Datasets:

wirthal1990-tech
/

USDA-Phytochemical-Database-JSON

Source	Version / Access Date	License
USDA Dr. Duke's Phytochemical and Ethnobotanical Databases	Archive (2024 retirement snapshot)	Public Domain (USDA)
PubMed / NCBI E-utilities	Accessed 2026-01 via `esearch.fcgi`	Open (NCBI Terms of Use)
ClinicalTrials.gov	API v2, accessed 2026-01	Public Domain (NLM)
ChEMBL	v35 REST API, accessed 2026-02	CC BY-SA 3.0
PatentsView (USPTO)	API v1, patents since 2020-01-01	Public Domain (USPTO)
PubChem (NCBI)	PUG REST API, accessed 2026-03	Public Domain (NCBI)

Schema v2.4

Field	Type	Null Count	Description
`chemical`	string	0	Compound name (natural key, from USDA)
`plant_species`	string	0	Botanical species name (natural key, from USDA)
`application`	string	38,149	Documented bioactivity / therapeutic use
`dosage`	string	67,132	Documented dosage from literature
`pubmed_mentions_2026`	Int64	0	PubMed publication mention count (title/abstract search, 2026)
`clinical_trials_count_2026`	Int64	0	ClinicalTrials.gov study count mentioning compound
`chembl_bioactivity_count`	Int64	0	ChEMBL bioactivity assay count
`patent_count_since_2020`	Int64	0	US patent count (USPTO PatentsView, since 2020-01-01)
`pubchem_cid`	Int64	13,265	PubChem Compound ID (CID) — 46.4% of unique compounds resolved
`canonical_smiles`	string	13,265	Canonical SMILES string (PubChem) — 46.4% of unique compounds resolved

Enrichment coverage:

Field	Non-zero %	Max	Mean
`pubmed_mentions_2026`	78.4%	349,640	8,646
`clinical_trials_count_2026`	24.2%	4,094	12
`chembl_bioactivity_count`	31.9%	7,679	85
`patent_count_since_2020`	37.2%	866,143	165

Note: Noise compounds (WATER, PROTEIN, GLUCOSE, etc.) and exact duplicates removed in DQA audit (2026-03-16). Post-DQA min is 0.

Enrichment Pipeline

1. PubMed (NCBI E-utilities)

Endpoint: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
Query logic: term={compound_name}[Title/Abstract] — substring match on title and abstract fields
Rate limiting: 3 requests/second (NCBI default without API key)
Output: Integer count of matching PubMed articles

2. ClinicalTrials.gov (Local XML Snapshot + Aho-Corasick)

Source: AllPublicXML archive, 575,349 studies (March 2026 snapshot)
Indexed studies: 517,205 studies with non-empty intervention_name fields (cached in ct_intervention_index.json)
Algorithm: Aho-Corasick multi-pattern string matching with word-boundary enforcement
Stereo-prefix normalization (v2.2): Compounds like (+)-CATECHIN are indexed as both (+)-catechin and catechin, covering 18 prefix types: (+)-, (-)-, (±)-, DL-, rac-, R-, S-, RS-, cis-, trans-, alpha-, beta-, gamma-, delta-, E-, Z-, L-, D-
Variants in automaton: 25,705 (from 24,698 unique compounds after skip filter)
Runtime: ~5 seconds (cached intervention index)
Output: Integer count of matching studies per compound

Why local instead of API: The ClinicalTrials.gov v2 API rejects IUPAC names containing brackets, arrows, and parentheses with HTTP 400 errors. The local XML approach eliminates rate limits, API failures, and network dependency entirely.

3. ChEMBL (REST API v35)

Endpoint: https://www.ebi.ac.uk/chembl/api/data/activity
Query logic: Direct compound name lookup → if no hit, PubChem canonical name resolution → ChEMBL molecule search → bioactivity count
Fallback chain: compound_name → PubChem → InChIKey → ChEMBL
Rate limiting: 3 requests/second (time.sleep(0.33))
Checkpoint: chembl_checkpoint.json — every 100 compounds
Error handling: -1 logged for API failures (see chembl_errors.log)

Attribution: ChEMBL data is from https://www.ebi.ac.uk/chembl/ (ChEMBL v35), licensed under CC BY-SA 3.0. Attribution required for downstream redistribution.

4. PatentsView (USPTO API v1)

Endpoint: https://api.patentsview.org/patents/query
Query logic: Patents since 2020-01-01 with compound name in title or abstract
Rate limiting: 45 requests/minute (PatentsView limit), semaphore(2) + 1.4s sleep
Checkpoint: patent_checkpoint.json — every 100 compounds
Requirement: Free API key via PATENTSVIEW_API_KEY environment variable

5. Merge & Export (`master_export_v2.py`)

Merges all 5 enrichment outputs (PubMed, ClinicalTrials, ChEMBL, Patents, PubChem SMILES/CID) into unified dataset
Exports: JSON (indent=2), Parquet (Snappy compressed), MANIFEST (SHA-256 checksums + statistics)
3-pass verification: record count, schema validation, checksum match

6. PubChem (PUG REST API)

Endpoint: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{name}/JSON
Query logic: Name-to-CID resolution, returns CID + CanonicalSMILES
Queries: 24,746 unique compound names
Resolved: 11,481 compounds (46.4% of unique chemicals)
Unresolved: 13,265 compounds (null in schema)
Rate limit: 0.35s between requests, checkpoint-resumable
Runtime: 3.2 hours (24,746 queries)
Output fields: canonical_smiles, pubchem_cid

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.

