{"id":39558,"date":"2026-03-11T10:27:04","date_gmt":"2026-03-11T09:27:04","guid":{"rendered":"https:\/\/www.graviton.at\/letterswaplibrary\/usda-phytochemical-database-enriched-with-pubmed-clinicaltrials-gov-chembl-and-uspto-patent-counts-free-sample-available\/"},"modified":"2026-03-11T10:27:04","modified_gmt":"2026-03-11T09:27:04","slug":"usda-phytochemical-database-enriched-with-pubmed-clinicaltrials-gov-chembl-and-uspto-patent-counts-free-sample-available","status":"publish","type":"post","link":"https:\/\/www.graviton.at\/letterswaplibrary\/usda-phytochemical-database-enriched-with-pubmed-clinicaltrials-gov-chembl-and-uspto-patent-counts-free-sample-available\/","title":{"rendered":"USDA Phytochemical Database Enriched With PubMed, ClinicalTrials.gov, ChEMBL, And USPTO Patent Counts \u2014 Free Sample Available"},"content":{"rendered":"<p><!-- SC_OFF --><\/p>\n<div class=\"md\">\n<p>Posting a dataset I&#8217;ve been building for a while:<\/p>\n<p><strong>What it is:<\/strong> The USDA Dr. Duke&#8217;s Phytochemical and Ethnobotanical Databases, restructured into a single flat table and enriched with four external data sources.<\/p>\n<p><strong>Schema (8 columns):<\/strong><\/p>\n<ul>\n<li><code>chemical<\/code> \u2014 compound name (USDA nomenclature)<\/li>\n<li><code>plant_species<\/code> \u2014 binomial species name<\/li>\n<li><code>application<\/code> \u2014 traditional medicinal use (where recorded)<\/li>\n<li><code>dosage<\/code> \u2014 reported effective dose or concentration<\/li>\n<li><code>pubmed_mentions_2026<\/code> \u2014 total PubMed publication count<\/li>\n<li><code>clinical_trials_count_2026<\/code> \u2014 <a href=\"http:\/\/clinicaltrials.gov\/\">ClinicalTrials.gov<\/a> study count<\/li>\n<li><code>chembl_bioactivity_count<\/code> \u2014 ChEMBL bioassay data points<\/li>\n<li><code>patent_count_since_2020<\/code> \u2014 USPTO patents since Jan 2020<\/li>\n<\/ul>\n<p><strong>Stats:<\/strong> 104,388 records, 24,771 unique compounds, 2,315 species.<\/p>\n<p><strong>Formats:<\/strong> JSON (~18 MB) and Parquet (~900 KB).<\/p>\n<p><strong>Free sample (400 rows, CC BY-NC 4.0):<\/strong> <a href=\"https:\/\/github.com\/wirthal1990-tech\/USDA-Phytochemical-Database-JSON\">https:\/\/github.com\/wirthal1990-tech\/USDA-Phytochemical-Database-JSON<\/a><\/p>\n<p>There&#8217;s also a quickstart Jupyter notebook in the repo if you want to run some DuckDB queries against the sample.<\/p>\n<p>The full dataset is commercial (one-time license). The base USDA data is public domain; the enrichment work is what you&#8217;re paying for.<\/p>\n<p>I built the dataset solo in Germany, server is a Hetzner VPS running PostgreSQL 15 and Python 3.12. Happy to answer methodology questions.<\/p>\n<\/div>\n<p><!-- SC_ON -->   submitted by   <a href=\"https:\/\/www.reddit.com\/user\/DoubleReception2962\"> \/u\/DoubleReception2962 <\/a> <br \/> <span><a href=\"https:\/\/www.reddit.com\/r\/datasets\/comments\/1rqp0u7\/usda_phytochemical_database_enriched_with_pubmed\/\">[link]<\/a><\/span>   <span><a href=\"https:\/\/www.reddit.com\/r\/datasets\/comments\/1rqp0u7\/usda_phytochemical_database_enriched_with_pubmed\/\">[comments]<\/a><\/span><\/p><div class='watch-action'><div class='watch-position align-right'><div class='action-like'><a class='lbg-style1 like-39558 jlk' href='javascript:void(0)' data-task='like' data-post_id='39558' data-nonce='bc39e8310e' rel='nofollow'><img class='wti-pixel' src='https:\/\/www.graviton.at\/letterswaplibrary\/wp-content\/plugins\/wti-like-post\/images\/pixel.gif' title='Like' \/><span class='lc-39558 lc'>0<\/span><\/a><\/div><\/div> <div class='status-39558 status align-right'><\/div><\/div><div class='wti-clear'><\/div>","protected":false},"excerpt":{"rendered":"<p>Posting a dataset I&#8217;ve been building for a while: What it is: The USDA Dr. Duke&#8217;s Phytochemical&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[85],"tags":[],"class_list":["post-39558","post","type-post","status-publish","format-standard","hentry","category-datatards","wpcat-85-id"],"_links":{"self":[{"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/posts\/39558","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/comments?post=39558"}],"version-history":[{"count":0,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/posts\/39558\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/media?parent=39558"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/categories?post=39558"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/tags?post=39558"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}