Gene expression databases and data mining. In silico is one of the modern and advanced methods has been used in pharmacology. In theory, data should be available for all endpoints that have been tested across a variety of guideline and non-standard approaches. The Pain Genes Database: an interactive web browser of pain-related transgenic knockout studies. (2002). doi: 10.1016/j.ddstr.2011.06.004, Luo, G., Shen, Y., Yang, L., Lu, A., and Xiang, Z. Toxicol. Toxicol. (1998). Chem. (2017). 44, D932–937. 14, 177–184. Probes &Drugs portal: an interactive, open data resource for chemical biology. Nucleic Acids Res. (2015). Aided Mol. Nucleic Acids Res. Br. The tools and approaches includes application of Thresholds of Toxicological Concern (TTC) of cosmetics related substances. (2014). doi: 10.1021/acs.chemrestox.7b00003, Hay, D. L., Garelja, M. L., Poyner, D. R., and Walker, C. S. (2018). A., Liu, Z., Gould, J., Mccarren, P., Hirschman, J. E., et al. 46, D1266–D1270. Disnor (Lo surdo et al., 2018), DrugSig (Wu et al., 2017), DisGeNet (Piñero et al., 2017), Drug Gene Interaction Database (DGIdb) (Griffith et al., 2013), Online Mendelian Inheritance in Man (OMIM) (Hamosh et al., 2005) are important resources for exploring the genes and disease domain. MedDRA provides a single standardised international medical terminology, which can be used for regulatory communication and evaluation of data pertaining to medicinal products for human use. The 11,688 samples were collected from 53 non-diseased tissue sites and 714 donors. doi: 10.18547/gcb.2017.vol3.iss1.e37. 32, D434–D437. 46, D36–D40. Nucleic Acids Res. Toxicol. 44, D463–D470. The end users are recommended to read and understand the licensing information correctly to know whether the contents are provided for commercial or educational research purposes only. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. Des. Please check your email for instructions on resetting your password. for chemical-protein target pair. The in chemico-in silico interface: challenges for integrating experimental and computational chemistry to identify toxicity. (2016). Open TG-GATEs: a large-scale toxicogenomics database. CanSAR is another translational platform, which integrates genomic, protein, pharmacological, drug, and chemical data with structural biology, protein networks, and druggability data. The desirable attributes included access to the metadata, study protocols, information on data quality assessment, ease of navigation, and other database statistics relating to the frequency of updates and number of compounds or drugs reported. The AMED cardiotoxicity database contains data on small molecules that bind to various ion channels and potentially cause cardiotoxic risk. (2010). However, overlap between the databases is not considered a major problem and it could be minimised by clearly identifying the origin of data and using primary sources where possible. Clin. Pathways based toxicity databases are useful in the development of AOPs. It contains interactions across 33 types of human cancers and also PPI information across 33 main normal tissues and cell types. It accepts all functional genomics data generated from micoarray or next-generation sequencing (NGS) platforms. Nucleic Acids Res. Protoc. However, a systematic review and grouping of databases, based on purpose and information content, consolidated in a single source, has been lacking. There are 30 databases with information on the effects of chemcials to the environment and non-human species29. The Biochemical Genetic and Genomic (BiGG) database (King et al., 2016) is a resource based on more than 70 genome-scale metabolic networks. Vigibase (Lindquist, 2008) is a unique World Health Organisation (WHO) global database of individual case safety reports (ICSRs), it is linked to medical and drug classifications, including terminologies such as WHO Adverse Reaction Terminology (ART), Medical Dictionary for Regulatory Activities (MedDRA) (Morley, 2014), WHO International Statistical Classification of Diseases (ICD), the medicinal products dictionary, and WHODrug. doi: 10.1002/minf.201500075, Davis, A. P., King, B. L., Mockus, S., Murphy, C. G., Saraceni-Richards, C., Rosenstein, M., et al. RefSeq (Nasko et al., 2018) is a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, 20,905,608 transcripts, and 100,043,962 proteins, and 73,996 organisms. The user can also access qPCR expression and MicroArray data. Cronin, M. (2005). 44, D1220–D1228. Thirty-eight ADME databases were identified which captured information on parameters such as area-under-the-plasma concentration-curve (AUC), maximum concentration (Cmax), Time to reach maximum concentration (Tmax), half-life (T1/2), volume of distribution (Vd), clearance (CL) etc13. Madden, J. C. (2013). It publishes original research papers and critical reviews at the interface of disciplines within the pharmaceutical and related sciences, and keeps pace with new research on how drug action may be optimized by new technologies. Nat. Toxicol. 42, 409–419. 44, 1107–1110. with over 70,000 chemicals and 2,116,700 data points. With the advent of high—throughput in-vitro technologies to systematically investigate new indications for existing drugs has led to the development of repurposing databases for personalized medicines such as RepurposeDB (Shameer et al., 2018), repoDB (Brown and Patel, 2017), The Drug Repurposing Hub (DRH) (Corsello et al., 2017), Promiscuous (Von Eichborn et al., 2011) etc. A., Ellrott, K., et al. Biol. It contains information of about 19,226 FDA approval applications for 31,815 products, 2,505 active ingredients, 1,629 molecular structures, 2.5 million adverse effects, and 36,963 experimental drug-target bioactivity data. Nat. (2010). Omics Discovery Index (Omics DI) (Perez-Riverol et al., 2017) is a great resource containing heterogeneous omics data covering 452,800 datasets, 65,200 species, 308,300 genomics, 1,600 tissues, 124,400 transcriptomics, 19 repositories, and 7,300 multiomics datasets. ACToR — Aggregated computational toxicology resource. GeneCards Version 3: the human gene integrator. (2014). databases, protein-protein interactions (PPIs), environmental exposure related, and finally databases relating to animal alternatives in support of 3Rs policies. doi: 10.1093/nar/gkw993, Veres, D. V., Gyurkó, D. M., Thaler, B., Szalay, K. Z., Fazekas, D., Korcsmáros, T., et al. 46, D440–D446. The choice of a particular API depends on the size of the database and the programming skills of the developer. 95, 496–498. doi: 10.1177/026119290903700508. LINCS (Liu et al., 2015) is a standalone library of molecular signatures describing how different types of cells respond to a variety of chemicals called “perbutagens.” At time of writing, this comprised 391 datasets covering 41,847 small molecules, 1,127 cell types derived from different organs, 978 genes, 1469 proteins/155 peptide probes, and 8 antibodies. Brief. CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. Nat. ChemSpider provides information on physical properties, biological activities (where available), interactive spectra, the name of chemical suppliers, and other miscellaneous information. Mapping of different databases depends on the technical content and architecture of the datasets.

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