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

Howe EA, de Souza A, Lahr DL, Chatwin S, Montgomery P, Alexander BR, Nguyen DT, Cruz Y, Stonich DA, Walzer G, Rose JT, Picard SC, Liu Z, Rose JN, Xiang X, Asiedu J, Durkin D, Levine J, Yang JJ, Schürer SC, Braisted JC, Southall N, Southern MR, Chung TD, Brudz S, Tanega C, Schreiber SL, Bittker JA, Guha R, Clemons PA - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA.

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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.
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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.

Mentions: The Web Query Client features an initial interface built around a single search bar. This search tool offers auto-suggest options for targets, gene names, KEGG pathways, GO terms, and other terms from the controlled vocabulary or referenced external ontologies. Queries are performed against the entire database, and results are returned for assay definitions, compounds, projects, and experiments in separate search tabs. These results can be examined and filtered by a variety of criteria such as protein target, GO biological process term, or assay format. Individual items can be stored for later comparison in the Query Cart, a user session-specific storage tool. Results can then be visualized using the web client's built-in Molecular Spreadsheet (Figure 4a) or by downloading to the BARD Desktop Client (Figure 5). The Query Cart can also be used as a workspace, where compounds, assay definitions, and projects can be added and removed as the user progressively refines their search criteria.


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

Howe EA, de Souza A, Lahr DL, Chatwin S, Montgomery P, Alexander BR, Nguyen DT, Cruz Y, Stonich DA, Walzer G, Rose JT, Picard SC, Liu Z, Rose JN, Xiang X, Asiedu J, Durkin D, Levine J, Yang JJ, Schürer SC, Braisted JC, Southall N, Southern MR, Chung TD, Brudz S, Tanega C, Schreiber SL, Bittker JA, Guha R, Clemons PA - Nucleic Acids Res. (2014)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4383997&req=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.
Mentions: The Web Query Client features an initial interface built around a single search bar. This search tool offers auto-suggest options for targets, gene names, KEGG pathways, GO terms, and other terms from the controlled vocabulary or referenced external ontologies. Queries are performed against the entire database, and results are returned for assay definitions, compounds, projects, and experiments in separate search tabs. These results can be examined and filtered by a variety of criteria such as protein target, GO biological process term, or assay format. Individual items can be stored for later comparison in the Query Cart, a user session-specific storage tool. Results can then be visualized using the web client's built-in Molecular Spreadsheet (Figure 4a) or by downloading to the BARD Desktop Client (Figure 5). The Query Cart can also be used as a workspace, where compounds, assay definitions, and projects can be added and removed as the user progressively refines their search criteria.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA.

Show MeSH