7. CTS Synonym Enrichment (v2.4)

Goal: Reduce the null-rate for pubchem_cid and canonical_smiles through systematic name variant resolution
Candidates: 14,197 compounds without PubChem CID (after excluding truncated names and length < 3)
CTS API test: UC Davis Chemical Translation Service tested first — 0% yield for all ethnobotanical trivial names → CTS not suitable for this nomenclature
PubChem PUG-REST name variants: 4 variants per compound:
1. Original (e.g. GALACTURONIC-ACID)
2. Hyphens → spaces (galacturonic acid)
3. Lowercase (galacturonic-acid)
4. Lowercase + spaces (galacturonic acid)
Checkpoint system: Resume-safe, persisted every 100 API calls
Runtime: ~3.5 hours at ~4.5 req/s
Result: 997 unique compounds newly resolved (7.0% of candidates), 2,741 records improved
Coverage improvement: 42.4% → 46.4% unique compounds (10,484 → 11,481), 71.8% → 75.4% records (55,217 → 57,958)
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

Known Limitations

ClinicalTrials.gov substring matching inflates counts for compounds with common names (e.g., "ACID" matches many unrelated trials). Consider filtering by exact intervention match for precision-critical uses.
PubMed counts include review articles — the search does not distinguish original research from reviews, meta-analyses, or editorials. Use as a relative popularity signal, not an absolute measure.
ChEMBL coverage ~34% — approximately two-thirds of compounds are too obscure for structural data in ChEMBL. These receive chembl_bioactivity_count = 0.
Species names — USDA synonyms are not always current binomial nomenclature. Some legacy names may not match modern taxonomic databases (e.g., NCBI Taxonomy, GBIF).
PubMed -1 values — historical API errors were present in pre-DQA data. Post-DQA (2026-03-16), all -1 values have been removed along with noise compounds.
Patent counts (PatentsView) — limited to US patents only. International patents (WIPO, EPO) are not included.

Noise Exclusion

117 compounds classified as noise (including generic biochemical terms like PROTEIN, PROTEINS, WATER, LEAD, GLUCOSE with inflated PubMed matches that are not specific phytochemicals) were identified. 24 of these were present in the dataset and removed during the DQA audit (2026-03-16), eliminating 11,744 records.

Exclusion criteria:

Solvents (e.g., ACETONE, ETHANOL, METHANOL)
Common elements and minerals (e.g., ALUMINUM, CALCIUM, IRON)
Generic or non-specific entries (e.g., ACIDS, ALCOHOL, ASH, FAT, FIBER, PROTEIN, WATER)
Industrial chemicals with no phytochemical relevance

Full list: noise_exclusion_list.txt

Reproducibility

All enrichment scripts are available in the repository:

Script	Purpose	Approx. Runtime
`clinicaltrials_enricher.py`	ClinicalTrials.gov enrichment	~2-3 hours
`chembl_enricher.py`	ChEMBL bioactivity enrichment	~51 hours
`patent_enricher.py`	PatentsView patent count enrichment	~10 hours
`master_export_v2.py`	Merge & export (JSON + Parquet + Manifest)	~5 minutes

Hardware: Hetzner CCX33 (8 vCPU, 32 GB RAM, AMD EPYC)
Checkpoint files enable resume after interruption — no need to restart from scratch
Deterministic output given the same API responses (APIs may return different counts over time as new publications/trials/patents are added)

License

Base USDA data: Public Domain (U.S. Government work)
Enrichment layer + compiled dataset:
- Free 400-row sample: CC BY 4.0
- Full dataset: Commercial license (single-entity, team, or enterprise)
Enrichment scripts: Available in this repository for transparency

Version History

Version	Date	Fields	Records	Changes
v1.0	2026-01	5 (chemical, plant_species, application, dosage, pubmed_mentions_2026)	104,388	Initial release with PubMed enrichment
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.
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)
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
v2.4	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
v2.4.0	2026-04	12 (+compound_type, patent_count_method)	76,907	CID audit, compound classification, patent method transparency, RESIN/RESINS CID correction, inorganic/generic reclassification

File Integrity

File	Size	SHA-256
`ethno_dataset_2026_v2.json`	16.3 MB	`cf517675c263eefb96c18a74a0238d0e142067eda2175259fde10db66a081bc3`
`ethno_dataset_2026_v2.parquet`	800 KB	`cd152dd830f769a8e86c2661f0650f20bd936452835d6ee4cad60549068c7b40`
`ethno_dataset_2026_v2.1_FINAL.json`	24.5 MB	`ae86ba33d76273dc52330ca5d75234d93f8a6d3a8db106186d39470a3c1a0db0`
`ethno_dataset_2026_v2.2.json`	25.4 MB	`7cb5719f9763f84f1cb8176b462d51fd9df5750e7cfa78e497263b7631ebba13`
`ethno_dataset_2026_v2.2.parquet`	1.2 MB	`118d28bf08b784868b60fc1445a0fdd6817d5d8a492015c51d975cf8e8e5a132`

Export timestamp: 2026-04-11T22:47:02Z (v2.4.0 final)

Methodology — Ethno-API Phytochemical Dataset v2.4.0

Data Sources