Metabases
| BIDD website | Provider: National University of Singapore |
| BioCyc | Caspi R., Altman T., Billington R., Dreher K., Foerster H., Fulcher C. A., Holland T. A., Keseler I. M., Kothari A., Kubo A., Krummenacker M., Latendresse M., Mueller L. A., Ong Q., Paley S., Subhraveti P., Weaver D. S., Weerasinghe D., Zhang P., Karp P. D., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research, 2014, 42, D459–D471. Abstract |
| BioDBCore | Gaudet P., Bairoch A., Field D., Sansone S.-A., Taylor C., Attwood T.K., Bateman A., Blake J.A., Bult C.J., Cherry J.M., Chisholm R.L., Cochrane G., Cook C.E., Eppig J.T., Galperin M.Y., Gentleman R., Goble C.A., Gojobori T., Hancock J.M., Howe D.G., Imanishi T., Kelso J., Landsman D., Lewis S.E., Karsch-Mizrachi I., Orchard S., Ouelette B.F.F., Ranganathan S., Richardson L., Rocca-Serra P., Schofield P.N., Smedley D., Southan C., Tan T.W., Tatusova T., Whetzel P.L., White O., Yamasaki C., Towards BioDBcore: a community-defined information specification for biological database. Database, 2011, Article No baq027. Abstract |
| BioSharing | McQuilton P., Gonzalez-Beltran A., Rocca-Serra P., Thurston M., Lister A., Maguire E., Sansone S.-A., BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. Database, 2016, Article No baw075. Abstract |
| Bio-TDS | Gnimpieba E. Z., VanDiermen M. S., Gustafson S. M., Conn B., Lushbough C. M., Bio-TDS: bioscience query tool discovery system. Nucleic Acids Research, 2017, 45, D1117–D1122. Abstract |
| CACTUS | Sitzmann M., Filippov I.V., Nicklaus M.C., Internet resources integrating many small molecular databases. SAR QSAR in Environmental Research, 2008, 19, 1-9. Abstract |
| Charité Structural Bioinformatics Group | Provider: Charité Universitätsmedizin Berlin |
| Chem2Bio2RDF | Chen B., Dong X., Jiao D., Wang H., Zhu Q., Ding Y., Wild D. J., Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics, 2010, 11, Article No, 255. Abstract |
| ChemAgora | Zanzi A., Wittwehr C., Searching online chemical data repositories via the ChemAgora portal. Journal of Chemical Information and Modeling, 2017, 57, 2905–2910. Abstract |
| Chemical Structure Lookup | Sitzmann M., Filippov I.V., Nicklaus M.C., Internet resources integrating many small molecular databases. SAR QSAR in Environmental Research, 2008, 19, 1-9. Abstract |
| Chemistry Databases | Providers: ChemPubSoc Europe and Wiley-VCh |
| ChemSpider | Pence H. E., Williams A., Chemspider: An online chemical information resource. Journal of Chemical Education, 2010, 87, 1123–1124. AbstractWilliams A., Tkachenko V., The Royal Society of Chemistry and the delivery of chemistry data repositories for the community. Journal of Computer Aided Molecular Design, 2014, 28, 1023–1030. Abstract |
| Click2Drug | Provider: Swiss Institute of Bioinformatics |
| ConsensusPathDB | Kamburov A., Stelzl U., Lehrach H., Herwig R., The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Research, 2013, 41, D793-D800. Abstract |
| CRDD | Provider: IMTECH/CSIR |
| DBD | Siva Kiran R. R., Setty M. V. N., Hanumatha Rao G., Bioinformatics glossary based Database of Biological Databases: DBD. Journal of Biochemical Technology, 2009, 1(3), 88-90. Abstract |
| EBI Chemical Biology | Provider: European Bioinformatics Institute |
| eChemPortal | Provider: OECD |
| Enzyme Portal | Alcántara R., Onwubiko J., Cao H., de Matos P., Cham J. A., Jacobsen J., Holliday G. L., Fischer J. D., Rahman S. A., Jassal B., Goujon M., Rowland R., Velankar S., López R., Overington J. P., Kleywegt G. J., Hermjakob H., O’Donovan C., Martín M. J., Thornton J. M., Steinbeck C., The EBI enzyme portal. Nucleic Acids Research, 2013, 41, D773–D780. Abstract |
| GlycomicsPortal | Provider: University of Georgia |
