SureChEMBL in 2026: an open database of chemical and biomedical annotations from the patent literature
- 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB101SD ,
Abstract
The patent literature is a major source of scientific and technical information for drug discovery, often disclosing chemical structures, biological targets, therapeutic indications, and structure-activity relationships before they appear in the scientific literature. However, patent documents are difficult to analyse at scale because of their volume, legal and technical language, heterogeneous formats, and frequent use of nonmachine-readable representations for chemical structures. Since 2015, SureChEMBL has provided open access to chemical information automatically extracted from patent documents. Here, we present a major redesign of the SureChEMBL resource. The updated platform is built on a modern architecture and includes redesigned extraction, chemistry registration, search and data-delivery workflows, together with large-scale reprocessing of the historical corpus through a unified standardization pipeline. SureChEMBL also introduces automatically generated biomedical annotations for genes, proteins, diseases, and mechanisms, linking patent chemistry to biological context. The resource currently contains 122 million patents, 44 million chemically annotated documents, 31 million chemical structures, and 1 million biomedical entity annotations, accessible through https://www.surechembl.org/, an API and the downloadable Bulk Data.
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BibTeX
@article{bosc2026surechembl,
title = {{SureChEMBL in 2026: an open database of chemical and biomedical annotations from the patent literature}},
author = {Nicolas Bosc and Tevfik Kizilören and Eloy Félix and Muhammad Arsalan and Carlos A Moreno-Vélez and James Webster and Ricardo Arcila and Melissa F Adasme and Idil Ismail and Michał Nowotka and Yury Zavarin and Maria P Magariños and Maria J Falaguera and Anna Gaulton and Anne Hersey and Andrew R Leach and Barbara Zdrazil and Noel M O’Boyle},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag1057},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1057/9002501},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - SureChEMBL in 2026: an open database of chemical and biomedical annotations from the patent literature
AU - Nicolas Bosc
AU - Tevfik Kizilören
AU - Eloy Félix
AU - Muhammad Arsalan
AU - Carlos A Moreno-Vélez
AU - James Webster
AU - Ricardo Arcila
AU - Melissa F Adasme
AU - Idil Ismail
AU - Michał Nowotka
AU - Yury Zavarin
AU - Maria P Magariños
AU - Maria J Falaguera
AU - Anna Gaulton
AU - Anne Hersey
AU - Andrew R Leach
AU - Barbara Zdrazil
AU - Noel M O’Boyle
PY - 2026
DA - 2026/10/27
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1057
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1057/9002501
AB - The patent literature is a major source of scientific and technical information for drug discovery, often disclosing chemical structures, biological targets, therapeutic indications, and structure-activity relationships before they appear in the scientific literature. However, patent documents are difficult to analyse at scale because of their volume, legal and technical language, heterogeneous formats, and frequent use of nonmachine-readable representations for chemical structures. Since 2015, SureChEMBL has provided open access to chemical information automatically extracted from patent documents. Here, we present a major redesign of the SureChEMBL resource. The updated platform is built on a modern architecture and includes redesigned extraction, chemistry registration, search and data-delivery workflows, together with large-scale reprocessing of the historical corpus through a unified standardization pipeline. SureChEMBL also introduces automatically generated biomedical annotations for genes, proteins, diseases, and mechanisms, linking patent chemistry to biological context. The resource currently contains 122 million patents, 44 million chemically annotated documents, 31 million chemical structures, and 1 million biomedical entity annotations, accessible through https://www.surechembl.org/, an API and the downloadable Bulk Data.
SN - 0305-1048
SN - 1362-4962
ER -