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Here we asked whether NP origin can be assigned from their molecular structure in a subset of 60,171 NPs in the recently reported Collection of Open Natural Products (COCONUT) database assigned to plants, fungi, or bacteria. Visualizing this subset in an interactive tree-map (TMAP) calculated using MAP4 (MinHashed atom pair fingerprint) clustered NPs according to their assigned origin (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/tm.gdb.tools\/map4\/coconut_tmap\/\">https:\/\/tm.gdb.tools\/map4\/coconut_tmap\/<\/jats:ext-link>\n                    ), and a support vector machine (SVM) trained with MAP4 correctly assigned the origin for 94% of plant, 89% of fungal, and 89% of bacterial NPs in this subset. An online tool based on an SVM trained with the entire subset correctly assigned the origin of further NPs with similar performance (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/np-svm-map4.gdb.tools\/\">https:\/\/np-svm-map4.gdb.tools\/<\/jats:ext-link>\n                    ). Origin information might be useful when searching for biosynthetic genes of NPs isolated from plants but produced by endophytic microorganisms.\n                  <\/jats:p>","DOI":"10.1186\/s13321-021-00559-3","type":"journal-article","created":{"date-parts":[[2021,10,18]],"date-time":"2021-10-18T15:28:00Z","timestamp":1634570880000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning"],"prefix":"10.1186","volume":"13","author":[{"given":"Alice","family":"Capecchi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2724-2942","authenticated-orcid":false,"given":"Jean-Louis","family":"Reymond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,10,18]]},"reference":[{"key":"559_CR1","doi-asserted-by":"publisher","first-page":"303","DOI":"10.3390\/metabo2020303","volume":"2","author":"DA Dias","year":"2012","unstructured":"Dias DA, Urban S, Roessner U (2012) A historical overview of natural products in drug discovery. 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