The European Chemical Biology Database (ECBD, https://ecbd.eu) serves as the central repository for data generated by the EU-OPENSCREEN research infrastructure consortium. It is developed according to FAIR principles, which emphasize findability, accessibility, interoperability and reusability of data. This data is made available to the scientific community following open access principles. The ECBD stores both positive and negative results from the entire chemical biology project pipeline, including data from primary or counter-screening assays. The assays utilize a defined and diverse library of over 107 000 compounds, the annotations of which are continuously enriched by external user supported screening projects and by internal EU-OPENSCREEN bioprofiling efforts. These compounds were screened in 89 currently deposited datasets (assays), with 48 already being publicly accessible, while the remaining will be published after a publication embargo period of up to 3 years. Together these datasets encompass ∼4.3 million experimental data points. All public data within ECBD can be accessed through its user interface, API or by database dump under the CC-BY 4.0 license.

CZ OPENSCREEN National Infrastructure for Chemical Biology Institute of Molecular Genetics of the Czech Academy of Sciences Vídeňská 1083 Prague 14220 Czech Republic

EU OPENSCREEN ERIC Robert Rössle Str 10 Berlin 13125 Germany

Nucleic Acids Res. 2025 Jan 24;53(3):gkaf026. doi: 10.1093/nar/gkaf026. PubMed

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Bajorath  J.  Integration of virtual and high-throughput screening. Nat. Rev. Drug Discov.  2002; 1:882–894. PubMed

Chen  C., Wang  J., Pan  D., Wang  X., Xu  Y., Yan  J., Wang  L., Yang  X., Yang  M., Liu  G.  Applications of multi-omics analysis in human diseases. MedComm.  2023; 4:e315. PubMed PMC

Thomas  J.R., Shelton  C., Murphy  J., Brittain  S., Bray  M.-A., Aspesi  P., Concannon  J., King  F.J., Ihry  R.J., Ho  D.J.  et al. .  Enhancing the small-scale screenable biological space beyond known chemogenomics libraries with gray chemical matter─compounds with novel mechanisms from high-throughput screening profiles. ACS Chem. Biol.  2024; 19:938–952. PubMed PMC

Wilkinson  M.D., Dumontier  M., Aalbersberg  I.J., Appleton  G., Axton  M., Baak  A., Blomberg  N., Boiten  J.-W., Da Silva Santos  L.B., Bourne  P.E.  et al. .  The FAIR guiding principles for scientific data management and stewardship. Sci. Data. 2016; 3:160018. PubMed PMC

Ginex  T., Madruga  E., Martinez  A., Gil  C.  MBC and ECBL libraries: outstanding tools for drug discovery. Front. Pharmacol.  2023; 14:1244317. PubMed PMC

Jalencas  X., Berg  H., Espeland  L.O., Sreeramulu  S., Kinnen  F., Richter  C., Georgiou  C., Yadrykhinsky  V., Specker  E., Jaudzems  K.  et al. .  Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection. RSC Med. Chem.  2024; 15:1176–1188. PubMed PMC

Kim  S., Chen  J., Cheng  T., Gindulyte  A., He  J., He  S., Li  Q., Shoemaker  B.A., Thiessen  P.A., Yu  B.  et al. .  PubChem 2023 update. Nucleic Acids Res.  2023; 51:D1373–D1380. PubMed PMC

Zdrazil  B., Felix  E., Hunter  F., Manners  E.J., Blackshaw  J., Corbett  S., de Veij  M., Ioannidis  H., Lopez  D.M., Mosquera  J.F.  et al. .  The ChEMBL database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods. Nucleic Acids Res.  2024; 52:D1180–D1192. PubMed PMC

Gilson  M.K., Liu  T., Baitaluk  M., Nicola  G., Hwang  L., Chong  J.  BindingDB in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res.  2016; 44:D1045–D1053. PubMed PMC

Irwin  J.J., Tang  K.G., Young  J., Dandarchuluun  C., Wong  B.R., Khurelbaatar  M., Moroz  Y.S., Mayfield  J., Sayle  R.A.  ZINC20—a free ultralarge-scale chemical database for ligand discovery. J. Chem. Inf. Model.  2020; 60:6065–6073. PubMed PMC

