Metabases

BIDD websiteProvider: National University of Singapore
BioCycCaspi 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
BioDBCoreGaudet 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
BioSharingMcQuilton 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-TDSGnimpieba 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
CACTUSSitzmann 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 
Chem2Bio2RDFChen 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
ChemAgoraZanzi 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 LookupSitzmann 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 DatabasesProviders: ChemPubSoc Europe and Wiley-VCh
ChemSpiderPence 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
Click2DrugProvider: Swiss Institute of Bioinformatics
ConsensusPathDBKamburov A., Stelzl U., Lehrach H., Herwig R., The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Research, 2013, 41, D793-D800. Abstract
CRDDProvider: IMTECH/CSIR
DBDSiva 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 BiologyProvider: European Bioinformatics Institute
eChemPortalProvider: OECD
Enzyme PortalAlcántara 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
GlycomicsPortalProvider: University of Georgia
Identifiers.orgBernal-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 – Raghava’s groupProvider: Indraprastha Institute of Information Technology, Delhi, India
ISDMKratochvíl M., Vondrášek J., Galgonek J., Interoperable chemical structure search service. Journal of Cheminformatics, 2019, 11, Article No 45. Abstract
KEGGKanehisa M., Sato Y., Furumichi M., Morishima K., Tanabe M., New approach for understanding genome variations in KEGG. Nucleic Acids Research, 2019, 47, D590–D595. Abstract
LabWormAuthors: Yoav BaumanRoy GranitAlon Vitenshtein
MetaBaseBolser 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
MUDProviders: MicroTech Solutions and University of Rajasthan
NAR CollectionRigden D. J., Fernández X. M., The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic Acids Research, 2022, 50, D1–D10. Abstract
NBDCProvider: Japan Science and Technology Agency
NIST Data Gateway 
NLMProvider: US Department of Health & Human Services
OpenPHACTSGray 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
pathDIPRahmati 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
PathGuideBader G. D., Cary M. P., Sander C., Pathguide: a pathway resource list. Nucleic Acids Research, 2006, 34, D504-D506. Abstract
PDSPProviders: National Institute of Mental Health, Bethesda, MD, USA and University of North Carolina, Chapel Hill, NC, USA
Peter Ertl website 
PRIMeSakurai 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 SourcesKim 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 RegistryIson 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
TOXNETFowler 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 
WishartlabProvider: University of Alberta