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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 TDY, Brudz S, Tanega C, Schreiber SL, Bittker JA, Guha R, Clemons PA. BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. Nucleic Acids Res 2014; 43:D1163-70. [PMID: 25477388 DOI: 10.1093/nar/gku1244] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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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Affiliation(s)
- E A Howe
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - A de Souza
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - D L Lahr
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - S Chatwin
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - P Montgomery
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - B R Alexander
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - D-T Nguyen
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Y Cruz
- The Translational Research Institute, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - D A Stonich
- Conrad Prebys Center for Chemical Genomics, Sanford
- Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - G Walzer
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - J T Rose
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - S C Picard
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Z Liu
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - J N Rose
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - X Xiang
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - J Asiedu
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - D Durkin
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - J Levine
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - J J Yang
- University of New Mexico Center for Molecular Discovery, University of New Mexico Health Sciences Center, 2500 Marble Avenue NE, Albuquerque, NM 87131, USA
| | - S C Schürer
- Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Gables One Tower, Coral Gables, FL 33146, USA
| | - J C Braisted
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - N Southall
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - M R Southern
- The Translational Research Institute, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - T D Y Chung
- Conrad Prebys Center for Chemical Genomics, Sanford
- Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - S Brudz
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - C Tanega
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - S L Schreiber
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - J A Bittker
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - R Guha
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - P A Clemons
- Center for the Science of Therapeutics, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
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