| Chemical databases |
| PubChem [28,29] |
https://pubchem.ncbi.nlm.nih.gov/ |
One of the largest chemical databases on the web. Created and maintained under the National Center for Biotechnology Information (NCBI). Contains over 68 million entries for compounds and over 198 million entries for substances, including mixtures, complexes, uncharacterized substances, etc. Each entry has a full description of the chemical and biological properties, utilization of the substance, information about vendors, etc. |
| Chemical Entities of Biological Interest (ChEBI) [30-32] |
https://www.ebi.ac.uk/chebi/ |
Free access chemical database focused mainly on small molecules. Every entry provides information about names, synonyms, registry number(s), molecular formula, and main chemical descriptors. This database is a part of the European molecular biology laboratory (EMBL) project. |
| ChEMBL [33-35] |
https://www.ebi.ac.uk/chembl/ |
Similar to ChEBI, but focused on compounds with drug-like or potential drug properties; contains over 1.7 million entries. Highlights the advantages of advanced search instruments. Search by ligand structure, current compound targets, and other keywords available on the web. Accepted by ELMB. |
| ChemSpider [36-38] |
http://www.chemspider.com/ |
Integrative chemical database from Royal Society of Chemistry. Includes 43 million chemical structures from 490 data sources. Provides information about patents, vendors, etc., related to each annotated compound. |
| Drugs databases |
| DrugBank [39-41] |
http://www.drugbank.ca |
Comprehensive resource indexing drugs at any stage—approved for human use, in clinical trials, and experimental drugs. Summarizes each drug's influence on molecular targets. Also provides information about pharmacology, side effects, etc. |
| The Pharmacogenomics Knowledgebase (PharmGKB) [43] |
https://www.pharmgkb.org/ |
Shows interactions between drugs and genes. |
| Side Effects Data Base [44] |
http://sideeffects.embl.de/ |
Describes over 4,000 side effects (adverse events) of 996 approved drugs. |
| Therapeutic Targets Database (TTD) [45,46] |
http://bidd.nus.edu.sg/group/cjttd |
Provides information about cell therapeutic targets, related metabolic pathways, and corresponding drugs. Provided by National University of Singapore. |
| Metabolic pathways databases |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) [47] |
http://www.genome.jp/kegg/ |
Resource including various databases such as chemical, biological, metabolic pathways, drug, and disease databases. Developed in Kyoto University. |
| The Human Metabolome Database (HMDB) [48,49] |
http://www.hmdb.ca/ |
Database of metabolites detectable in the human body. First resource designed for metabolomics; now contains over 42,000 entries. |
| Toxicology databases |
| TOXNET [50] |
http://toxnet.nlm.nih.gov |
Contains a variety of resources related to toxicology, linked to original peer-reviewed articles. |
| Liver Tox [51] |
http://livertox.nih.gov/ |
Provides data on hundreds of compounds with known or potential liver toxicity. |
| Gene Expression |
| Gene Expression Omnibus [52,53] |
http://www.ncbi.nlm.nih.gov/geo |
International public repository archiving microarray, next generation sequencing, and other genomics data; user submitted. |
| L1000 [54] |
http://www.broadinstitute.org/LINCS |
Project of the Broad Institute. Utilizes computationally selected 1000 landmark genes to infer the transcriptome. |
| Protein databases |
| UniProt [55] |
http://www.uniprot.org/ |
The largest database of the annotated proteins. |
| Clinical trials databases |
| Clinical Trials [56,57] |
https://clinicaltrials.gov/ |
The largest web catalog of registered clinical trials launched by the US National Laboratory of Medicine; contains over 200 clinical trials conducted in US and nearly 200 more conducted abroad. Describes protocols, conditions, studied drugs, etc. |
| Other sources |
| MeSH (Medical Subject Headings) |
https://www.nlm.nih.gov/mesh/ |
US National Library of Medicine's controlled vocabulary thesaurus. |
| Reference.MD |
http://www.reference.md/ |
Resource that integrates medical information from MeSH, Drugs@FDA, FDA Adverse Event Reporting System, etc. |
| Commercial organizations (Chemical vendors) |
| Chemnet |
http://www.chemnet.com/cas/ |
China-based company; platform of providing comprehensive service to chemicals; database of 300,000 products. |
| Sigma Aldrich |
http://www.sigmaaldrich.com/ |
US-based company; manufactures over 230,000 chemicals, biochemicals, and other essential products; 1.4 million customers globally. |
| Enzo Life Sciences |
http://www.enzolifesciences.com/ |
US-based manufacturer of health and biological sciences research products. |
| Santa Cruz Biotechnology, Inc. |
http://www.scbt.com/ |
US-based developer of products for biomedical research worldwide. |
