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For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.","is_dataset_classified":null,"base_score":8.615770754777232,"endowment":8.615770754777232,"datacite_reuse_total":25,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"26400175","pmcid":"PMC4702940","openalex_id":"https://openalex.org/W2177317049","authors":[],"funders":[{"funder_name":"Intramural NIH HHS","grant_id":"","title":null},{"funder_name":"Intramural NIH HHS","grant_id":"","title":null}],"total_grants":2,"fwci":318.6428,"citation_percentile":1.0,"influential_citations":0,"citation_trend":[{"year":2013,"count":2},{"year":2015,"count":3},{"year":2016,"count":163},{"year":2017,"count":286},{"year":2018,"count":500},{"year":2019,"count":509},{"year":2020,"count":619},{"year":2021,"count":640},{"year":2022,"count":577},{"year":2023,"count":631},{"year":2024,"count":661},{"year":2025,"count":638},{"year":2026,"count":283}],"oa_status":"gold","license":"public-domain","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/44/D1/D1202/9484096/gkv951.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/44/D1/D1202/9484096/gkv951.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/44/D1/D1202/9484096/gkv951.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkv951","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/26400175","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4702940","host_type":"repository"},{"url":"http://nar.oxfordjournals.org/cgi/content/short/44/D1/D1202","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC4702940","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC4702940?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Computational Drug Discovery Methods","Biomedical Text Mining and Ontologies","Metabolomics and Mass Spectrometry Studies","Databases, Chemical","Internet","Molecular Structure","Pharmaceutical Preparations","Software"],"mesh_terms":["Pharmaceutical Preparations","Software","Molecular Structure","Internet","Databases, Chemical"],"keywords":["PubChem","Database","Resource (disambiguation)","Information resource","Upload","Computer science","World Wide Web","Biology","Computational biology"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.26581916","title":"Additional file 7 of Investigation of chemical structure recognition by encoder–decoder models in learning progress","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26581916.v1","title":"Additional file 7 of Investigation of chemical structure recognition by encoder–decoder models in learning progress","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26581913.v1","title":"Additional file 6 of Investigation of chemical structure recognition by encoder–decoder models in learning progress","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26581913","title":"Additional file 6 of Investigation of chemical structure recognition by encoder–decoder models in learning progress","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26581910.v1","title":"Additional file 5 of Investigation of chemical structure recognition by encoder–decoder models in learning progress","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26581910","title":"Additional file 5 of Investigation of chemical structure recognition by encoder–decoder models in learning progress","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26581907.v1","title":"Additional file 4 of Investigation of chemical structure recognition by encoder–decoder models in learning progress","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26581907","title":"Additional file 4 of Investigation of chemical structure recognition by encoder–decoder models in learning progress","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.13257687.v1","title":"Additional file 4 of Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) 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