chore: Update documentation for v2.2 release (42.4% SMILES coverage, 76907 records)

METHODOLOGY.md

@@ -1,6 +1,6 @@
-# Methodology — Ethno-API Phytochemical Dataset v2.1
+# Methodology — Ethno-API Phytochemical Dataset v2.2
 
-> **Schema v2.1 · 76,907 records · 24,746 compounds · 2,313 species · 10 fields**
+> **Schema v2.2 · 76,907 records · 24,746 compounds · 2,313 species · 10 fields**
 
 ---
 
@@ -17,7 +17,7 @@
 
 ---
 
-## Schema v2.1
+## Schema v2.2
 
 | Field | Type | Null Count | Description |
 |---|---|---|---|
@@ -29,8 +29,8 @@
 | `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 | 21,690 | PubChem Compound ID (CID) |
-| `canonical_smiles` | string | 21,690 | Canonical SMILES string (PubChem) |
+| `pubchem_cid` | Int64 | 44,329 | PubChem Compound ID (CID) — 42.4% of unique compounds resolved |
+| `canonical_smiles` | string | 44,329 | Canonical SMILES string (PubChem) — 42.4% of unique compounds resolved |
 
 **Enrichment coverage:**
 
@@ -54,13 +54,17 @@
 - **Rate limiting:** 3 requests/second (NCBI default without API key)
 - **Output:** Integer count of matching PubMed articles
 
-### 2. ClinicalTrials.gov (API v2)
+### 2. ClinicalTrials.gov (Local XML Snapshot + Aho-Corasick)
 
-- **Endpoint:** `https://clinicaltrials.gov/api/v2/studies`
-- **Query logic:** Free-text search for compound name across study titles and interventions
-- **Rate limiting:** 5 requests/second, checkpoint every 100 compounds
-- **Runtime:** ~2-3 hours for 24,746 unique compounds
-- **Checkpoint:** `ct_checkpoint.json` — enables resume after interruption
+- **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)
 
@@ -83,10 +87,23 @@
 
 ### 5. Merge & Export (`master_export_v2.py`)
 
-- Merges all 4 enrichment outputs into unified dataset
-- Exports: JSON (compact), Parquet (Snappy compressed), MANIFEST (SHA-256 checksums + statistics)
+- Merges all 4 enrichment outputs + 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:** 10,484 compounds (42.4% of unique chemicals)
+- **Unresolved:** 14,262 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 57.6% 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.
+
 ---
 
 ## Known Limitations
@@ -152,7 +169,8 @@ All enrichment scripts are available in the repository:
 |---|---|---|---|---|
 | 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 |
-| v2.1 | 2026-03 | 10 (+pubchem_cid, canonical_smiles) | 76,907 | PubChem CID + SMILES enrichment (10,484 chemicals resolved, 71.8% record coverage) |
+| 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 |
 
 ---
 
@@ -163,5 +181,7 @@ All enrichment scripts are available in the repository:
 | `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: `2026-03-16T21:10:00+00:00` (post-DQA)
+Export timestamp: `2026-03-22T14:29:03Z` (v2.2 final)

README.md

@@ -7,7 +7,7 @@ language:
 - en
 license: cc-by-4.0
 multilinguality: monolingual
-pretty_name: "USDA Phytochemical & Ethnobotanical Database — Enriched v2.1"
+pretty_name: "USDA Phytochemical & Ethnobotanical Database — Enriched v2.2"
 size_categories:
 - 100K<n<1M
 source_datasets:
@@ -70,12 +70,12 @@ dataset_info:
 If you use this dataset in your research, please cite:
 
 ```
-Wirth, A. (2026). USDA Phytochemical Database — Enriched v2.1 (Sample). Zenodo. https://doi.org/10.5281/zenodo.19053087
+Wirth, A. (2026). USDA Phytochemical Database — Enriched v2.2 (Sample). Zenodo. https://doi.org/10.5281/zenodo.19053087
 ```
 
 ---
 
-# USDA Phytochemical & Ethnobotanical Database — Enriched v2.1
+# USDA Phytochemical & Ethnobotanical Database — Enriched v2.2
 
 **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.**
 
@@ -111,7 +111,7 @@ The full IP Discrepancy Report, including Freedom-to-Operate indicators and comp
 
 ---
 
-## Schema (v2.1)
+## Schema (v2.2)
 
 | Column | Type | Nulls | Description |
 |--------|------|-------|-------------|
@@ -123,8 +123,8 @@ The full IP Discrepancy Report, including Freedom-to-Operate indicators and comp
 | `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) |
-| `pubchem_cid` | `int64` | ~28% | PubChem Compound ID (CID) — resolved via PubChem PUG REST (March 2026) |
-| `canonical_smiles` | `string` | ~28% | Canonical SMILES notation — molecular structure from PubChem |
+| `pubchem_cid` | `int64` | ~58% | PubChem Compound ID (CID) — resolved via PubChem PUG REST (March 2026) |
+| `canonical_smiles` | `string` | ~58% | Canonical SMILES notation — molecular structure from PubChem (42.4% of unique compounds resolved) |
 
 ---
 
@@ -240,7 +240,7 @@ Below is a real record from the dataset — QUERCETIN, one of the most-studied p
 }
 ```
 
-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 71.8% of records (10,484 unique chemicals resolved via PubChem); `application` (~50% null) and `dosage` (~87% null) reflect USDA source gaps.
+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 42.4% of unique compounds (10,484 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.
 The free 400-row sample contains real, final enrichment values across all four layers.
 
 ## File Manifest
@@ -288,7 +288,8 @@ Enrichment methodology is documented in [`METHODOLOGY.md`](METHODOLOGY.md). Sour
 |---------|--------:|--------|--------|
 | v1.0 | 104,388 | 5 columns (USDA baseline) | Deprecated |
 | v2.0 | 76,907 | 8 columns (+ PubMed, ClinicalTrials, ChEMBL, Patents) | Superseded |
-| **v2.1** | **76,907** | **10 columns (+ PubChem CID, Canonical SMILES)** | **Current** |
+| v2.1 | 76,907 | 10 columns (+ PubChem CID, Canonical SMILES) | Superseded |
+| **v2.2** | **76,907** | **10 columns (stereo-prefix CT normalization, corrected SMILES coverage)** | **Current** |
 
 The free sample (`ethno_sample_400.json`) uses the v2.0 schema with final enrichment values across all four layers.
 
@@ -325,13 +326,13 @@ Ethno-API is the deterministic answer to these pipeline requirements.
 
 ```bibtex
 @misc{ethno_api_v2_2026,
-  title     = {USDA Phytochemical \& Ethnobotanical Database --- Enriched v2.1},
+  title     = {USDA Phytochemical \& Ethnobotanical Database --- Enriched v2.2},
   author    = {Wirth, Alexander},
   year      = {2026},
   publisher = {Ethno-API},
   url       = {https://ethno-api.com},
   doi       = {10.5281/zenodo.19053087},
-  note      = {76,907 records, 24,746 unique chemicals, 2,313 plant species, 8-column schema with PubMed, ClinicalTrials, ChEMBL, and PatentsView enrichment}
+  note      = {76,907 records, 24,746 unique chemicals, 2,313 plant species, 10-column schema with PubMed, ClinicalTrials, ChEMBL, PatentsView, PubChem CID/SMILES enrichment}
 }
 ```