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. 2015 Jan;43(Database issue):D1163-70.
doi: 10.1093/nar/gku1244. Epub 2014 Dec 4.

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types

E A Howe  1 , A de Souza  2 , D L Lahr  1 , S Chatwin  1 , P Montgomery  1 , B R Alexander  1 , D-T Nguyen  3 , Y Cruz  4 , D A Stonich  5 , G Walzer  1 , J T Rose  1 , S C Picard  1 , Z Liu  1 , J N Rose  1 , X Xiang  1 , J Asiedu  1 , D Durkin  1 , J Levine  1 , J J Yang  6 , S C Schürer  7 , J C Braisted  3 , N Southall  3 , M R Southern  4 , T D Y Chung  5 , S Brudz  1 , C Tanega  3 , S L Schreiber  1 , J A Bittker  1 , R Guha  8 , P A Clemons  9
Affiliations

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types

E A Howe et al. Nucleic Acids Res. 2015 Jan.

Abstract

BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource.

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Figures

Figure 1.
Figure 1.
BARD data access and entry. BARD data are entered by data depositors, using the web-based data-entry interface (purple). Data miners can explore BARD data using several tools, developed both by BARD developers and the larger developer community (blue and green). Software developers can create new tools that access BARD data using the API and deploy them either as stand-alone tools or as plug-ins that can be integrated into the BARD website (green and orange).
Figure 2.
Figure 2.
Loading data into BARD. New screening experiments can be entered into BARD using the web-based data-entry tool, available on the BARD website. The BARD UI guides the user through the process of creating an assay protocol to describe the experimental design. It then creates an upload template file that contains all of the required fields necessary to deposit a completed set of experimental results.
Figure 3.
Figure 3.
The Project Flow Diagram. The Project Flow Diagram illustrates the relationships between experiments in a project. Experiments like primary screens can be connected to downstream experiments, like confirmatory assays and counter-screens.
Figure 4.
Figure 4.
The Web Query Client results. Rich search results are available in the Web Query Client. (a) The Molecular Spreadsheet displays a summary table of characteristics of selected compounds, including structure, active versus inactive counts, a complete record of the assays and experiments in which the compounds were active, the concentrations at which they were active, and dose–response curves when they are available. (b) The Linked Hierarchy enables investigation of compound annotations. The individual pie or sunburst charts summarize the number of compound hits from assays broken down by several different criteria: biological process, assay format, protein target class, and assay type. These charts are interactive: clicking on an item in the sunburst causes the sunburst to be redrawn to show only those items belonging to the selected item and its children. The remaining three pie charts are also redrawn to display the distribution of items that belong to the selected assay results.
Figure 5.
Figure 5.
The Desktop Client. The Desktop Client downloads data stored in the user's Query Cart, and displays it alongside local, private data for further analysis. (a) The compound-level information is displayed in a tabular format similar to Web Query Client results and includes compound structure and promiscuity information as well as compound class and full name. (b) The Assays tab summarizes results for the selected compound in each assay, displaying dose–response curves and other summary statistics.
Figure 6.
Figure 6.
The BADAPPLE plug-in is embedded within the BARD website. The BADAPPLE plug-in accesses the BARD data warehouse using the REST API and implements the plug-in interface, allowing it to be deployed as part of the BARD website. The results are then displayed as part of the compound details. BADAPPLE predicts compound scaffold promiscuity using assay information about compounds containing that scaffold.
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