{"doi":"10.1093/nar/gkad1004","title":"The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods","abstract":"ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated, high-quality, large-scale, open, FAIR and Global Core Biodata Resource of bioactive molecules with drug-like properties, previously described in the 2012, 2014, 2017 and 2019 Nucleic Acids Research Database Issues. Since its introduction in 2009, ChEMBL's content has changed dramatically in size and diversity of data types. Through incorporation of multiple new datasets from depositors since the 2019 update, ChEMBL now contains slightly more bioactivity data from deposited data vs data extracted from literature. In collaboration with the EUbOPEN consortium, chemical probe data is now regularly deposited into ChEMBL. Release 27 made curated data available for compounds screened for potential anti-SARS-CoV-2 activity from several large-scale drug repurposing screens. In addition, new patent bioactivity data have been added to the latest ChEMBL releases, and various new features have been incorporated, including a Natural Product likeness score, updated flags for Natural Products, a new flag for Chemical Probes, and the initial annotation of the action type for ∼270 000 bioactivity measurements.","journal":"Nucleic Acids Research","year":2023,"id":314642,"datarank":5.469724030791308,"base_score":7.133295954896068,"endowment":7.133295954896068,"self_citation_contribution":1.0699943932344105,"citation_network_contribution":4.399729637556898,"self_endowment_contribution":1.0699943932344105,"citer_contribution":4.399729637556898,"corpus_percentile":96.24042701322813,"corpus_rank":487,"citation_count":1252,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9468,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":79.1667,"fair_percentile":97.67655151329869,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":75390,"name":"Eloy Félix","orcid":"0000-0002-5512-6810","position":1,"is_corresponding":false},{"id":34541,"name":"Fiona Hunter","orcid":"0000-0001-7160-1880","position":2,"is_corresponding":false},{"id":106693,"name":"Emma J. Manners","orcid":"0000-0001-7875-1259","position":3,"is_corresponding":false},{"id":1013664,"name":"James Blackshaw","orcid":"0000-0002-0343-0319","position":4,"is_corresponding":false},{"id":1015138,"name":"Sybilla Corbett","orcid":null,"position":5,"is_corresponding":false},{"id":75389,"name":"Marleen De Veij","orcid":"0000-0003-2587-8752","position":6,"is_corresponding":false},{"id":1013665,"name":"Harris Ioannidis","orcid":"0000-0003-3470-6055","position":7,"is_corresponding":false},{"id":75405,"name":"David Méndez","orcid":"0000-0002-0294-5484","position":8,"is_corresponding":false},{"id":1015139,"name":"Juan F Mosquera","orcid":null,"position":9,"is_corresponding":false},{"id":75391,"name":"María Paula Magariños","orcid":"0000-0003-2769-4105","position":10,"is_corresponding":false},{"id":75400,"name":"Nicolas Bosc","orcid":"0000-0003-3562-1328","position":11,"is_corresponding":false},{"id":24384,"name":"Ricardo Arcila","orcid":"0000-0002-8253-7375","position":12,"is_corresponding":false},{"id":992672,"name":"Tevfik Kizilören","orcid":"0000-0001-8129-6488","position":13,"is_corresponding":false},{"id":75386,"name":"Anna Gaulton","orcid":"0000-0003-2634-7400","position":14,"is_corresponding":false},{"id":75387,"name":"A. Patrícia Bento","orcid":"0000-0003-1424-480X","position":15,"is_corresponding":false},{"id":1013666,"name":"Melissa F. Adasme","orcid":"0000-0003-2217-4629","position":16,"is_corresponding":false},{"id":1015140,"name":"Peter Monecke","orcid":null,"position":17,"is_corresponding":false},{"id":1013667,"name":"Gregory A. Landrum","orcid":"0000-0001-6279-4481","position":18,"is_corresponding":false},{"id":75404,"name":"Andrew R. Leach","orcid":"0000-0001-8178-0253","position":19,"is_corresponding":false},{"id":36036,"name":"Barbara Zdrazil","orcid":"0000-0001-9395-1515","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-19T01:06:02.898877Z","pmid":"37933841","pmcid":"PMC10767899","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":50.0,"fair_a":81.25,"fair_i":60.0,"fair_r":100.0,"fair_zscore":1.77,"fair_rationale":{"fair_score":79.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_33/","grounded":true,"rationale":"The paper gives a URL (FTP path) for the data, not a persistent identifier scheme.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The ChEMBL database is made available under a Creative Commons Attribution-ShareAlike 3.0 Unported license","grounded":true,"rationale":"The holder named is the ChEMBL database itself, which is a recognised repository (ELIXIR core data resource). [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The ChEMBL database is made available under a Creative Commons Attribution-ShareAlike 3.0 Unported license ( http://creativecommons.org/licenses/by-sa/3.0 )","grounded":true,"rationale":"The statement points to a license, not a repository record with an accession.","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"In total, release 33 of the ChEMBL database (prepared on 31/05/2023) contains information extracted from > 88000 publications and patents (of which 2564 are patents), 420 deposited datasets, and two books for a grand total of >20.3 Million bioactivity measurements and 2.4 Million unique compounds.","grounded":false,"rationale":"The dataset size and content are described in running prose, not in an itemized inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"ChEMBL ( https://www.ebi.ac.uk/chembl/ )","grounded":true,"rationale":"The dataset identifier appears only in the body text, not as a reference-list entry. 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[majority verdict 'partial' (4/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No open file format token is explicitly named for the released data. [majority verdict 'no' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Each withdrawn drug includes a citation to a regulatory document or similar; the specific (granular) withdrawn reason is mapped to EFO","grounded":true,"rationale":"The paper uses EFO, a community standard ontology, to map withdrawn drug reasons.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"The FPSim2 Python package (10.5281/zenodo.7781320) was developed and open-sourced","grounded":true,"rationale":"The paper gives a DOI for the FPSim2 software, a resource other than the own dataset. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":100.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The ChEMBL database is made available under a Creative Commons Attribution-ShareAlike 3.0 Unported license","grounded":true,"rationale":"The license is an open standard Creative Commons license.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The FPSim2 Python package (10.5281/zenodo.7781320) was developed and open-sourced ( https://github.com/chembl/FPSim2 ) with the intention of replacing RDKit's PostgreSQL cartridge","grounded":true,"rationale":"The paper names specific software tools (RDKit, FPSim2) used to produce the data. 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A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_33/","why":"The paper gives a URL (FTP path) for the data, not a persistent identifier scheme.","gain":8.33,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No open file format token is explicitly named for the released data. [majority verdict 'no' (4/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"ChEMBL ( https://www.ebi.ac.uk/chembl/ )","why":"The dataset identifier appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The ChEMBL database is made available under a Creative Commons Attribution-ShareAlike 3.0 Unported license ( http://creativecommons.org/licenses/by-sa/3.0 )","why":"The statement points to a license, not a repository record with an accession.","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. 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[downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive human-subject data; no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The ChEMBL database is made available under a Creative Commons Attribution-ShareAlike 3.0 Unported license","why":"The paper states the data are available now but does not specify a retention period or persistence commitment. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:46:56.082126Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}