DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

Abstract

DrugBank (http://www.drugbank.ca) is a richly annotated database of drug and drug target information. It contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pharmaceutical properties of both small molecule and large molecule (biotech) drugs. It also contains comprehensive information on the target diseases, proteins, genes and organisms on which these drugs act. First released in 2006, DrugBank has become widely used by pharmacists, medicinal chemists, pharmaceutical researchers, clinicians, educators and the general public. Since its last update in 2008, DrugBank has been greatly expanded through the addition of new drugs, new targets and the inclusion of more than 40 new data fields per drug entry (a 40% increase in data ‘depth’). These data field additions include illustrated drug-action pathways, drug transporter data, drug metabolite data, pharmacogenomic data, adverse drug response data, ADMET data, pharmacokinetic data, computed property data and chemical classification data. DrugBank 3.0 also offers expanded database links, improved search tools for drug–drug and food–drug interaction, new resources for querying and viewing drug pathways and hundreds of new drug entries with detailed patent, pricing and manufacturer data. These additions have been complemented by enhancements to the quality and quantity of existing data, particularly with regard to drug target, drug description and drug action data. DrugBank 3.0 represents the result of 2 years of manual annotation work aimed at making the database much more useful for a wide range of ‘omics’ (i.e. pharmacogenomic, pharmacoproteomic, pharmacometabolomic and even pharmacoeconomic) applications.

The Protein Data Bank archive as an open data resource

“…More than 400 million coordinate sets were downloaded in 2013 from the wwPDB partner sites. Both the utility and the uniformity of PDB data have enabled the development of other databases and datarelated resources, including resources for drug discovery (for a review see [32]); resources focused on small molecules and ligands such as ChEMBL [33], DrugBank [34], BindingDB [35], BindingMOAD [36], and PDBBind [37]; protein structure classification and annotation resources, such as CATH [38,39], SCOP [40][41][42], and PDBsum [43,44]; and focused, specialty annotation resources such as Protein Data Bank of Transmembrane Proteins (PDBTM) [45], ArchDB for functional loops in structures [46], and 3did for protein-protein interaction surfaces [47]. These resources are frequently compiled in the annual Database Issue of Nucleic Acids Research.…”

Adaptation of machine translation for multilingual information retrieval in the medical domain

“…The in-domain monolingual corpora include (cf. Table 2): the Cochrane database of reviews of primary research in human health care and health policy [63], DrugBank -a bioinformatics and cheminformatics resource describing drugs [64], Gene Regulation Event Corpus (GREC) -a semantically annotated English corpus of abstracts of biomedical texts [65], the GENIA corpus of biomedical literature compiled and annotated within the GENIA project [66], the Foundational Model of Anatomy Ontology (FMA) -a knowledge source for biomedical informatics concerned with symbolic representation of the phenotypic structure of the human body [67], English texts extracted from the UMLS Metathesaurus [40], the Patient Information Leaflet Corpus (PIL) -a collection of documents giving instructions to patients about their medication [69], and finally, a large set of texts extracted from HONcode-certified sites (HON) that have been identified by language-detection libraries [70,71] to be English-language [72].…”

Finding type 2 diabetes causal single nucleotide polymorphism combinations and functional modules from genome-wide association data

“…T2D genes are collected from public disease gene databases such as OMIM [23], KEGG [24], and GAD [25]. From DrugBank [26], KEGG Drug and PharmGKB Drug [27] databases, 36 T2D drug targets were collected.…”