{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:16Z","timestamp":1772138056748,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,2]],"date-time":"2022-11-02T00:00:00Z","timestamp":1667347200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Education and Research","award":["01GM2003A"],"award-info":[{"award-number":["01GM2003A"]}]},{"name":"European Union\u2019s Horizon 2020 programme","award":["824087"],"award-info":[{"award-number":["824087"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Drug discovery practitioners in industry and academia use semantic tools to extract information from online scientific literature to generate new insights into targets, therapeutics and diseases. However, due to complexities in access and analysis, patent-based literature is often overlooked as a source of information. As drug discovery is a highly competitive field, naturally, tools that tap into patent literature can provide any actor in the field an advantage in terms of better informed decision-making. Hence, we aim to facilitate access to patent literature through the creation of an automatic tool for extracting information from patents described in existing public resources.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present PEMT, a novel patent enrichment tool, that takes advantage of public databases like ChEMBL and SureChEMBL to extract relevant patent information linked to chemical structures and\/or gene names described through FAIR principles and metadata annotations. PEMT aims at supporting drug discovery and research by establishing a patent landscape around genes of interest. The pharmaceutical focus of the tool is mainly due to the subselection of International Patent Classification codes, but in principle, it can be used for other patent fields, provided that a link between a concept and chemical structure is investigated. Finally, we demonstrate a use-case in rare diseases by generating a gene-patent list based on the epidemiological prevalence of these diseases and exploring their underlying patent landscapes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PEMT is an open-source Python tool and its source code and PyPi package are available at https:\/\/github.com\/Fraunhofer-ITMP\/PEMT and https:\/\/pypi.org\/project\/PEMT\/, respectively.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac716","type":"journal-article","created":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T09:13:06Z","timestamp":1667293986000},"source":"Crossref","is-referenced-by-count":9,"title":["PEMT: a patent enrichment tool for drug discovery"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7683-0452","authenticated-orcid":false,"given":"Yojana","family":"Gadiya","sequence":"first","affiliation":[{"name":"Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) , Hamburg 22525, Germany"},{"name":"Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) , Frankfurt 60590, Germany"}]},{"given":"Andrea","family":"Zaliani","sequence":"additional","affiliation":[{"name":"Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) , Hamburg 22525, Germany"},{"name":"Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) , Frankfurt 60590, Germany"}]},{"given":"Philip","family":"Gribbon","sequence":"additional","affiliation":[{"name":"Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) , Hamburg 22525, Germany"},{"name":"Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) , Frankfurt 60590, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9012-6720","authenticated-orcid":false,"given":"Martin","family":"Hofmann-Apitius","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Sankt Augustin 53754, Germany"},{"name":"Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn , Bonn 53113, Germany"}]}],"member":"286","published-online":{"date-parts":[[2022,11,2]]},"reference":[{"key":"2023122218555095600_btac716-B1","doi-asserted-by":"crossref","first-page":"16052","DOI":"10.18632\/oncotarget.14109","article-title":"Inhibition of the fibroblast growth factor receptor (FGFR) pathway: the current landscape and barriers to clinical application","volume":"8","author":"Chae","year":"2017","journal-title":"Oncotarget"},{"key":"2023122218555095600_btac716-B2","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1080\/13543776.2018.1438409","article-title":"Tips for reading patents: a concise introduction for scientists","volume":"28","author":"Donald","year":"2018","journal-title":"Exp. Opin. Ther. Pat"},{"key":"2023122218555095600_btac716-B3","doi-asserted-by":"crossref","first-page":"D1100","DOI":"10.1093\/nar\/gkr777","article-title":"ChEMBL: a large-scale bioactivity database for drug discovery","volume":"40","author":"Gaulton","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023122218555095600_btac716-B4","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1038\/sj.leu.2403347","article-title":"Targeting FGFR3 in multiple myeloma: inhibition of t (4; 14)-positive cells by SU5402 and PD173074","volume":"18","author":"Grand","year":"2004","journal-title":"Leukemia"},{"key":"2023122218555095600_btac716-B5","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1016\/j.drudis.2013.11.005","article-title":"Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines","volume":"19","author":"Jin","year":"2014","journal-title":"Drug Discov. 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