",
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"pubmed_mentions_2026",
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"clinical_trials_count_2026",
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"chembl_bioactivity_count",
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"patent_count_since_2020",
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"pubchem_cid",
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"canonical_smiles"
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],
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"null_counts": {
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"application": 38149,
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"dosage": 67132,
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"pubchem_cid": 21690,
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"canonical_smiles": 21690
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},
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"enrichment_statistics": {
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"pubchem_cid_filled": 55217,
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"canonical_smiles_filled": 55217,
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"pubchem_fill_rate_pct": 71.8
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},
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"data_sources": [
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"USDA Dr. Duke Phytochemical and Ethnobotanical Databases",
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"NCBI PubMed (E-utilities API, 2026 snapshot)",
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"ClinicalTrials.gov (API v2, 2026 snapshot)",
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"ChEMBL v35 REST API",
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"USPTO PatentsView (2020-2026)",
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"PubChem REST API (CID + CanonicalSMILES, 2026)"
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],
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"license": "CC BY 4.0",
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"zenodo_doi": "10.5281/zenodo.19053087"
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}
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ethno_sample_400.json
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See raw diff
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quickstart.ipynb
CHANGED
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@@ -17,7 +17,7 @@
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"cell_type": "markdown",
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"id": "cell-01",
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"metadata": {},
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"source": "# USDA Phytochemical & Ethnobotanical Database — Enriched v2.
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},
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{
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"cell_type": "code",
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"import duckdb\n",
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"\n",
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"# Load the free 400-row sample\n",
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"# To use full dataset: replace path with 'ethno_dataset_2026_v2.json'\n",
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"SAMPLE = 'ethno_sample_400.json'\n",
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"\n",
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"df = pd.read_json(SAMPLE)\n",
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"cell_type": "markdown",
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"id": "cell-07",
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"metadata": {},
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"source": "## What's Included in Each Tier\n\n### Team License (
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},
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{
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"cell_type": "code",
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"cell_type": "markdown",
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"id": "cell-09",
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"metadata": {},
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"source": "## Citation\n\n```bibtex\n@misc{
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}
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]
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}
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"cell_type": "markdown",
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"id": "cell-01",
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"metadata": {},
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"source": "# USDA Phytochemical & Ethnobotanical Database — Enriched v2.1\n\n**76,907 records · 24,746 compounds · 2,313 species · 5 enrichment layers**\n\n| Tier | Price | Includes |\n|------|-------|----------|\n| **Single Entity** | [€699](https://buy.stripe.com/00w6oGgFh58v6Toeqsebu02?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03) | JSON + Parquet + SHA-256 Manifest |\n| **Team** | [€1,349](https://buy.stripe.com/dRm7sK9cP1Wj0v06Y0ebu03?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03) | + `duckdb_queries.sql` (20 queries) + `compound_priority_score.py` + 4 Pre-computed Views |\n| **Enterprise** | [€1,699](https://buy.stripe.com/dRm28q0Gj1WjdhM6Y0ebu04?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03) | + `snowflake_load.sql` + `chromadb_ingest.py` + `pinecone_ingest.py` + `embedding_guide.md` + Opportunity Matrix |\n\n**Full dataset:** [ethno-api.com](https://ethno-api.com) · **This notebook runs on the free 400-row sample.**\n"
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},
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{
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"cell_type": "code",
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"import duckdb\n",
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"\n",
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"# Load the free 400-row sample\n",
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"# To use full dataset: replace path with 'ethno_dataset_2026_v2.1_FINAL.json'\n",
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"SAMPLE = 'ethno_sample_400.json'\n",
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"\n",
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"df = pd.read_json(SAMPLE)\n",
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"cell_type": "markdown",
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"id": "cell-07",
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"metadata": {},
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"source": "## What's Included in Each Tier\n\n### Team License (€1,349, reg. €1.349) — adds to Single:\n| File | Description |\n|------|-------------|\n| `duckdb_queries.sql` | 20 production-ready queries across 5 categories (compound discovery, evidence scoring, species analysis, application intelligence, IP/pipeline) |\n| `compound_priority_score.py` | Combined evidence score calculator across all 4 layers |\n| `top500_by_pubmed.parquet` | Pre-computed Top 500 compounds by PubMed score |\n| `top500_by_trials.parquet` | Pre-computed Top 500 by ClinicalTrials count |\n| `top500_by_patent_density.parquet` | Pre-computed Top 500 by patent density |\n| `anti_inflammatory_panel.parquet` | All anti-inflammatory application records |\n\n### Enterprise License (€1,699, reg. €1.699) — adds to Team:\n| File | Description |\n|------|-------------|\n| `snowflake_load.sql` | Drop-in Snowflake import script (Stage + COPY INTO + Verify) |\n| `chromadb_ingest.py` | ChromaDB vector ingest with batch upload, --resume, verification |\n| `pinecone_ingest.py` | Pinecone ingest supporting OpenAI, sentence-transformers, Pinecone inference |\n| `embedding_guide.md` | ClinicalBERT, RAG pipeline templates, cost benchmarks |\n| `compound_opportunity_matrix.csv` | Ranked compound candidates: high bioactivity × low patent density |\n| `clinical_pipeline_gaps.csv` | High-PubMed, low-trial compounds: drug discovery pipeline gaps |\n| `ethno_rag_chunks.jsonl` | Pre-chunked JSONL for direct LLM embedding (ChromaDB / Pinecone) |\n\n---\n\n**→ Purchase the full dataset:**\n\n[**Single €699 →**](https://buy.stripe.com/00w6oGgFh58v6Toeqsebu02?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03) [**Team €1,349 →**](https://buy.stripe.com/dRm7sK9cP1Wj0v06Y0ebu03?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03) [**Enterprise €1,699 →**](https://buy.stripe.com/dRm28q0Gj1WjdhM6Y0ebu04?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03)\n"
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},
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{
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"cell_type": "code",
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"cell_type": "markdown",
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"id": "cell-09",
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"metadata": {},
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"source": "## Citation\n\n```bibtex\n@misc{ethno_api_v2.1_2026,\n title = {USDA Phytochemical \\& Ethnobotanical Database --- Enriched v2.1},\n author = {Wirth, Alexander},\n year = {2026},\n publisher = {Ethno-API},\n url = {https://ethno-api.com},\n note = {76,907 records, 24,746 unique chemicals, 2,313 plant species,\n 10-column schema with PubMed, ClinicalTrials, ChEMBL, and PatentsView enrichment}\n}\n```\n\n**Links:** [ethno-api.com](https://ethno-api.com) · [GitHub](https://github.com/wirthal1990-tech/USDA-Phytochemical-Database-JSON) · [HuggingFace](https://huggingface.co/datasets/wirthal1990-tech/USDA-Phytochemical-Database-JSON)\n\n\n---\n\n## Purchase Full Dataset\n\n| Tier | Price | |\n|------|-------|---|\n| Single Entity | ⚡ €299 (reg. €699) | [**Buy →**](https://buy.stripe.com/00w6oGgFh58v6Toeqsebu02?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03) |\n| Team | ⚡ €549 (reg. €1.349) | [**Buy →**](https://buy.stripe.com/dRm7sK9cP1Wj0v06Y0ebu03?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03) |\n| Enterprise | ⚡ €899 (reg. €1.699) | [**Buy →**](https://buy.stripe.com/dRm28q0Gj1WjdhM6Y0ebu04?utm_source=github&utm_medium=notebook&utm_campaign=launch_2026_03) |\n\n> Gemäß § 19 UStG keine Umsatzsteuer.\n"
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}
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]
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}
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