An overview of the challenges in designing, integrating, and delivering BARD: A public chemical-biology resource and query portal for multiple organizations, locations, and disciplines

Andrea De Souza, Joshua A. Bittker, David L. Lahr, Steve Brudz, Simon Chatwin, Tudor I. Oprea, Anna Waller, Jeremy J. Yang, Noel Southall, Rajarshi Guha, Stephan C Schuerer, Uma D. Vempati, Mark R. Southern, Eric S. Dawson, Paul A. Clemons, Thomas D Y Chung

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Recent industry-academic partnerships involve collaboration among disciplines, locations, and organizations using publicly funded "open-access" and proprietary commercial data sources. These require the effective integration of chemical and biological information from diverse data sources, which presents key informatics, personnel, and organizational challenges. The BioAssay Research Database (BARD) was conceived to address these challenges and serve as a community-wide resource and intuitive web portal for public-sector chemical-biology data. Its initial focus is to enable scientists to more effectively use the National Institutes of Health Roadmap Molecular Libraries Program (MLP) data generated from the 3-year pilot and 6-year production phases of the Molecular Libraries Probe Production Centers Network (MLPCN), which is currently in its final year. BARD evolves the current data standards through structured assay and result annotations that leverage BioAssay Ontology and other industry-standard ontologies, and a core hierarchy of assay definition terms and data standards defined specifically for small-molecule assay data. We initially focused on migrating the highest-value MLP data into BARD and bringing it up to this new standard. We review the technical and organizational challenges overcome by the interdisciplinary BARD team, veterans of public- and private-sector data-integration projects, who are collaborating to describe (functional specifications), design (technical specifications), and implement this next-generation software solution.

Original languageEnglish
Pages (from-to)614-627
Number of pages14
JournalJournal of Biomolecular Screening
Volume19
Issue number5
DOIs
StatePublished - Jan 1 2014

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Bioassay
Biological Assay
Organizations
Databases
Assays
Research
Public Sector
Information Storage and Retrieval
Ontology
Industry
Specifications
Molecular Probes
Informatics
Private Sector
Data integration
National Institutes of Health (U.S.)
Veterans
Software
Health
Personnel

Keywords

  • Chemical biological database standards
  • Visualization
  • Web portal

ASJC Scopus subject areas

  • Analytical Chemistry
  • Drug Discovery
  • Pharmacology
  • Biochemistry
  • Molecular Medicine
  • Biotechnology

Cite this

An overview of the challenges in designing, integrating, and delivering BARD : A public chemical-biology resource and query portal for multiple organizations, locations, and disciplines. / De Souza, Andrea; Bittker, Joshua A.; Lahr, David L.; Brudz, Steve; Chatwin, Simon; Oprea, Tudor I.; Waller, Anna; Yang, Jeremy J.; Southall, Noel; Guha, Rajarshi; Schuerer, Stephan C; Vempati, Uma D.; Southern, Mark R.; Dawson, Eric S.; Clemons, Paul A.; Chung, Thomas D Y.

In: Journal of Biomolecular Screening, Vol. 19, No. 5, 01.01.2014, p. 614-627.

Research output: Contribution to journalArticle

De Souza, A, Bittker, JA, Lahr, DL, Brudz, S, Chatwin, S, Oprea, TI, Waller, A, Yang, JJ, Southall, N, Guha, R, Schuerer, SC, Vempati, UD, Southern, MR, Dawson, ES, Clemons, PA & Chung, TDY 2014, 'An overview of the challenges in designing, integrating, and delivering BARD: A public chemical-biology resource and query portal for multiple organizations, locations, and disciplines', Journal of Biomolecular Screening, vol. 19, no. 5, pp. 614-627. https://doi.org/10.1177/1087057113517139
De Souza, Andrea ; Bittker, Joshua A. ; Lahr, David L. ; Brudz, Steve ; Chatwin, Simon ; Oprea, Tudor I. ; Waller, Anna ; Yang, Jeremy J. ; Southall, Noel ; Guha, Rajarshi ; Schuerer, Stephan C ; Vempati, Uma D. ; Southern, Mark R. ; Dawson, Eric S. ; Clemons, Paul A. ; Chung, Thomas D Y. / An overview of the challenges in designing, integrating, and delivering BARD : A public chemical-biology resource and query portal for multiple organizations, locations, and disciplines. In: Journal of Biomolecular Screening. 2014 ; Vol. 19, No. 5. pp. 614-627.
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