| Identifiers.org | Bernal-Llinares M., Ferrer-Gómez J., Juty N., Goble C., Wimalaratne S. M., Hermjakob H., Identifiers.org: Compact identifier services in the cloud. Bioinformatics, 2021, 37, 1781–1782. Abstract |
| IIIT – Complex Systems Lab | Goel M., Bagler G., Computational gastronomy: A data science approach to food. Journal of Bioscience, 2022, 47, Article No 12. Abstract |
| IIIT – Raghava’s group | Provider: Indraprastha Institute of Information Technology, Delhi, India |
| ISDM | Kratochvíl M., Vondrášek J., Galgonek J., Interoperable chemical structure search service. Journal of Cheminformatics, 2019, 11, Article No 45. Abstract |
| KEGG | Kanehisa M., Furumichi M., Sato Y., Kawashima M., Ishiguro-Watanabe M., KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Research, 2023, 51, D587–D592. Abstract |
| LabWorm | Authors: Yoav Bauman, Roy Granit, Alon Vitenshtein |
| MetaBase | Bolser D.M., Chibon P.Y., Palopoli N., Gong S., Jacob D., Dominguez Del Angel V., Swan D., Bassi S., González V., Suravajhala P., Hwang S., Romano P., Edwards R., Bishop B., Eargle J., Shtatland T., Provart N.J., Clements D., Renfro D.P., Bhak D., Bhak J., MetaBase-the wiki-database of biological databases. Nucleic Acids Research, 2012, 40, D1250–D1254. Abstract |
| MUD | Providers: MicroTech Solutions and University of Rajasthan |
| NAR Collection | Rigden D. J., Fernández X. M., The 2025 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic Acids Research, 2025, 53, D1–D9. Abstract |
| NBDC | Provider: Japan Science and Technology Agency |
| NIST Data Gateway | Provider: National Institute of Standards and Technology |
| NLM | Provider: US Department of Health & Human Services |
| OpenPHACTS | Gray A. J. G., Groth P., Loizou A., Askjaer S., Brenninkmeijer C., Burger K., Chichester C., Evelo C. T., Goble C., Harland L., Pettifer S., Thompson M., Waagmeester A., Williams A. J., Applying linked data approaches to pharmacology: architectural decisions and implementation. Semantic Web Journal, 2012. Abstract |
| pathDIP | Rahmati S., Abovsky M., Pastrello C., Kotlyar M., Lu R., Cumbaa C. A., Rahman P., Chandran V., Jurisica I., pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species. Nucleic Acids Research, 2020, 48, D479–D488. Abstract |
| PathGuide | Bader G. D., Cary M. P., Sander C., Pathguide: a pathway resource list. Nucleic Acids Research, 2006, 34, D504-D506. Abstract |
| PDSP | Providers: National Institute of Mental Health, Bethesda, MD, USA and University of North Carolina, Chapel Hill, NC, USA |
| Peter Ertl website | |
| PRIMe | Sakurai T., Yamada Y., Sawada Y., Matsuda F., Akiyama K., Shinozaki K., Hirai M.Y., Saito K., PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. Plant & Cell Physiology, 2013, 54, Article No e5. Abstract |
| PubChem Sources | Kim S., Chen J., Cheng T., Gindulyte A., He J., He S., Li Q., Shoemaker B. A., Thiessen P. A., Yu B., Zaslavsky L., Zhang J., Bolton E. E., PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Research, 2021, 49, D1388–D1395. Abstract |
| SIRCh | |
| Tools and Data Services Registry | Ison J., Ménager H., Brancotte B., Jaaniso E., Salumets A., Raček T., Lamprecht A.-L., Palmblad M., Kalaš M., Chmura P., Hancock J. M., Schwämmle V., Ienasescu H.-I., Community curation of bioinformatics software and data resources. Briefings in Bioinformatics, 2020, 21, 1697–1705. Abstract |
| TOXNET | Fowler S., Schnall J. G., TOXNET: Information on toxicology and environmental health. American Journal of Nursing, 2014, 114, 61-63. Abstract |
| Wikipedia biological databases | |
| Wikipedia chemical databases | |
| Wishartlab | Provider: University of Alberta |
Last Updated on 10-01-2025 by Piotr Minkiewicz