Skuta  C., Popr  M., Muller  T., Jindrich  J., Kahle  M., Sedlak  D., Svozil  D., Bartunek  P.  Probes & Drugs portal: an interactive, open data resource for chemical biology. Nat. Methods. 2017; 14:759–760. PubMed

Harding  S.D., Armstrong  J.F., Faccenda  E., Southan  C., Alexander  S.P.H., Davenport  A.P., Spedding  M., Davies  J.A.  The IUPHAR/BPS guide to pharmacology in 2024. Nucleic Acids Res.  2024; 52:D1438–D1449. PubMed PMC

Knox  C., Wilson  M., Klinger  C.M., Franklin  M., Oler  E., Wilson  A., Pon  A., Cox  J., Chin  N.E.L., Strawbridge  S.A.  et al. .  DrugBank 6.0: the DrugBank knowledgebase for 2024. Nucleic Acids Res.  2024; 52:D1265–D1275. PubMed PMC

Avram  S., Wilson  T.B., Curpan  R., Halip  L., Borota  A., Bora  A., Bologa  C.G., Holmes  J., Knockel  J., Yang  J.J.  et al. .  DrugCentral 2023 extends human clinical data and integrates veterinary drugs. Nucleic Acids Res.  2023; 51:D1276–D1287. PubMed PMC

Edfeldt  K., Edwards  A.M., Engkvist  O., Günther  J., Hartley  M., Hulcoop  D.G., Leach  A.R., Marsden  B.D., Menge  A., Misquitta  L.  et al. .  A data science roadmap for open science organizations engaged in early-stage drug discovery. Nat. Commun.  2024; 15:5640. PubMed PMC

Freedman  L.P., Inglese  J.  The increasing urgency for standards in basic biologic research. Cancer Res.  2014; 74:4024–4029. PubMed PMC

Arrowsmith  C.H., Audia  J.E., Austin  C., Baell  J., Bennett  J., Blagg  J., Bountra  C., Brennan  P.E., Brown  P.J., Bunnage  M.E.  et al. .  The promise and peril of chemical probes. Nat. Chem. Biol.  2015; 11:536–541. PubMed PMC

Hoch  J.C., Baskaran  K., Burr  H., Chin  J., Eghbalnia  H.R., Fujiwara  T., Gryk  M.R., Iwata  T., Kojima  C., Kurisu  G.  et al. .  Biological Magnetic Resonance Data Bank. Nucleic Acids Res.  2023; 51:D368–D376. PubMed PMC

Masters  J.R., Thomson  J.A., Daly-Burns  B., Reid  Y.A., Dirks  W.G., Packer  P., Toji  L.H., Ohno  T., Tanabe  H., Arlett  C.F.  et al. .  Short tandem repeat profiling provides an international reference standard for human cell lines. Proc. Natl. Acad. Sci. U.S.A.  2001; 98:8012–8017. PubMed PMC

Visser  U., Abeyruwan  S., Vempati  U., Smith  R.P., Lemmon  V., Schürer  S.C.  BioAssay ontology (BAO): a semantic description of bioassays and high-throughput screening results. BMC Bioinf.  2011; 12:257. PubMed PMC

Gkoutos  G.V., Schofield  P.N., Hoehndorf  R.  The Units ontology: a tool for integrating units of measurement in science. Database. 2012; 2012:bas033–bas033. PubMed PMC

Bairoch  A.  The Cellosaurus, a cell-line knowledge resource. J. Biomol. Tech.  2018; 29:25–38. PubMed PMC

Chang  A., Jeske  L., Ulbrich  S., Hofmann  J., Koblitz  J., Schomburg  I., Neumann-Schaal  M., Jahn  D., Schomburg  D.  BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res.  2021; 49:D498–D508. PubMed PMC

Ashburner  M., Ball  C.A., Blake  J.A., Botstein  D., Butler  H., Cherry  J.M., Davis  A.P., Dolinski  K., Dwight  S.S., Eppig  J.T.  et al. .  Gene ontology: tool for the unification of biology. Nat. Genet.  2000; 25:25–29. PubMed PMC

