{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T20:26:26Z","timestamp":1780345586849,"version":"3.54.1"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T00:00:00Z","timestamp":1722902400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T00:00:00Z","timestamp":1722902400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["MSCA-ITN-H2020"],"award-info":[{"award-number":["MSCA-ITN-H2020"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001537","name":"University of Auckland","doi-asserted-by":"publisher","award":["Doctoral Scholarship"],"award-info":[{"award-number":["Doctoral Scholarship"]}],"id":[{"id":"10.13039\/501100001537","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"abstract":"<jats:sec>\n                    <jats:title>Abstract<\/jats:title>\n                    <jats:p>enviPath is a widely used database and prediction system for microbial biotransformation pathways of primarily xenobiotic compounds. Data and prediction system are freely available both via a web interface and a public REST API. Since its initial release in 2016, we extended the data available in enviPath and improved the performance of the prediction system and usability of the overall system. We now provide three diverse data sets, covering microbial biotransformation in different environments and under different experimental conditions. This also enabled developing a pathway prediction model that is applicable to a more diverse set of chemicals. In the prediction engine, we implemented a new evaluation tailored towards pathway prediction, which returns a more honest and holistic view on the performance. We also implemented a novel applicability domain algorithm, which allows the user to estimate how well the model will perform on their data. Finally, we improved the implementation to speed up the overall system and provide new functionality via a plugin system.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Scientific contribution<\/jats:title>\n                    <jats:p>The main scientific contributions are the development of a pathway prediction model applicable to diverse chemicals, a specialized evaluation method for holistic performance assessment, and a novel applicability domain algorithm for user-specific performance estimation. The introduction of two new data sets, and the creation of links to EC classes make enviPath a unique resource in microbial biotransformation research.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13321-024-00881-6","type":"journal-article","created":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T14:04:41Z","timestamp":1722953081000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath"],"prefix":"10.1186","volume":"16","author":[{"given":"Jasmin","family":"Hafner","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Lorsbach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liam","family":"Brydon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katharina","family":"Dost","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunyang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathrin","family":"Fenner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00f6rg","family":"Wicker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,8,6]]},"reference":[{"issue":"D1","key":"881_CR1","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1093\/nar\/gkv1229","volume":"44","author":"J Wicker","year":"2016","unstructured":"Wicker J, Lorsbach T, G\u00fctlein M, Schmid E, Latino D, Kramer S, Fenner K (2016) envipath-the environmental contaminant biotransformation pathway resource. 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J Cheminform 15:53","journal-title":"J Cheminform"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-024-00881-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13321-024-00881-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-024-00881-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T02:30:14Z","timestamp":1722997814000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-024-00881-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,6]]},"references-count":29,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["881"],"URL":"https:\/\/doi.org\/10.1186\/s13321-024-00881-6","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-3607847\/v1","asserted-by":"object"}]},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,6]]},"assertion":[{"value":"14 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 August 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"JSW is one of the founders of enviPath UG & Co. KG, a scientific software development company that develops and maintains enviPath. JSW, TL, and KD are employees of enviPath UG & Co. KG. SS is an employee of Bayer AG, a manufacturer of pharmaceutical, agricultural, and consumer health chemicals. The authors declare no Conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"93"}}