Webinar for Drug Related Gene Database is available through NIF. Click the picture below to watch the webinar.
Funded by National Institute of Drug Abuse (NIDA), the DRG database was created to facilitate discovery and use of resources relevant to drug abuse research. The database and associated tools were specifically created for providing data that is contained in tables, figures and supplementary materials from published papers in a way that facilitates search across the results of these studies. These data are extracted from published journal articles that directly test hypotheses relevant to the neuroscience of addiction and addictive behavior. The current database mainly focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data types include the effects of a particular drug, strain, or knock out on a particular gene, in a particular anatomical region. Once loaded, these data are available for query through the NIF interface. During this process, the content is standardized using a generic high level description of a relevant study and study terms are mapped to ontologies available through the NIF project (NIFSTD) to enhance semantic search of such data. During this project, many of the concepts relevant for drug abuse research were added to the NIFSTD, e.g., drug of abuse.
The Data Federation tab shows many results. Open the Dataset or Gene category by clicking on the + to the right of it and then click on the Drug Related Gene DB.
In addition to the data visible through the interface are a variety of other data that can be accessed through the Export button on the top right of the results pane. In the Export options, all columns must be selected to export the additional information.
The exported data includes the data visible on the interface as well as additional details gathered from the paper about each result including the experimental values, control values, experimental / control ratio, experimental paradigm, statistical test performed, comments, accession ID (gene ID), platform, PubMed ID (PMID), explanation of significance criteria, etc., where available. Results are exported in Excel.
The search results went from over 210,000 records when we searched cocaine alone, down to 8 when we searched for a particular gene and cocaine. Adding a brain region, such as hippocampus, to this search would narrow the results down even further.
The results for this search show the publications and the specific table, or figure, within that publication that looked at the AQP4 gene under cocaine conditions. The results show the effect (increased expression, decreased expression, no change, etc.) on the AQP4 gene, in a particular brain region of a particular organism (listed) when given cocaine under a particular paradigm (chronic cocaine, acute cocaine, acute binge cocaine, or chronic binge cocaine). Additionally, you can follow the treatment link to the methods within the paper (when available) to gather additional details. The results show what the experimental variant and control were and which kind of protocol / assay type was used. Furthermore, the experimental paradigm, experimental values, statistical tests used, platform, and a wealth of other information, is provided through the Export button in an Excel spreadsheet. (All fields must be selected for export to get the additional fields.)
A glance at the results from various studies can help researchers see trends in the effects of a drug on a particular gene in a particular brain region. One can see which genes are up-regulated by a specific drug in a particular organism in a particular brain region, or a variety of other scenarios. The view provides enough information to the user to know if they are interested in a study and be able to attain additional information through the Export button, as well as links back to the original publication.
NIF Version: 5.0
Ontology Version: 2.5
Level 2.5/3.0 Resources: 889
Registry Entries: 6,339
Total Records: 356,197,652