The Gene Ontology Consortium Aleksander  S.A., Balhoff  J., Carbon  S., Cherry  J.M., Drabkin  H.J., Ebert  D., Feuermann  M., Gaudet  P., Harris  N.L.  et al. .  The gene ontology knowledgebase in 2023. Genetics. 2023; 224:iyad031. PubMed PMC

Mutowo  P., Bento  A.P., Dedman  N., Gaulton  A., Hersey  A., Lomax  J., Overington  J.P.  A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL. J. Biomed. Semant.  2016; 7:59. PubMed PMC

Schoch  C.L., Ciufo  S., Domrachev  M., Hotton  C.L., Kannan  S., Khovanskaya  R., Leipe  D., Mcveigh  R., O’Neill  K., Robbertse  B.  et al. .  NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database. 2020; 2020:baaa062. PubMed PMC

Milacic  M., Beavers  D., Conley  P., Gong  C., Gillespie  M., Griss  J., Haw  R., Jassal  B., Matthews  L., May  B.  et al. .  The Reactome Pathway Knowledgebase 2024. Nucleic Acids Res.  2024; 52:D672–D678. PubMed PMC

Heller  S.R., McNaught  A., Pletnev  I., Stein  S., Tchekhovskoi  D.  InChI, the IUPAC International Chemical Identifier. J. Cheminform.  2015; 7:23. PubMed PMC

Goodman  J.M., Pletnev  I., Thiessen  P., Bolton  E., Heller  S.R.  InChI version 1.06: now more than 99.99% reliable. J. Cheminform.  2021; 13:40. PubMed PMC

Lipinski  C.A., Lombardo  F., Dominy  B.W., Feeney  P.J.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1. Adv. Drug. Deliv. Rev.  2001; 46:3–26. PubMed

Baell  J.B., Holloway  G.A.  New substructure filters for removal of pan-assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J. Med. Chem.  2010; 53:2719–2740. PubMed

Baell  J.B., Nissink  J.W.M.  Seven year Itch: pan-assay interference compounds (PAINS) in 2017-utility and limitations. ACS Chem. Biol.  2018; 13:36–44. PubMed PMC

Chambers  J., Davies  M., Gaulton  A., Hersey  A., Velankar  S., Petryszak  R., Hastings  J., Bellis  L., McGlinchey  S., Overington  J.P.  UniChem: a unified chemical structure cross-referencing and identifier tracking system. J. Cheminform.  2013; 5:3. PubMed PMC

Consortium  T.U.P., Bateman  A., Martin  M.-J., Orchard  S., Magrane  M., Agivetova  R., Ahmad  S., Alpi  E., Bowler-Barnett  E.H., Britto  R.  et al. .  UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res.  2021; 49:D480–D489. PubMed PMC

Sayers  E.W., Cavanaugh  M., Clark  K., Pruitt  K.D., Schoch  C.L., Sherry  S.T., Karsch-Mizrachi  I.  GenBank. Nucleic Acids Res.  2021; 49:D92–D96. PubMed PMC

Harrison  P.W., Lopez  R., Rahman  N., Allen  S.G., Aslam  R., Buso  N., Cummins  C., Fathy  Y., Felix  E., Glont  M.  et al. .  The COVID-19 data portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. Nucleic Acids Res.  2021; 49:W619–W623. PubMed PMC

Škuta  C., Bartůněk  P., Svozil  D.  InCHlib—interactive cluster heatmap for web applications. J. Cheminform.  2014; 6:44. PubMed PMC

Karulin  B., Kozhevnikov  M.  Ketcher: web-based chemical structure editor. J. Cheminform.  2011; 3:P3.

Berthold  M.R., Cebron  N., Dill  F., Gabriel  T.R., Kötter  T., Meinl  T., Ohl  P., Thiel  K., Wiswedel  B.  KNIME—the Konstanz information miner: version 2.0 and beyond. SIGKDD Explor. Newsl.  2009; 11:26–31.

Bray  M.-A., Singh  S., Han  H., Davis  C.T., Borgeson  B., Hartland  C., Kost-Alimova  M., Gustafsdottir  S.M., Gibson  C.C., Carpenter  A.E.  Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat. Protoc.  2016; 11:1757–1774. PubMed PMC

Morphological profiling data resource enables prediction of chemical compound properties